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ticket/1674_TMX (diff) – NEMO

Changes between Version 1 and Version 2 of ticket/1674_TMX


Ignore:
Timestamp:
2016-02-05T03:41:03+01:00 (8 years ago)
Author:
gm
Comment:

--

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  • ticket/1674_TMX

    v1 v2  
    55'''ticket''' : #1674 
    66 
    7 '''Branch''' : [https://forge.ipsl.jussieu.fr/nemo/wiki/ticket/1674_TMX   2015/dev_r5721_CNRS9_NOC3_LDF] 
    8  
    9 '''WP2015 Action''' : CNRS-9 and NOC-3 
    10  
    11 '''===>>>   NOW''' moved on the '''trunk''' (revision: [https://forge.ipsl.jussieu.fr/nemo/log/trunk/NEMOGCM?rev=5838 ​5836]) 
     7'''Branch''' : [https://forge.ipsl.jussieu.fr/nemo/browser/branches/2015/dev_r6287_ZDFTMX_new 2015/dev_r6287_ZDFTMX_new] 
    128 
    139---- 
    1410= Description = 
    15 Development branch related to CNRS-9 and NOC-3 actions of 2015 work plan :[[BR]]        • simplify and improve the tracer advection and the lateral diffusion and dissipation in NEMO/OPA[[BR]]        • generalization of the use of surface scale factors (e1e2 at T, U, V, F points) 
     11Introduce in the v3.6_STABLE a non intrusive version of a new parameterization of internal wave-driven mixing. 
    1612 
    17 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. 
     13The original parameterization that has been developed is implemented with the two following undesirable features for the v3.6_STABLE:[[BR]] (1) a module replacing the existing zdftmx.F90 module (impossible to use the old param); [[BR]] (2) avt and avs arrays always defined (suppression of zdfddm_substitute.h90 which introduces changes in ~25 modules) 
    1814 
    19 ''Simplification'': [[BR]](1) define bilaplacian operators on dynamics and tracers as re-entrant laplacian ;[[BR]](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) ;[[BR]](3) generalize of the use of surface scale factors and their inverse ;[[BR]](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).[[BR]](5) suppress some CPP keys : key_ldfslp ; ley_ldftra_eiv ; key_traldf_ano ; key_traldf_c1d, _c2d, c3d ; key_dynldf_c1d, _c2d, c3d ; key_esopa (from traldf and traadv routines) ;[[BR]](6) remove Smagorinsky dependent eddy viscosity and diffusivity 
    20  
    21 ''Improvements'': [[BR]] (1) introduce Beckers et al. (2000) compact stencil in the cross-isoneutral direction in triads formalism ; [[BR]] (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 bi-laplacian iso-neutral operators (Lemarié et al. (2012). 
     15  Here, the parameterization is introduced as an additional option, making both the current parameterization and the new one available, and the new one will only be available if double diffusion mixing is activated (key_zdfddm defined). Therefore changes in the code are restricted to the namlist and zdftmx.F90 (+ an update of the ZDF chapter of the Documentation). 
    2216 
    2317---- 
    2418= Strategy = 
    25 Three steps: [[BR]] 
    26  
    27 == I. Phasing of horizontal scale factors == 
    28   ===>>> '''            OK'''             see revision  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5737]                                                                   '''                                                                  + minor correction'''                                                                   revision  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5737]                                                              (SETTE OK) 
    29  
    30 === (I.1)  standardisation of the name === 
    31 The chosen names of quantities derived from horizontal scale factors are:[[BR]] - inverse of scale factors : r1_e1t, r1_e2t, r1_e1u, r1_e2u, r1_e1v, r1_e2v, r1_e1f, r1_e2f ;[[BR]] - surfaces and their inverse:    e1e2t, e1e2u , e1e2v, e1e2f  and, r1_e1e2t , r1_e1e2u , r1_e1e2v, r1_e1e2f ;[[BR]] - ratio (used in traldf...) : e2_e1u , e1_e2v(I.1) generalize of the use of surface scale factors ;[[BR]] These quantities are defined in memory in dom_oce.F90, and set to their proper value in domhgr.F90 
    32  
    33 === (I.2) domhgr: add a optional read of surface scale factors === 
    34   An optional read of surface scale factors at velocity points ( e1e2u and e1e2v) is needed in coordinate file. Indeed, in case of reduction of a scale factor (e1u or e2v) in a strait, the surface at u- and v-points must remain unchanged.[[BR]]              This allows to suppress the dom_vvl_orca_fix routine from dlmvvl.F90 module.[[BR]]           ''           Note that this change modifies the model results''           , as it contains a better handling of reduced strait width (i.e. reduced face between 2 adjacent T-points, but unchanged U and V points volume).[[BR]]              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. [[BR]]              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 coordinates.nc file together with the e1e2u & e1e2v surfaces.  ===>>> OK see '''           revision  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5755]           ''' 
    35  
    36 == [[BR]][[BR]]II. Phasing of the advective/diffusive trends on tracers == 
    37 === II.1 —''' '''LDF on tracers''' (both TRA & TRC) - Diffusive trends''' === 
    38   ===>>> '''         OK'''          see revision  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5758]           &  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5759]           and  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5760]           with SETTE OK 
    39  
    40   '''         ====>>>> Bug in triad operator TO BE CHECKED'''         [[BR]]           triad operator is neither restartable not repro  in the branche (it was the case in v3.6 stable) 
    41  
    42 ''operator'': [[BR]]- laplacian operator: re-entrant laplacian for iso-level, standard iso-neutral, and triad iso-neutral operators ;[[BR]]- bilaplacian operator: traldf_blp.F90 module: use of the re-entrant laplacian [[BR]]- both standard and triad iso-neutral operators includes  the Method of Stabilizing Correction (Lemarié et al. (2012) which allows bilaplacian along iso-neutral surfaces ;[[BR]]- triad operator: introduce Beckers et al. (2000) compact stencil in the cross-isoneutral direction ; make the triad operator available in TOP[[BR]]- change name:  traldf_iso_grif.F90 becomes traldf_iso_triad.F90[[BR]]- suppression of traadv_eiv.F90 ; traldf_bilap.F90 ; traldf_bilapg.F90 ;[[BR]]- remove the possibility to compute the lateral diffusion from T-S anomalies (key_traldf_ano) 
    43  
    44 ''lateral mixing coefficient'':[[BR]]- new user interface (namelist) : 
     19(1) in zdftmx:  introduce in zdftmx.F90 a new CPP key : key_zdftmx_new so that: [[BR]] 
    4520 
    4621{{{ 
    47 !---------------------------------------------------------------------------------- 
    48 &namtra_ldf    !   lateral diffusion scheme for tracers 
    49 !---------------------------------------------------------------------------------- 
    50    !                       !  Operator type: 
    51    ln_traldf_lap   =  .false.  !    laplacian operator 
    52    ln_traldf_blp   =  .false.  !  bilaplacian operator 
    53    !                       !  Direction of action: 
    54    ln_traldf_lev   =  .false.  !  iso-level 
    55    ln_traldf_hor   =  .false.  !  horizontal (geopotential) 
    56    ln_traldf_iso   =  .true.   !  iso-neutral 
    57    ln_traldf_triad =  .false.  !  iso-neutral using Griffies triads 
    58    ! 
    59    !                             !  iso-neutral options:         
    60    ln_traldf_msc   =  .true.   !  Method of Stabilizing Correction (both operators) 
    61    rn_slpmax       =   0.01    !  slope limit                      (both operators) 
    62    ln_triad_iso    =  .false.  !  pure horizontal mixing in ML     (triad only) 
    63    rn_sw_triad     =  1        !  =1 switching triad ; =0 all 4 triads used (triad only) 
    64    ln_botmix_triad =  .false.  !  lateral mixing on bottom         (triad only) 
    65    ! 
    66    !                       !  Coefficients: 
    67    nn_aht_ijk_t    = 21        !  space/time variation of eddy coef 
    68    !                                !   =-20 (=-30)    read in eddy_diffusivity_2D.nc (..._3D.nc) file 
    69    !                                !   =  0           constant  
    70    !                                !   = 10 F(k)      =ldf_c1d  
    71    !                                !   = 20 F(i,j)    =ldf_c2d  
    72    !                                !   = 21 F(i,j,t)  =Treguier et al. JPO 1997 formulation 
    73    !                                !   = 30 F(i,j,k)  =ldf_c2d + ldf_c1d 
    74    !                                !   = 31 F(i,j,k,t)=F(local velocity) 
    75    rn_aht_0        = 2000.     !  lateral eddy diffusivity   (lap. operator) [m2/s] 
    76    rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s] 
    77 / 
    78 !---------------------------------------------------------------------------------- 
    79 &namtra_ldfeiv !   eddy induced velocity param. 
    80 !---------------------------------------------------------------------------------- 
    81    ln_ldfeiv     =.true.   ! use eddy induced velocity parameterization 
    82    ln_ldfeiv_dia =.true.   ! diagnose eiv stream function and velocities 
    83    rn_aeiv_0     = 2000.   ! eddy induced velocity coefficient   [m2/s] 
    84    nn_aei_ijk_t  = 21      ! space/time variation of the eiv coeficient 
    85    !                                !   =-20 (=-30)    read in eddy_induced_velocity_2D.nc (..._3D.nc) file 
    86    !                                !   =  0           constant  
    87    !                                !   = 10 F(k)      =ldf_c1d  
    88    !                                !   = 20 F(i,j)    =ldf_c2d  
    89    !                                !   = 21 F(i,j,t)  =Treguier et al. JPO 1997 formulation 
    90    !                                !   = 30 F(i,j,k)  =ldf_c2d + ldf_c1d 
    91 / 
     22MODULE zdftmx 
     23... 
     24#if defined key_zdftmx   ||   defined key_esopa 
     25   !!---------------------------------------------------------------------- 
     26   !!   'key_zdftmx'                                  Tidal vertical mixing   <<<==OLD version 
     27   !!---------------------------------------------------------------------- 
     28   !!   zdf_tmx      : global     momentum & tracer Kz with tidal induced Kz 
     29   !!   tmx_itf      : Indonesian momentum & tracer Kz with tidal induced Kz  
     30   !!   zdf_tmx_init : initialisation of tidal induced Kz 
     31   !!---------------------------------------------------------------------- 
     32   ... 
     33   LOGICAL, PUBLIC, PARAMETER ::   lk_zdftmx = .TRUE.    !: tidal mixing flag     <<=== same flag 
     34   ... 
     35#elif defined key_zdftmx_new 
     36   !!---------------------------------------------------------------------- 
     37   !!   'key_zdftmx_new'                          New Tidal vertical mixing   <<<==NEW version 
     38   !!---------------------------------------------------------------------- 
     39   !!   zdf_tmx      : global     momentum & tracer Kz with tidal induced Kz 
     40   !!   zdf_tmx_init : initialisation of tidal induced Kz 
     41   !!---------------------------------------------------------------------- 
     42   ... 
     43   LOGICAL, PUBLIC, PARAMETER ::   lk_zdftmx = .TRUE.    !: tidal mixing flag     <<=== same flag 
     44   ... 
     45#else 
     46   !!---------------------------------------------------------------------- 
     47   !!   Default option          Dummy module                NO Tidal MiXing 
     48   !!---------------------------------------------------------------------- 
     49   ... 
     50#endif 
    9251}}} 
    93 [[BR]]- default value of the namelist: ''no operator chosen'': lln_traldf_lap=traldf_blp=0 No lateral diffusion applied on tracers.[[BR]]-  bi-laplacian eddy coefficient defined as SQRT(bhm)[[BR]]- ah and bh coefficients defined only at u- and v-points.[[BR]]- 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) [[BR]]- 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, a module share with ldftra.F90) ; ldftra_oce.F90 (now included in ldftra.F90) [[BR]]- remove ldftra_smag.F90 (suppression of smagorinski option)  '''==>>> TO BE re-add in the new framework by someone...[[BR]]'''- 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[[BR]]- suppression of key_esopa in traldf.F90[[BR]]- zpshde.F90 correct an issue with position of optional argument in zps_hde_isf routine[[BR]]- change in all standard namelist_cfg and 1_namelist_cfg 
    9452 
    95 ''passive tracers''[[BR]]- all changes in the management of diffusive coefficients and operator has been taken into account in TOP[[BR]]- change in all standard namelist_top_cfg 
     53(2) introduce in the Namelist_ref, a new namelist: namzdf_tmx_new used if key_zdftmx_new is defined. 
    9654 
    97 '''Pending issues''' : [[BR]]- verify diaptr.F90  : not sure it is OK[[BR]]- 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[[BR]]- test all 6 operators.[[BR]]- In field_def.xml  add a comment to say where is the routine calling the corresponding iom_put[[BR]]- in the documentation, add a change in the DOCTOR norm: np_ is now a prefix used for PARAMETER 
    98  
    99 === [[BR]]II.2 — Advective trends (TRA/traadv....) === 
    100   ===>>> '''        OK'''         see revision  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5770]         &  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5771]           ===>> SETTE OK with revision [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5774]         &  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5737 5775] 
    101  
    102   - traadv_muscl2.F90  removed[[BR]]- traadv_muscl.F90 renamed traadv_mus.F90[[BR]]- traadv_cen2.F90  replaced by traadv_cen which provides 2nd and 4th order centered scheme on both horizontal and vertical directions.[[BR]]- name TVD has been changed to the more commonly used FCT (Flux Correction Transport)[[BR]]- FCT offers now 2nd and 4th order centered scheme on both horizontal and vertical directions.[[BR]]- UBS offers now in option either a 2nd order FCT or a 4th order COMPACT scheme in the vertical direction[[BR]]- NB in case of 4th order in the vertical, CEN, UBS and FCT use a compact 4th order scheme[[BR]]- key_esopa removed from traadv.F90[[BR]]- Surface boundary condition in ISF case has been added in all cases (except 4th order COMPACT scheme which have not been tested with ISF) 
    103  
    104 {{{ 
    105 !----------------------------------------------------------------------- 
    106 &namtra_adv    !   advection scheme for tracer 
    107 !----------------------------------------------------------------------- 
    108    ln_traadv_cen =  .false.  !  2nd order centered scheme 
    109       nn_cen_h   =  4               !  =2/4, horizontal 2nd order CEN / 4th order CEN 
    110       nn_cen_v   =  4               !  =2/4, vertical   2nd order CEN / 4th order COMPACT 
    111    ln_traadv_fct =  .false.  !  FCT scheme 
    112       nn_fct_h   =  2               !  =2/4, horizontal 2nd / 4th order  
    113       nn_fct_v   =  2               !  =2/4, vertical   2nd / COMPACT 4th order  
    114       nn_fct_zts =  0               !  > 1 , 2nd order FCT scheme with vertical sub-timestepping 
    115       !                             !        (number of sub-timestep = nn_fct_zts) 
    116    ln_traadv_mus =  .false.  !  MUSCL scheme 
    117       ln_mus_ups =  .false.         !  use upstream scheme near river mouths 
    118    ln_traadv_ubs =  .false.  !  UBS scheme 
    119       nn_ubs_v   =  2               !  =2  , vertical 2nd order FCT 
    120    ln_traadv_qck =  .false.  !  QUICKEST scheme 
    121 / 
    122 }}} 
    123 '''Unresolved issues/improvement''' on TRAADV: [[BR]]- QCK: cross terms are missing. alternate direction should be added....[[BR]]- Bug in FCT with sub-time-stepping and key_vvl. The change in e3 should be taken into account in the sub-timesteps.[[BR]]- traadv_mus.F90   some rather simple optimization can be added...[[BR]]- traadv_qck.F90 : possibility to add a 4th order COMPACT scheme on the vertical. [[BR]]- 4th order COMPACT have not been tested with ISF. The routine needs probably to be modified. 
    124  
    125 === [[BR]]II.3 — Miscellaneous === 
    126  * Atmospheric pressure forcing: change to a systematic call of sbc_apr in step.F90 (with or without BDY) and remove its call from sbcmod 
    127  * remove key_vectopt_loop from all the code except in vectopt_loop_substitute.h90 (it is an obsolescent feature only adapted to vector computers) 
    128  * remove all "!CDIR " lines = NEC vector compiler instructions 
    129  
    130 == [[BR]][[BR]][[BR]]III. Phasing of momentum trends == 
    131   ===>>> '''        OK'''         see revision  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5777 5777]                                          & [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5778 5778]                                          and   [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5782 5782]                                          with SETTE OK 
    132  
    133 === [[BR]]III.1 — LDF on dynamics  - viscous trends === 
    134 ''operator'': [[BR]]- laplacian operator: re-entrant laplacian for iso-level operators (routine dyn_ldf_lap found in dynldf_lap_blp);[[BR]]- bilaplacian operator: dynldf_blp.F90 module: use of the re-entrant iso-level laplacian (routine dyn_ldf_blp found in dynldf_lap_blp.F90)[[BR]]- suppression of dynnept.F90  to finalize the suppression of Neptune effect param. ;[[BR]]- suppression of dynldf_lap.F90 and dynldf_bilap.F90 replaced by dynldf_lap_blp.F90 (which contains dyn_ldf_lap & dyn_ldf_blp routines) ; dynldf_bilapg.F90 (remove old and approximative rotated bi-laplacian on momentum)[[BR]]- rotb and rotn arrays suppressed (even from the restart file) NB: the viscous operator now uses the full before velocity field (i.e. including the asselin filter)[[BR]]- hdivb array is suppressed. hdivn and hdivb are removed from restart[[BR]]- associate with rotn and rotb suppression comes the suppression of no-slip accurate option (key_noslip_accurate is removed)[[BR]]- divcur.F90 becomes divhor.F90 and only computes the horizontal divergence 
    135  
    136 [[BR]]''lateral mixing coefficient'':[[BR]]- new user interface (namelist) : 
    137  
    138 {{{ 
    139 !----------------------------------------------------------------------- 
    140 &namdyn_ldf    !   lateral diffusion on momentum 
    141 !----------------------------------------------------------------------- 
    142    !                       !  Type of the operator : 
    143    !                           !  no diffusion: set ln_dynldf_lap=..._blp=F  
    144    ln_dynldf_lap =  .false.    !    laplacian operator 
    145    ln_dynldf_blp =  .false.    !  bilaplacian operator 
    146    !                       !  Direction of action  : 
    147    ln_dynldf_lev =  .false.    !  iso-level 
    148    ln_dynldf_hor =  .false.    !  horizontal (geopotential) 
    149    ln_dynldf_iso =  .false.    !  iso-neutral 
    150    !                       !  Coefficient 
    151    nn_ahm_ijk_t  = 0           !  space/time variation of eddy coef 
    152    !                                !  =-30  read in eddy_viscosity_3D.nc file 
    153    !                                !  =-20  read in eddy_viscosity_3D.nc file 
    154    !                                !  =  0  constant  
    155    !                                !  = 10  F(k)=c1d 
    156    !                                !  = 20  F(i,j)=F(grid spacing)=c2d 
    157    !                                !  = 30  F(i,j,k)=c2d*c1d 
    158    !                                !  = 31  F(i,j,k)=F(grid spacing and local velocity) 
    159    rn_ahm_0      =  40000.     !  horizontal laplacian eddy viscosity   [m2/s] 
    160    rn_ahm_b      =      0.     !  background eddy viscosity for ldf_iso [m2/s] 
    161    rn_bhm_0      = 1.e+12      !  horizontal bilaplacian eddy viscosity [m4/s] 
    162    ! 
    163    ! Caution in 20 and 30 cases the coefficient have to be given for a 1 degree grid (~111km) 
    164 / 
    165 }}} 
    166 [[BR]]- default value of the namelist: ''no operator chosen'': ln_dynldf_lap=dyndf_blp=0   ==>>>   No lateral diffusion applied on momentum[[BR]]- create the 2D and 3D ahmt and ahmf file for ORCA_R2      '''===>>>  TO BE DONE for ORCA_R1''' . nn_ahm_ijk_t must be set to -20 or -30 for ORCA2 and ORCA1 (read in a file) [[BR]]- both laplacian and bi-laplacian coef. are always 3D arrays defined at T- and F- points. Bi-laplacian eddy coefficient defined as SQRT(bhm)    [[BR]]'''                  ====>>> TO BE DONE: explore the possibility of u- and v-points'''[[BR]]- redesign of space variation of the eddy viscosity: suppression of: ldfdyn_substitute.h90 ; ldfdyn_c1d.h90 , ldfdyn_c2d.h90 and ldfdyn_c3d.h90 (replaced by ldfc1d_c2d.F90, a module share with ldftra.F90) ; ldfdyn_oce.F90 (now included in ldfdyn.F90)[[BR]]- remove ldfdyn_smag.F90 (suppression of smagorinsky option)  '''==>>> TO BE re-add in the new framework by  someone...'''[[BR]]- suppression of key_esopa in dynldf.F90[[BR]]- suppression of key_dynldf_c1d, key_dynldf_c2d, key_dynldf_c3d[[BR]]- change in all standard namelist_cfg and 1_namelist_cfg [[BR]]- Namelist default values : NO operator ; NO direction  ===>>> No lateral mixing applied on momentum   ===>>> must be specified in all CONFIG 
    167  
    168 === [[BR]]III.2 —''' '''ADV on dynamics''' - advective trends''' === 
    169   ===>>> '''        OK'''         see revision  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5778 5778]         and  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5786 5786]        with SETTE OK 
    170  
    171 ''dynvor.F90 (impact also dynspg_ts.F90)''[[BR]]                   - remove key_esopa[[BR]]                   - remove dyn_vor_mix : now successive call of den_vor_ene (Coriolis) and din_vor_ens (relative voricity)[[BR]]                   - replace rotn by its calculation everywhere in dynvor.F90[[BR]]                   - remove the use of fmask from standard vorticity calculation in dynvor.F90 but add a namelist parameter (ln_dynvor_msk) to multiply by fmask the vorticity term[[BR]]- add an namelist option to mask or not the vorticity (including Coriolis) '''CAUTION''' : the mask option does not work: set to FALSE by default with comment DO NOT set it to TRUE  (see '''  [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5827 5827]''' )[[BR]]- change ln_dynvor_een_old into nn_een_e3f = 0/1 
    172  
    173 namdyn_vor becomes: 
    174  
    175 {{{ 
    176 !----------------------------------------------------------------------- 
    177 &namdyn_vor    !   option of physics/algorithm (not control by CPP keys) 
    178 !----------------------------------------------------------------------- 
    179    ln_dynvor_ene = .false. !  enstrophy conserving scheme 
    180    ln_dynvor_ens = .false. !  energy conserving scheme 
    181    ln_dynvor_mix = .false. !  mixed scheme 
    182    ln_dynvor_een = .true.  !  energy & enstrophy scheme 
    183       nn_een_e3f = 1             !  e3f = masked averaging of e3t divided by 4 (=0) or by the sum of mask (=1) 
    184    ln_dynvor_msk = .false. !  vorticity multiplied by fmask (=T) or not (=F) (all vorticity schemes) 
    185 / 
    186 }}} 
    187 ''dynadv.F90[[BR]]''- remove key_esopa[[BR]]- introduce parameter in the SELECT CASE 
    188  
    189 namlist_ref and all CONFIG namelists updated 
    190  
    191 === [[BR]]III.3 Miscellaneous === 
    192  * key_esopa has been remove from the whole NEMO code '''DONE''' see rev. [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5778 5778] 
    193  * remove key_noslip_accurate from dom_oce.F90 and domsk.F90. '''DONE''' see rev. [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5829 5829] 
    194  * remove duplicate print of "W A R N I N G" and "E R R O R" in ctl_nam routine  '''DONE''' see rev. [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5829 5829] 
    195  * remove ll_is_orca and its associated use in domvvl.F90 (no used anymore)  '''DONE''' see rev [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5829 5829] 
    196  * remove ttrdmp & strdmp arrays (not used anymore)     '''DONE see rev'''.''' [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5830 5830]''' 
    197  * remove the remaining use of ua,va as workspace (changes in trazdf_imp.F90, zdfevd.F90, zdftmx.F90 and oce_trc.F90)   '''DONE''' see rev. [https://forge.ipsl.jussieu.fr/nemo/log/branches/2015/dev_r5721_CNRS9_NOC3_LDF?rev=5831 5831] 
    198  
    199 == [[BR]]IV. Pending issues : need to be solved before v3.7 release == 
    200 '''•''' Update the documentation. 
    201  
    202 '''•''' ensure the restartability & reproducibility for triad operator. 
    203  
    204 '''• ''' specification of eddy viscosity/diffusivity coefficients in case of grid-size dependency. 
    205  
    206 Issue:  define the grid-size dependency in such a way that does not require the Equator being inside the domain.[[BR]]Solution: [[BR]]'''- 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. [[BR]]In addition:[[BR]]- '''add''' in NEMOGCM/TOOLS directory a program that read a coordinates.nc file apply a reduction of scale factors in some straits, and create the associated extended coordinates file (coordinates_e1e2u_v.nc)[[BR]]- '''create''' the extended coordinates files form ORCA 2°, 1°, and 0.5°. ===>>> Done for ORCA 2° and 1°,  '''1/2° and 1/4° missing...[[BR]]'''- '''explore''' the possibility of defining ahm coef. at u- and v-points.  This will improve the velocity dependent case. 
    207  
    208 '''• '''specification of lateral friction at the coast.[[BR]]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 [[BR]]Solution: 
    209  
    210 == [[BR]][[BR]]V. Pending issues : to be solved in 2016 ? == 
    211 '''(V.1)''' Add a proper coding of Smagorinsky eddy viscosity and diffusivity... 
    212  
    213 '''(V.2)''' It should be possible to remove hdivn ... think about that 
    214  
    215 ---- 
    216 = [[BR]] Next Step = 
    217 Starting from the '''trunk''' (revision: [https://forge.ipsl.jussieu.fr/nemo/log/trunk/NEMOGCM?rev=5838 ​5836]), which has been phased with the branch described here, several branches are created which will contain the following item: 
    218  
    219 • Documentation : create a branch (shared among all developers) to document both the changes in revision [https://forge.ipsl.jussieu.fr/nemo/log/trunk/NEMOGCM?rev=5838 ​5836] and those in branches starting from this revision. 
    220  
    221 • Non linear free surface by default ([https://forge.ipsl.jussieu.fr/nemo/browser/branches/2015/dev_r5836_NOC3_vvl_by_default ​dev_r5836_NOC3_vvl_by_default]). see Wiki page [https://forge.ipsl.jussieu.fr/nemo/wiki/ticket/5836_NOC3_vvl_by_default 5836_NOC3_vvl_by_default] 
    222  
    223 • ZDF simplification: introduce a vertical physics manager that allows to save MPP communications. remove avmu, avmv. remove all key_zdfxxx  (a Gurvan's branch) 
    224  
    225 • create trptra.F90 which compute the effective velocity for both TRC and TRA  (a Gurvan's branch) 
    226  
    227 • remove all remaining hard coded parts specific to a configuration (especially ORCA2): see a description of the remaining work here: [https://forge.ipsl.jussieu.fr/nemo/wiki/2014WP/2014_SystemSimplification_hard_coding SystemSimplification_hard_coding] 
    228  
    229 • remove most of the remaining CPP keys (key_trabbl, key_zdf...) 
    230  
    231 • remove the solver, keeping only split-explicit scheme for free-surface time stepping. (Jérome's branch) 
    232  
    233 .... 
    234  
    235 ---- 
    236 = To be CHECKED = 
    237 (not necessary associated with this branch) 
    238  
    239  * find ''!!gm'' everywhere in the fortran code, and try to solve the issues raised ! 
    240  * check that task_i use ssmask, i.e. that it takes into account the under ice shelf seas. 
    241  * CRS : the new arrays derived from horizontal scale factors MUST be added in CRS. 
    242  * Bug in diawri.F90 when NOT using key_iomput (OK ==>> see ticket #1596) 
    243  
    244  * Idea for finalization of domhgr.F90 :[[BR]]'''add''' 2 modules (from domhgr.F90), domhgr_read.F90 and domhgr_ana.F90, which contains:[[BR]]- domhgr_read.F90: the CASE jphgr_msh=0 of domhgr.F90 (i.e. read the coordinates file)[[BR]]- domhgr_ana.F90: the CASE jphgr_msh=5 of domhgr.F90 (i.e. the GYRE analytical definition of the coordinates)[[BR]]'''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)[[BR]]'''remove''' from the namelist_ref/namdom all variable related to the horizontal mesh, and add a flag, ln_mesh_read, =T read the coordinates.nc file ; =F analytical mesh (by default GYRE mesh). 
    245  * sbcisf.F90 : use of hard coded staff associated with EOS (in situ temperature and co ...) 
    246  * sbcwave.F90   :  lot of modifications has been done, but I'm still uncomfortable with the calculation of stokes drift velocities....[[BR]][[BR]] 
    247  
    248 ... 
    249  
    250 ---- 
     55(3) add in the input file  of both ORCA2 and ORCA1 the input files of the new TMX