Changes between Version 25 and Version 26 of ticket/1593_CNRS9_NOC3_LDF


Ignore:
Timestamp:
2015-10-03T09:50:50+02:00 (5 years ago)
Author:
gm
Comment:

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  • ticket/1593_CNRS9_NOC3_LDF

    v25 v26  
    1717''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) ; 
    1818 
    19 ''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)''' '''; 
    20  
    21 (3) implement bilaplacian iso-neutral operators (Lemarié et al. (2012). 
     19''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). 
    2220 
    2321---- 
     
    2523Three steps: [[BR]] 
    2624 
    27   '''                                                  I. Phasing of horizontal scale factors                         '''                        ===>>> 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)''' 
     25  '''                                                     I. Phasing of horizontal scale factors                         '''                           ===>>> 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)''' 
    2826 
    2927'''   (I.1)''' standardisation of the name of quantities derived from horizontal scale factors (many modules of NEMO)[[BR]]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 
    3028 
    31 '''   (I.2)''' add a optional read of surface scale factors at velocity points in coordinate file (domhgr.F90)[[BR]]        The input coordinate file have to include e1e2u and e1e2v in case of reduction of the scale factors in some straits.[[BR]]        When e1u or e2v are reduced in some straits, the surface at u- and v-points remains 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 surface between 2 adjacent U or V 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]''' 
    32  
    33   '''                                                 II. Phasing of the advective/diffusive trends on tracers''' 
     29'''   (I.2)''' add a optional read of surface scale factors at velocity points in coordinate file (domhgr.F90)[[BR]]   The input coordinate file have to include e1e2u and e1e2v in case of reduction of the scale factors in some straits.[[BR]]        When e1u or e2v are reduced in some straits, the surface at u- and v-points remains 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 surface between 2 adjacent U or V 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]''' 
     30 
     31  ''' [[BR]] [[BR]] II. Phasing of the advective/diffusive trends on tracers''' 
    3432 
    3533'''II.1 —''' '''LDF on tracers''' (both TRA & TRC) - Diffusive trends :    ''' '''===>>> 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''' 
     
    8886/ 
    8987}}} 
    90 [[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 
    91  
    92 ''passive tracers''[[BR]]- all changes in the management of diffusive coefficients and operator has been taken into account in TOP 
    93  
    94  * '''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]]- change default option in the namelist ! [[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 
    95  
    96 '''II.2 —''' '''Advective trends''' :TRA/traadv....     ===>>> 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]''' 
    97  
    98  * 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 
    99  
    100  * Surface boundary condition in ISF case has been added in all cases (except 4th order COMPACT scheme which currently don't work with ISF) 
     88[[BR]]- default value of the namelist: ''no operator chosen'': lln_traldf_lap=traldf_blp=0 No lateral diffusion applied on tracers '''  ===>>> CHECK THAT'''[[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 
     89 
     90''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 
     91 
     92'''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]]- change default option in the namelist ! [[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 
     93 
     94'''[[BR]]II.2 —''' '''Advective trends''' :TRA/traadv....     ===>>> 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]''' 
     95 
     96- 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 
     97 
     98[[BR]]- Surface boundary condition in ISF case has been added in all cases (except 4th order COMPACT scheme which currently don't work with ISF) 
    10199 
    102100{{{ 
     
    125123 * Atmospheric pressure forcing: change to a systematic call of sbc_apr in step.F90 (with or without BDY) and remove its call from sbcmod[[BR]]- remove key_ldftra_smag and associated module (ldftra_smag.F90)[[BR]]- remove key_vectopt_loop from all the code except in domzgr_substitute.h90 (it is an obsolescent feature only adapted to vector computers)[[BR]]- remove all "!CDIR " lines = NEC vector compiler instructions 
    126124 
    127   '''                                                  III. Phasing of viscous trends''' 
     125  '''  [[BR]]  [[BR]]  III. Phasing of viscous trends''' 
    128126 
    129127'''III.1 —''' '''LDF on dynamics'''  - viscous trends :  ===>>> OK see '''revision  ....     and  .....   with SETTE OK''' 
    130128 
    131 ''operator'': [[BR]]- laplacian operator: re-entrant laplacian for iso-level operators (dynldf_lap);[[BR]]- bilaplacian operator: dynldf_blp.F90 module: use of the re-entrant iso-level laplacian [[BR]]- suppression of traadv_eiv.F90 ; traldf_bilap.F90 ; traldf_bilapg.F90 ;[[BR]]- rotb and rotn arrays suppressed (even from the restart file) [[BR]]- hdivn and hdivb removed from restart too [[BR]]- divcur.F90 becomes divhor and only computes the horizontal divergence 
     129''operator'': [[BR]]- laplacian operator: re-entrant laplacian for iso-level operators (dynldf_lap);[[BR]]- bilaplacian operator: dynldf_blp.F90 module: use of the re-entrant iso-level laplacian [[BR]]- suppression of .... ;[[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]]- hdivn and hdivb removed from restart too [[BR]]- divcur.F90 becomes divhor.F90 and only computes the horizontal divergence 
    132130 
    133131[[BR]]''lateral mixing coefficient'':[[BR]]- new user interface (namelist) : 
     
    161159/ 
    162160}}} 
    163 [[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 ahtu and ahtv 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)    '''====>>> 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 traldf.F90 
     161[[BR]]- default value of the namelist: ''no operator chosen'': ln_dynldf_lap=dyndf_blp=0 No lateral diffusion applied on momentum   '''===>>> check THAT'''[[BR]]- create the 2D and 3D ahtu and ahtv 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 traldf.F90[[BR]]- change in all standard namelist_cfg and 1_namelist_cfg  ''' ===>>> TO BE DONE''' 
    164162 
    165163[[BR]]'''IV. Solve the pending issues''' 
    166164 
    167   '''                                                 (IV.1) '''                                specification of eddy viscosity/diffusivity coefficients in case of grid-size dependency.[[BR]]                                Issue:  define the grid-size dependency in such a way that does not require the Equator being inside the domain.[[BR]]                                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[[BR]]                                and use this scalar to compute the grid-size dependency of the coefficients.  [[BR]]'''(IV.2) '''                                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: 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[[BR]]                                and use this scalar to compute the grid-size dependency of the coefficients. [[BR]]'''(IV.3)'''    Add a proper coding of Smagorinsky eddy viscosity and diffusivity 
     165  '''                                                    (IV.1) '''                                   specification of eddy viscosity/diffusivity coefficients in case of grid-size dependency.[[BR]]                                   Issue:  define the grid-size dependency in such a way that does not require the Equator being inside the domain.[[BR]]                                   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[[BR]]                                   and use this scalar to compute the grid-size dependency of the coefficients.  [[BR]]   '''   (IV.2) '''                                   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: 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[[BR]]                                   and use this scalar to compute the grid-size dependency of the coefficients. [[BR]]   '''   (IV.3)'''       Add a proper coding of Smagorinsky eddy viscosity and diffusivity 
    168166 
    169167... 
     
    177175 * test with SETTE (especially restartability and reproducibility ) 
    178176 
    179  [[BR]] '''  V. Finalize the simplification''' 
    180  
    181   '''                                (V.1) 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]]'''(V.2) 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]]'''(V.3) create''' in NEMOGCM/TOOLS directory a program that create the ORCA2 and ORCA1 eddy viscosity''' ????''' 
     177  [[BR]]    '''     V. Finalize the simplification''' 
     178 
     179  '''                                   (V.1) 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]]   '''   (V.2) 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]]   '''   (V.3) create'''    in NEMOGCM/TOOLS directory a program that create the ORCA2 and ORCA1 eddy viscosity'''    ????''' 
    182180 
    183181...