Changes between Version 33 and Version 34 of ticket/0927_Energy_diag


Ignore:
Timestamp:
2012-03-20T18:49:03+01:00 (9 years ago)
Author:
fabien.roquet
Comment:

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  • ticket/0927_Energy_diag

    v33 v34  
    1 [[PageOutline]] Last edited [[Timestamp]]  !'''Author!''' : Gurvan Madec  !'''Ticket !''' : !#927  !'''Branch!''' : ![https://forge.ipsl.jussieu.fr/nemo/browser/branches/2012/dev_r3309_LOCEAN12_Ediag 2012/dev_r3309_LOCEAN12_Ediag]  ---- == !'''LOCEAN .12 - Energy diagnostics!''' == !'''     Motivation: !'''    output 3D trends of tracers, momentum, kinetic energy and potential energy.  !'''     Status :!''' the extraction of trends terms exists, but not the 3D output of the trends     !'''     Main tasks :!'''              (1) implement the 3D output of tracers and momentum trends using iom_put            (2) compute and output the 3D trends of PE and KE                 (3) validatation + documentation       !'''     Science Reviewer:!''' NOCS guy?           !'''     System Reviewer:!'''  NOCS guy?          !'''     Deadline:!'''   spring 2012     !'''     Priority:!'''      high      !'''     Depends on:!'''    gurvan disponibilities     !'''     Principal Investigator : !'''      Gurvan Madec and Simona Flavoni (simona.flavoni@locean-ipsl.upmc.fr)       ---- == !''' Detail of the implementation!''' == ---- === !''' Step I : add the 3D output !''' === see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3316 revision 3316]    !'''        trdmod_oce!'''         module and !'''        namtrd namelist!'''              logical flags added in namlist namtrd which now controls what is done with the trends.   All the types of treatment of a given trend are available at the same time. The memory requirement will only increase due to the time averaged arrays defined in IOM.  !{{{    LOGICAL , PUBLIC  ::   ln_dyn_trd   = .FALSE.        !: (T) 3D momentum             trends or (F) not    LOGICAL , PUBLIC  ::   ln_tra_trd   = .FALSE.        !: (T) 3D tracer               trends or (F) not    LOGICAL , PUBLIC  ::   ln_PE_trd    = .FALSE.        !: (T) 3D Potential Energy     trends or (F) not    LOGICAL , PUBLIC  ::   ln_KE_trd    = .FALSE.        !: (T) 3D Kinetic   Energy     trends or (F) not    LOGICAL , PUBLIC  ::   ln_vor_trd   = .FALSE.        !: (T) 3D barotropic vorticity trends or (F) not    LOGICAL , PUBLIC  ::   ln_glo_trd   = .FALSE.        !: (T) global domain averaged diag for T, T^2, KE, and PE    LOGICAL , PUBLIC  ::   ln_dyn_mld   = .FALSE.        !: (T) 2D tracer   trends averaged over the mixed layer     LOGICAL , PUBLIC  ::   ln_tra_mld   = .FALSE.        !: (T) 2D momentum trends averaged over the mixed layer  }}} Add these new logical in the namelist. !'''==>>> CAUTION only in the ORCA2_LIM directory!'''   NB: here is the new name set in revision number 3318     !'''        trdtra!'''         module     Add a systematic mask of the trend.  Change the comments to better describe the purpose of this module. Its purpose is:      'TRA' case:  to regroup T & S trends and send them to trd_mod, with, in case of advection, transform the incoming advective fluxes into advctive trend (U.grad[T])           'TRC' case:  send trend to ted_mod_trc, with,  in case of advection,  transform the incoming advective fluxes into advective trend            all cases  : mask the trend    (!'''        ===>>>   PROBABLY add in the module a lbc_lnk so that the trend is defined everywhere!'''        )    !'''        dynadv_cen2 and _ubs!'''         modules     change jpdyn_trd_had  into jpdyn_trd_keg. Now in flux form _keg corresponds to the horizontal advection trends and _rvo to the metric terms       !'''        dynnxt!'''         module     add the output using mom of the total den trend (except asselin time filter) ("utrd_tot", "vtrd_tot") and of the asselin time filter trend ("utrd_atf", "vtrd_atf") but with a shift by one time step       !'''        dynvor, trdvor and trdmod_oce!'''         modules     suppress the call to trd_mod in the jpdyn_trd_dat case (computation of beta.V) add add the calculation of beta.V term in 'trdvor' in jpvor_pvo case. And obviously suppress jpdyn_trd_dat from trdmod_oce   Also suppress the jpdyn_trd_had case  horizontal advection for the dynamics is 'keg' + 'vor'  ; in case of flux form,  'had' is put in 'keg' and the metric terms is put in 'vor'   there is now only 10 trends on the dynamics instead of 12       !'''        trdmod!'''         module     1- introduce the new logical namelist parameters  2- introduce new subroutines : !'''trd_budget!''' : computation of the domain averaged T,T!^2!^, PE, KE trends formerly computes in trd_mod routine)  !''' trd_3Diom!''': output of the 3D trends using IOM        !'''        trdicp!'''         module     add in trd_twr routine the computation of the vertical diffusive trend on T & S in case of iso-neutral diffusion (ln_traldf_iso=T). These trends ("ttrd_zdfp", "strd_zdfp")  name zdfp for "PURE" vertical diffusion trends are output so that by difference with "zdf" trends we can access to the vertical contribution of the iso-neutral operator        !'''        iodef.xml!'''         file     add all the trends nick name : !'''==>>> CAUTION only in the ORCA2_LIM directory!'''      ---- === !''' Step II : simplification of the structure !''' ===   !'''        trdicp and trdicp_oce!'''         modules     see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3317 revision 3317]  1- suppress trdicp_oce module (put required variables in trdmod_oce parameters)  2- use the jptra_trd_...  instead of jpicp_...  3- move trd_budget subroutine from trdmod to trdicp.F90. Suppress trd_icp routine (i.e. trd_2d, trd_3d) as the work is now simply done in trd_budget.  4- rescan all dyn/tra trend indices. add jptra_trd_zdfp for "PURE Kz dissusive trend when ln_traldf_iso=T (see also changes in tranxt where a call to trd_tra is done just before the swap, so that PURE Kz trends can be diagnosed in tra_trd. See also xml file).  5- jptra_trd_nsr and jptra_trd_cdt are 3D trends as their incorporate both surface forcing AND runoff, the later being possibly spread in depth (!'''==>>> probably to be changed!''')  6- suppress the key_trddyn key trdtra  from trdicp     !'''        trdtra - trddyn - trdmod - trdvor!'''         modules : impact on !'''        TRA!'''        , !'''        DYN!'''        , !'''        TRD!'''         and almost all !'''        TOP_SRC!'''         modules     see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3318 revision 3318]  Change the logic : split DYN and TRA trend diagnostics in separate modules   move the call to trd_... from the end of step to the select CASE(jp..._atf) i.e. when the last trend is send to trdtra or trddyn   Change the name of the trend indices from jptra_trd_xxx to jptra_xxx and from jpdyn_trd_yyy to jpdyn_yyy. This impact TRA,DYN, TRD but also all TOP_SRC   0- move trdmod_oce into trd_oce  1- trdvor: move the trdvor 1st part from trdmod to trevor module. Suppress the call of trd_vor from step (now called in trddyn for each trend, with the output done for the last trend (_atf).   2- create a trddyn that manage the distribution to iom, global mean, KE, vor, mld   3- trdtra in TRC case pre-process advective trends and then call trdmod_trc ; in TRA case: it regroups T & S trend in one and calla local routine to manage the distribution to iom, global mean, PE, mld  4- trdmod now contains only the trdmod_init routine. Rename all as trdini.F90 and ted_init subroutine 5- suppress all !'''key_trd...!''' keys (thanks to dynamical allocation) except for the top key: !'''key_trdmld_trc!'''.   !''' ==>>> To be done!'''    ---- === !''' Step III : addition of 3D KE diagnostics !''' ===   !'''        trdken!'''         module     see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3325 revision 3325]  0- bug correction:  in trddyn.F90  (ji,jj) ==>> (:,:) in surface stress computation   1- create a trdken.F90 module which compute the KE trends at T-point and out them using IOM  TO BE DONE: diagnose the KE local dissipation and associated diffusive fluxes ; diagnose bottom friction in all cases (implicit/explicit) ; in flux form, remove the KE*divh(U) from the H/V advection trends  NB: Missing the KE trends in the xml files ; Bug in trdtra: 2 call to ted_tra_mng in case of jptra_zdfp. Both corrected in Step IV release (see below)  ---- === !''' Step IV : addition of 3D PE diagnostics !''' ===   !'''        trdpen!'''         module     see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3326 revision 3326] and ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3327 revision 3327] 0- correct a bug in trdtra and trdken  1- add xml name for both PE and KE   2- create a trdpen.F90 module which compute the PE trends at T-point and out them using IOM  3- introduce in eosbn2 a subroutine, eos_drau_dtds, that computes the partial derivative off in situ density with respect to T and S (NB: only coded the 2 linear eos, !'''TO BE DONE  for the UNESCO eos!''' (nn_eos=0)  4- correct a few bugs and adopt almost systematic CASE structure in trdtra (see revision 3327)  NB: to be verified: the addition of a ssh term in PE for NOT lk_vvl case  NB: runoff put as a source term in the divergence computation since v3.3 (see divcur), implication for source term in PE, but also tracer trends ? !'''Think about that!'''''!''''                    !'''Pending issues!''' :    atmospheric pressure gradient trend not taken into account (see dynspg.F90  !'''        To be done !!!!'''                !'''    kpp non-local trend put in zdf trends !!!  this will not work ! a additional trend term should be add !'''        To be done !!!!'''                !'''    problems to be solved: vvl case for tracer sad trends ; flux form case for had (keg) and zad momentum trends       add separate modules for each option ...    create the momentum diag over the ML    reshape trdtra so that T and S are treated separately in all ted routine (including mld diag...)  !'''Changes done by Fabien R.!'''    In trdtra.F90:   * removed semi-colon on lines 118 and 267.  * replaced ln_glo_trd by ln_PE_trd in line 239.  * Moved wrk_alloc and wrk_dealloc  in the IF (.NOT.lk_vvl ) structure.  In trddyn.F90:   * Added wrk_alloc, wrk_dealloc and lbc_lnk in trd_dyn_iom.    Remove unused variables ztswu, ztswv.  * Following norm in the code, utrd_bfr and vtrd_bfr should be filled only when ln_bfrimp=.FALSE. (non implicit bottom friction).  * Implicit bottom friction is calculated at the end of each timestep, in dynzdf_imp.    The diagnostic of bottom friction in the implicit case is saved in separate variable names to avoid confusion: utrd_bfr_imp and vtrd_bfr_imp.    Similarly, diagnostics of wind stress inputs are provided in 2D fields utrd_tau and vtrd_tau.  In step.F90:   * Added "IF( .NOT.ln_bfrimp)" before the "CALL dyn_bfr( kstp )" to clarify that dyn_bfr is called only if bottom friction is explicit, as proposed by gm.  In trdglo.F90:   * In trd_glo_init, corrected definition for tvolt:             tvolt = tvolt + SUM( e1e2t(:,:) * fse3t(:,:,jk) * tmask(:,:,jk) * tmask_i(:,:) )  * Treatment of bfr has been clarified: if bfr is implicit (ln_bfrimp=.TRUE.), the bottom friction term remain 0, as bottom friction is implicitly included in the vertical diffusion term.  In trd_oce.F90    ---- === Testing === Testing could consider (where appropriate) other configurations in addition to NVTK].  || NVTK Tested || !!'''YES/NO!!''' || || Other model configurations || !!'''YES/NO!!''' || || Processor configurations tested || [ Enter processor configs tested here ] || || If adding new functionality please confirm that the ![[BR]]New code doesn't change results when it is switched off ![[BR]]and !!''works!!'' when switched on || !!'''YES/NO/NA!!''' ||  (Answering UNSURE is likely to generate further questions from reviewers.)  'Please add further summary details here'   * Processor configurations tested  * etc----  === Bit Comparability === || Does this change preserve answers in your tested standard configurations (to the last bit) ? || !!'''YES/NO !!''' || || Does this change bit compare across various processor configurations. (1xM, Nx1 and MxN are recommended) || !!'''YES/NO!!''' || || Is this change expected to preserve answers in all possible model configurations? || !!'''YES/NO!!''' || || Is this change expected to preserve all diagnostics? ![[BR]]!!,,!!''Preserving answers in model runs does not necessarily imply preserved diagnostics. !!'' || !!'''YES/NO!!''' ||  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  * What is needed to achieve regression with the previous model release (e.g. a regression branch, hand-edits etc). If this is not possible, explain why not.  * What do you expect to see occur in the test harness jobs?  * Which diagnostics have you altered and why have they changed?Please add details here........  ---- === System Changes === || Does your change alter namelists? || !!'''YES/NO !!''' || || Does your change require a change in compiler options? || !!'''YES/NO !!''' ||  If any of these apply, please document the changes required here.......  ---- === Resources === !''Please !''summarize!'' any changes in runtime or memory use caused by this change......!''  ---- === IPR issues === || Has the code been wholly (100%) produced by NEMO developers staff working exclusively on NEMO? || !!'''YES/ NO !!''' ||  If No:   * Identify the collaboration agreement details  * Ensure the code routine header is in accordance with the agreement, (Copyright/Redistribution etc).Add further details here if required.......... 
     1[[PageOutline]] Last edited [[Timestamp]]  !'''Author!''' : Gurvan Madec  !'''Ticket !''' : !#927  !'''Branch!''' : ![https://forge.ipsl.jussieu.fr/nemo/browser/branches/2012/dev_r3309_LOCEAN12_Ediag 2012/dev_r3309_LOCEAN12_Ediag]  ---- == !'''LOCEAN .12 - Energy diagnostics!''' == !'''     Motivation: !'''    output 3D trends of tracers, momentum, kinetic energy and potential energy.  !'''     Status :!''' the extraction of trends terms exists, but not the 3D output of the trends     !'''     Main tasks :!'''              (1) implement the 3D output of tracers and momentum trends using iom_put            (2) compute and output the 3D trends of PE and KE                 (3) validatation + documentation       !'''     Science Reviewer:! ''' NOCS guy?           !'''     System Reviewer:! '''  NOCS guy?          !'''     Deadline:! '''   spring 2012     !'''     Priority:! '''      high      !'''     Depends on:! '''    gurvan disponibilities     !'''     Principal Investigator : !'''      Gurvan Madec and Simona Flavoni (simona.flavoni@locean-ipsl.upmc.fr)       ---- == !''' Detail of the implementation!''' == ---- === !''' Step I : add the 3D output !''' === see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3316 revision 3316]    !'''        trdmod_oce!'''         module and !'''        namtrd namelist!'''              logical flags added in namlist namtrd which now controls what is done with the trends.   All the types of treatment of a given trend are available at the same time. The memory requirement will only increase due to the time averaged arrays defined in IOM.  !{{{    LOGICAL , PUBLIC  ::   ln_dyn_trd   = .FALSE.        !: (T) 3D momentum             trends or (F) not    LOGICAL , PUBLIC  ::   ln_tra_trd   = .FALSE.        !: (T) 3D tracer               trends or (F) not    LOGICAL , PUBLIC  ::   ln_PE_trd    = .FALSE.        !: (T) 3D Potential Energy     trends or (F) not    LOGICAL , PUBLIC  ::   ln_KE_trd    = .FALSE.        !: (T) 3D Kinetic   Energy     trends or (F) not    LOGICAL , PUBLIC  ::   ln_vor_trd   = .FALSE.        !: (T) 3D barotropic vorticity trends or (F) not    LOGICAL , PUBLIC  ::   ln_glo_trd   = .FALSE.        !: (T) global domain averaged diag for T, T^2, KE, and PE    LOGICAL , PUBLIC  ::   ln_dyn_mld   = .FALSE.        !: (T) 2D tracer   trends averaged over the mixed layer     LOGICAL , PUBLIC  ::   ln_tra_mld   = .FALSE.        !: (T) 2D momentum trends averaged over the mixed layer  }}} Add these new logical in the namelist. !'''==>>> CAUTION only in the ORCA2_LIM directory!'''   NB: here is the new name set in revision number 3318     !'''        trdtra!'''         module     Add a systematic mask of the trend.  Change the comments to better describe the purpose of this module. Its purpose is:      'TRA' case:  to regroup T & S trends and send them to trd_mod, with, in case of advection, transform the incoming advective fluxes into advctive trend (U.grad[T])           'TRC' case:  send trend to ted_mod_trc, with,  in case of advection,  transform the incoming advective fluxes into advective trend            all cases  : mask the trend    (!'''        ===>>>   PROBABLY add in the module a lbc_lnk so that the trend is defined everywhere!'''        )    !'''        dynadv_cen2 and _ubs!'''         modules     change jpdyn_trd_had  into jpdyn_trd_keg. Now in flux form _keg corresponds to the horizontal advection trends and _rvo to the metric terms       !'''        dynnxt!'''         module     add the output using mom of the total den trend (except asselin time filter) ("utrd_tot", "vtrd_tot") and of the asselin time filter trend ("utrd_atf", "vtrd_atf") but with a shift by one time step       !'''        dynvor, trdvor and trdmod_oce!'''         modules     suppress the call to trd_mod in the jpdyn_trd_dat case (computation of beta.V) add add the calculation of beta.V term in 'trdvor' in jpvor_pvo case. And obviously suppress jpdyn_trd_dat from trdmod_oce   Also suppress the jpdyn_trd_had case  horizontal advection for the dynamics is 'keg' + 'vor'  ; in case of flux form,  'had' is put in 'keg' and the metric terms is put in 'vor'   there is now only 10 trends on the dynamics instead of 12       !'''        trdmod!'''         module     1- introduce the new logical namelist parameters  2- introduce new subroutines : !'''trd_budget!''' : computation of the domain averaged T,T!^2!^, PE, KE trends formerly computes in trd_mod routine)  !''' trd_3Diom!''': output of the 3D trends using IOM        !'''        trdicp!'''         module     add in trd_twr routine the computation of the vertical diffusive trend on T & S in case of iso-neutral diffusion (ln_traldf_iso=T). These trends ("ttrd_zdfp", "strd_zdfp")  name zdfp for "PURE" vertical diffusion trends are output so that by difference with "zdf" trends we can access to the vertical contribution of the iso-neutral operator        !'''        iodef.xml!'''         file     add all the trends nick name : !'''==>>> CAUTION only in the ORCA2_LIM directory!'''      ---- === !''' Step II : simplification of the structure !''' ===   !'''        trdicp and trdicp_oce!'''         modules     see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3317 revision 3317]  1- suppress trdicp_oce module (put required variables in trdmod_oce parameters)  2- use the jptra_trd_...  instead of jpicp_...  3- move trd_budget subroutine from trdmod to trdicp.F90. Suppress trd_icp routine (i.e. trd_2d, trd_3d) as the work is now simply done in trd_budget.  4- rescan all dyn/tra trend indices. add jptra_trd_zdfp for "PURE Kz dissusive trend when ln_traldf_iso=T (see also changes in tranxt where a call to trd_tra is done just before the swap, so that PURE Kz trends can be diagnosed in tra_trd. See also xml file).  5- jptra_trd_nsr and jptra_trd_cdt are 3D trends as their incorporate both surface forcing AND runoff, the later being possibly spread in depth (!'''==>>> probably to be changed!''')  6- suppress the key_trddyn key trdtra  from trdicp     !'''        trdtra - trddyn - trdmod - trdvor!'''         modules : impact on !'''        TRA!'''        , !'''        DYN!'''        , !'''        TRD!'''         and almost all !'''        TOP_SRC!'''         modules     see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3318 revision 3318]  Change the logic : split DYN and TRA trend diagnostics in separate modules   move the call to trd_... from the end of step to the select CASE(jp..._atf) i.e. when the last trend is send to trdtra or trddyn   Change the name of the trend indices from jptra_trd_xxx to jptra_xxx and from jpdyn_trd_yyy to jpdyn_yyy. This impact TRA,DYN, TRD but also all TOP_SRC   0- move trdmod_oce into trd_oce  1- trdvor: move the trdvor 1st part from trdmod to trevor module. Suppress the call of trd_vor from step (now called in trddyn for each trend, with the output done for the last trend (_atf).   2- create a trddyn that manage the distribution to iom, global mean, KE, vor, mld   3- trdtra in TRC case pre-process advective trends and then call trdmod_trc ; in TRA case: it regroups T & S trend in one and calla local routine to manage the distribution to iom, global mean, PE, mld  4- trdmod now contains only the trdmod_init routine. Rename all as trdini.F90 and ted_init subroutine 5- suppress all !'''key_trd...!''' keys (thanks to dynamical allocation) except for the top key: !'''key_trdmld_trc!'''.   !''' ==>>> To be done!'''    ---- === !''' Step III : addition of 3D KE diagnostics !''' ===   !'''        trdken!'''         module     see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3325 revision 3325]  0- bug correction:  in trddyn.F90  (ji,jj) ==>> (:,:) in surface stress computation   1- create a trdken.F90 module which compute the KE trends at T-point and out them using IOM  TO BE DONE: diagnose the KE local dissipation and associated diffusive fluxes ; diagnose bottom friction in all cases (implicit/explicit) ; in flux form, remove the KE*divh(U) from the H/V advection trends  NB: Missing the KE trends in the xml files ; Bug in trdtra: 2 call to ted_tra_mng in case of jptra_zdfp. Both corrected in Step IV release (see below)  ---- === !''' Step IV : addition of 3D PE diagnostics !''' ===   !'''        trdpen!'''         module     see ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3326 revision 3326] and ![https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3327 revision 3327] 0- correct a bug in trdtra and trdken  1- add xml name for both PE and KE   2- create a trdpen.F90 module which compute the PE trends at T-point and out them using IOM  3- introduce in eosbn2 a subroutine, eos_drau_dtds, that computes the partial derivative off in situ density with respect to T and S (NB: only coded the 2 linear eos, !'''TO BE DONE  for the UNESCO eos!''' (nn_eos=0)  4- correct a few bugs and adopt almost systematic CASE structure in trdtra (see revision 3327)  NB: to be verified: the addition of a ssh term in PE for NOT lk_vvl case  NB: runoff put as a source term in the divergence computation since v3.3 (see divcur), implication for source term in PE, but also tracer trends ? !'''Think about that!'''''!''''                    !'''Pending issues!''' :    atmospheric pressure gradient trend not taken into account (see dynspg.F90  !'''        To be done !!!!'''                !'''    kpp non-local trend put in zdf trends !!!  this will not work ! a additional trend term should be add !'''        To be done !!!!'''                !'''    problems to be solved: vvl case for tracer sad trends ; flux form case for had (keg) and zad momentum trends       add separate modules for each option ...    create the momentum diag over the ML    reshape trdtra so that T and S are treated separately in all ted routine (including mld diag...)  !'''Changes done by Fabien R.!'''    In trdtra.F90:   * removed semi-colon on lines 118 and 267.  * replaced ln_glo_trd by ln_PE_trd in line 239.  * Moved wrk_alloc and wrk_dealloc  in the IF (.NOT.lk_vvl ) structure.  In trddyn.F90:   * Added wrk_alloc, wrk_dealloc and lbc_lnk in trd_dyn_iom.    Remove unused variables ztswu, ztswv.  * Following norm in the code, utrd_bfr and vtrd_bfr should be filled only when ln_bfrimp=.FALSE. (non implicit bottom friction).  * Implicit bottom friction is calculated at the end of each timestep, in dynzdf_imp.    The diagnostic of bottom friction in the implicit case is saved in separate variable names to avoid confusion: utrd_bfr_imp and vtrd_bfr_imp.    Similarly, diagnostics of wind stress inputs are provided in 2D fields utrd_tau and vtrd_tau.  In step.F90:   * Added "IF( .NOT.ln_bfrimp)" before the "CALL dyn_bfr( kstp )" to clarify that dyn_bfr is called only if bottom friction is explicit, as proposed by gm.  In trdglo.F90:   * In trd_glo_init, corrected definition for tvolt:             tvolt = tvolt + SUM( e1e2t(:,:) * fse3t(:,:,jk) * tmask(:,:,jk) * tmask_i(:,:) )  * Treatment of bfr has been clarified: if bfr is implicit (ln_bfrimp=.TRUE.), the bottom friction term remain 0, as bottom friction is implicitly included in the vertical diffusion term.  In trd_oce.F90    ---- === Testing === Testing could consider (where appropriate) other configurations in addition to NVTK].  ''' 
     2 
     3|| NVTK Tested || !!'''YES/NO!!''' || || Other model configurations || !!'''YES/NO!!''' || || Processor configurations tested || [ Enter processor configs tested here ] || || If adding new functionality please confirm that the ![[BR]]New code doesn't change results when it is switched off ![[BR]]and !!''works!!'' when switched on || !!'''YES/NO/NA!!''' || (Answering UNSURE is likely to generate further questions from reviewers.)  'Please add further summary details here'   * Processor configurations tested  * etc----  === Bit Comparability === || Does this change preserve answers in your tested standard configurations (to the last bit) ? || !!'''YES/NO !!''' || || Does this change bit compare across various processor configurations. (1xM, Nx1 and MxN are recommended) || !!'''YES/NO!!''' || || Is this change expected to preserve answers in all possible model configurations? || !!'''YES/NO!!''' || || Is this change expected to preserve all diagnostics? ![[BR]]!!,,!!''Preserving answers in model runs does not necessarily imply preserved diagnostics. !!'' || !!'''YES/NO!!''' || 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  * What is needed to achieve regression with the previous model release (e.g. a regression branch, hand-edits etc). If this is not possible, explain why not.  * What do you expect to see occur in the test harness jobs?  * Which diagnostics have you altered and why have they changed?Please add details here........  ---- === System Changes === || Does your change alter namelists? || !!'''YES/NO !!''' || || Does your change require a change in compiler options? || !!'''YES/NO !!''' || If any of these apply, please document the changes required here.......  ---- === Resources === !''Please !''summarize!'' any changes in runtime or memory use caused by this change......!''  ---- === IPR issues === || Has the code been wholly (100%) produced by NEMO developers staff working exclusively on NEMO? || !!'''YES/ NO !!''' || If No:   * Identify the collaboration agreement details  * Ensure the code routine header is in accordance with the agreement, (Copyright/Redistribution etc).Add further details here if required.......... || 
    24 
    35[[PageOutline]] Last edited [[Timestamp]] 
     
    1315'''     Motivation: '''    output 3D trends of tracers, momentum, kinetic energy and potential energy.[[BR]] '''     Status :''' the extraction of trends terms exists, but not the 3D output of the trends   [[BR]] '''     Main tasks :'''         [[BR]] 
    1416 
    15   (1) implement the 3D output of tracers and momentum trends using iom_put [[BR]]        (2) compute and output the 3D trends of PE and KE [[BR]]             (3) validatation + documentation  [[BR]] 
     17  (1) implement the 3D output of tracers and momentum trends using iom_put [[BR]]         (2) compute and output the 3D trends of PE and KE [[BR]]              (3) validatation + documentation  [[BR]] 
    1618 
    1719'''     Science Reviewer:''' NOCS guy?     [[BR]]     '''     System Reviewer:'''  NOCS guy?     [[BR]]    '''     Deadline:'''   spring 2012   [[BR]] '''     Priority:'''      high    [[BR]] '''     Depends on:'''    gurvan disponibilities   [[BR]] '''     Principal Investigator : '''      Gurvan Madec and Simona Flavoni (simona.flavoni@locean-ipsl.upmc.fr)  [[BR]] [[BR]] 
     
    2325see [https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3316 revision 3316] 
    2426 
    25   '''        trdmod_oce'''         module and '''        namtrd namelist'''         [[BR]] 
     27  '''         trdmod_oce'''          module and '''         namtrd namelist'''          [[BR]] 
    2628 
    2729logical flags added in namlist namtrd which now controls what is done with the trends. [[BR]] All the types of treatment of a given trend are available at the same time. The memory requirement will only increase due to the time averaged arrays defined in IOM. 
     
    3941Add these new logical in the namelist. '''==>>> CAUTION only in the ORCA2_LIM directory''' [[BR]] NB: here is the new name set in revision number 3318[[BR]] 
    4042 
    41   '''        trdtra'''         module[[BR]] 
     43  '''         trdtra'''          module[[BR]] 
    4244 
    4345Add a systematic mask of the trend.[[BR]] Change the comments to better describe the purpose of this module. Its purpose is: [[BR]] 
    4446 
    45   'TRA' case:  to regroup T & S trends and send them to trd_mod, with, in case of advection, transform the incoming advective fluxes into advctive trend (U.grad[T])[[BR]]        'TRC' case:  send trend to ted_mod_trc, with,  in case of advection,  transform the incoming advective fluxes into advective trend [[BR]]        all cases  : mask the trend    ('''        ===>>>   PROBABLY add in the module a lbc_lnk so that the trend is defined everywhere'''        ) 
    46  
    47   '''        dynadv_cen2 and _ubs'''         modules[[BR]] 
     47  'TRA' case:  to regroup T & S trends and send them to trd_mod, with, in case of advection, transform the incoming advective fluxes into advctive trend (U.grad[T])[[BR]]         'TRC' case:  send trend to ted_mod_trc, with,  in case of advection,  transform the incoming advective fluxes into advective trend [[BR]]         all cases  : mask the trend    ('''         ===>>>   PROBABLY add in the module a lbc_lnk so that the trend is defined everywhere'''         ) 
     48 
     49  '''         dynadv_cen2 and _ubs'''          modules[[BR]] 
    4850 
    4951change jpdyn_trd_had  into jpdyn_trd_keg. Now in flux form _keg corresponds to the horizontal advection trends and _rvo to the metric terms[[BR]] [[BR]] 
    5052 
    51   '''        dynnxt'''         module[[BR]] 
     53  '''         dynnxt'''          module[[BR]] 
    5254 
    5355add the output using mom of the total den trend (except asselin time filter) ("utrd_tot", "vtrd_tot") and of the asselin time filter trend ("utrd_atf", "vtrd_atf") but with a shift by one time step[[BR]] [[BR]] 
    5456 
    55   '''        dynvor, trdvor and trdmod_oce'''         modules[[BR]] 
     57  '''         dynvor, trdvor and trdmod_oce'''          modules[[BR]] 
    5658 
    5759suppress the call to trd_mod in the jpdyn_trd_dat case (computation of beta.V) add add the calculation of beta.V term in 'trdvor' in jpvor_pvo case. And obviously suppress jpdyn_trd_dat from trdmod_oce [[BR]] Also suppress the jpdyn_trd_had case  horizontal advection for the dynamics is 'keg' + 'vor'  ; in case of flux form,  'had' is put in 'keg' and the metric terms is put in 'vor' [[BR]] there is now only 10 trends on the dynamics instead of 12[[BR]] [[BR]] 
    5860 
    59   '''        trdmod'''         module[[BR]] 
     61  '''         trdmod'''          module[[BR]] 
    6062 
    61631- introduce the new logical namelist parameters[[BR]] 2- introduce new subroutines : '''trd_budget''' : computation of the domain averaged T,T^2^, PE, KE trends formerly computes in trd_mod routine)[[BR]] ''' trd_3Diom''': output of the 3D trends using IOM [[BR]] [[BR]] 
    6264 
    63   '''        trdicp'''         module[[BR]] 
     65  '''         trdicp'''          module[[BR]] 
    6466 
    6567add in trd_twr routine the computation of the vertical diffusive trend on T & S in case of iso-neutral diffusion (ln_traldf_iso=T). These trends ("ttrd_zdfp", "strd_zdfp")  name zdfp for "PURE" vertical diffusion trends are output so that by difference with "zdf" trends we can access to the vertical contribution of the iso-neutral operator [[BR]] [[BR]] 
    6668 
    67   '''        iodef.xml'''         file[[BR]] 
     69  '''         iodef.xml'''          file[[BR]] 
    6870 
    6971add all the trends nick name : '''==>>> CAUTION only in the ORCA2_LIM directory''' [[BR]] [[BR]] 
     
    7173---- 
    7274=== ''' Step II : simplification of the structure ''' === 
    73   '''        trdicp and trdicp_oce'''         modules[[BR]] 
     75  '''         trdicp and trdicp_oce'''          modules[[BR]] 
    7476 
    7577see [https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3317 revision 3317] 
     
    77791- suppress trdicp_oce module (put required variables in trdmod_oce parameters)[[BR]] 2- use the jptra_trd_...  instead of jpicp_...  3- move trd_budget subroutine from trdmod to trdicp.F90. Suppress trd_icp routine (i.e. trd_2d, trd_3d) as the work is now simply done in trd_budget.[[BR]] 4- rescan all dyn/tra trend indices. add jptra_trd_zdfp for "PURE Kz dissusive trend when ln_traldf_iso=T (see also changes in tranxt where a call to trd_tra is done just before the swap, so that PURE Kz trends can be diagnosed in tra_trd. See also xml file).  5- jptra_trd_nsr and jptra_trd_cdt are 3D trends as their incorporate both surface forcing AND runoff, the later being possibly spread in depth ('''==>>> probably to be changed''')[[BR]] 6- suppress the key_trddyn key trdtra  from trdicp[[BR]] 
    7880 
    79   '''        trdtra - trddyn - trdmod - trdvor'''         modules : impact on '''        TRA'''        , '''        DYN'''        , '''        TRD'''         and almost all '''        TOP_SRC'''         modules[[BR]] 
     81  '''         trdtra - trddyn - trdmod - trdvor'''          modules : impact on '''         TRA'''         , '''         DYN'''         , '''         TRD'''          and almost all '''         TOP_SRC'''          modules[[BR]] 
    8082 
    8183see [https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3318 revision 3318] 
     
    9193---- 
    9294=== ''' Step III : addition of 3D KE diagnostics ''' === 
    93   '''        trdken'''         module[[BR]] 
     95  '''         trdken'''          module[[BR]] 
    9496 
    9597see [https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3325 revision 3325] 
     
    105107---- 
    106108=== ''' Step IV : addition of 3D PE diagnostics ''' === 
    107   '''        trdpen'''         module[[BR]] 
     109  '''         trdpen'''          module[[BR]] 
    108110 
    109111see [https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3326 revision 3326] and [https://forge.ipsl.jussieu.fr/nemo/log/branches/2012/dev_r3309_LOCEAN12_Ediag/NEMOGCM/NEMO/OPA_SRC?rev=3327 revision 3327] 0- correct a bug in trdtra and trdken 
     
    121123[[BR]] [[BR]] [[BR]] [[BR]] [[BR]] [[BR]] [[BR]] [[BR]] [[BR]] '''Pending issues''' : 
    122124 
    123   atmospheric pressure gradient trend not taken into account (see dynspg.F90  '''        To be done !!!!'''        [[BR]]       ''' 
    124  
    125   kpp non-local trend put in zdf trends !!!  this will not work ! a additional trend term should be add '''        To be done !!!!'''        [[BR]]       ''' 
     125  atmospheric pressure gradient trend not taken into account (see dynspg.F90  '''         To be done !!!!'''         [[BR]]        ''' 
     126 
     127  kpp non-local trend put in zdf trends !!!  this will not work ! a additional trend term should be add '''         To be done !!!!'''         [[BR]]        ''' 
    126128 
    127129  problems to be solved: vvl case for tracer sad trends ; flux form case for had (keg) and zad momentum trends[[BR]] 
     
    155157 * In trd_glo_init, corrected definition for tvolt:[[BR]]         tvolt = tvolt + SUM( e1e2t(:,:) * fse3t(:,:,jk) * tmask(:,:,jk) * tmask_i(:,:) ) 
    156158 * Treatment of bfr has been clarified: if bfr is implicit (ln_bfrimp=.TRUE.), the bottom friction term remain 0, as bottom friction is implicitly included in the vertical diffusion term. 
    157  * Correction of outputs of dynamic trends and hke 
     159 * Correction of outputs of dynamic trends and hke. 
    158160 
    159161In trd_oce.F90