Changes between Version 2 and Version 3 of ticket/1775_TOP_Offline_vvl

Timestamp:

2016-09-21T11:24:41+02:00 (8 years ago)

Author:

cetlod

Comment:

--

ticket/1775_TOP_Offline_vvl

@@ -1 @@
-= [[PageOutline]] Last edited [[Timestamp]]
+= [[PageOutline]] Last edited [[Timestamp]] =
+'''Author''' : Christian Ethé
 
-'''Author''' : Simona Flavoni
+'''ticket''' : [ticket:1692 #]1788
 
-'''ticket''' : #1692
+'''Branch''' : [https://forge.ipsl.jussieu.fr/nemo/browser/branches/2016/dev_r6409_SIMPLIF_2_usrdef 2016/dev_r6]665_TOP_Offline_vvl
 
-'''Branch''' : [https://forge.ipsl.jussieu.fr/nemo/browser/branches/2016/dev_r6409_SIMPLIF_2_usrdef 2016/dev_r6409_SIMPLIF_2_usrdef]
+'''WP2016 Action''' : 
 
-'''WP2016 Action''' : SIMPLIF-2
+= Purpose : =
+Run passive tracers offline with linear free surface
 
-----
-[[BR]]'''REMARK:'''
+= Method : =
+Compute ssh evolution and vertical scale factors at each time step using dynamical fields previously stored on files
 
-look at this old page (2014) : https://forge.ipsl.jussieu.fr/nemo/wiki/2014WP/2014_SystemSimplification_hard_coding to see '''what is STILL missing''' (for example diafwb, closea, etc..)
+= Hypothesis : =
+ *  zstar coordinate only
+ * No advective bbl
+ *  '''in a first step : no time interpolation ====> at least 5 days-mean fields are needed'''
 
-Notes of development of simplification-2 strategy
 
- =
-= Modification from revision '''6593''' to next one (revision '''6595''') =
-= These changes doesn’t change de GYRE results (in both ln_read_cfg = T and F)'''[[BR]]'''[[BR]][[BR]]'''domwri.F90''' and '''par_oce.F90'''[[BR]]Add jpkglo in par_oce[[BR]]Add jpiglo, jpjglo and jpkglo in mesh_mask file[[BR]][[BR]]'''domhgr.F90''', '''usrdef.F90''', and '''nemogcm.F90 '''[[BR]]create usr_def_nam to read the namusr_def which allows to specify the global domain sizes (jpiglo,jpjglo,jpkglo) [[BR]]change nn_bench into ln_bench read in namusr_def. ln_bench is now a variable known only by usrdef.F90 module. Remove nbench and nn_bench everywhere else (namelist_ref, nemogcm.F90, sbcana, in_out_manager.F90)[[BR]]nemo_init : add read of jpiglo, jpjglo and jpkglo or their setting in usr_def_nam'''[[BR]][[BR]]domhgr.F90''', and''' usrdef.F90[[BR]]'''add all hgr arrays in argument of hgr_read and usr_def_hgr [[BR]]remove kbench and k_cfg from usr_def_hgr arguments (same argueent in [[BR]]both hgr_read and usr_def_hgr)[[BR]]domhgr: - remove useless local variable declaration[[BR]]- add control print for iff and ie1e2u_v cases'''[[BR]][[BR]][[BR]]sbcana.F90 '''and''' namsbc_ana '''removed from the code'''[[BR]]'''ln_ana replaced by ln_usr in namsbc[[BR]]jp_ana replaced by jp_usr in sbcmod.F90[[BR]]remove sbcana.F90 from the code'''[[BR]][[BR]]usrdef_sbc.F90 [[BR]]'''remove the use of ln_bench by constraining the use of key_mpp_rep[[BR]]CAUTION : this changes the results of the reference GYRE which is without[[BR]]this key ===>>> update the reference run used to compare the results, with [[BR]]a new run with the key_mpp_rep[[BR]]'''[[BR]][[BR]]Namelist of all configuration + namelist_ref :[[BR]]'''- namelist_ref /namsbc : ln_blk_core = .true. ===>>> = .false.[[BR]]and thus add ln_blk_core = .true. in all ORCA configuration namelist_cfg[[BR]]Change ln_ana into ln_usr and thus also change all GYRE configuration[[BR]]'''[[BR]]'''
 
- =
-= Modification from revision '''6595''' to next one (revision '''6596''') =
-= These changes doesn’t change de GYRE results (in both ln_read_cfg = T and F)[[BR]]
+{{{
+ssh(n+dt) = ssh(n) + dt * ( div2D(DT) - emp(DT) ) where div2D is the vertically integrated divergence transport and DT is the frequency of dynamical fields
+}}}
+=  =
+= Dynamics : =
+ * e3t, e3u, e3v, e3w  : vertical scale factor
+ * U, V, W : effective transport ( e1*e2*e3 * u where u is velocity including eiv, mle etc ...)
+ * hdiv * e3t :  horizontal divergence
+ * emp
+ * 3D runoffs
+ * Kz
+ * T,S, qsr, mld
 
-Revision 6596 includes step.I and II that follow.[[BR]]'''[[BR]][[BR]]Idea : simplification of the namelist resulting from modification in hgr[[BR]][[BR]][[BR]]Step I : '''remove from namelist : jphgr_msh , [[BR]]ppglam0, ppgphi0 [[BR]]ppe1_deg, ppe2_deg, ppe1_m, ppe2_m[[BR]][[BR]]This requires the following changes:'''[[BR]][[BR]]'''LIM2 and LIM3 needs the Coriolis parameter at T-points[[BR]]==>> Introduce in dom_oce both Coriolis at T- and F-point : '''ff_t and ff_f,''' resp.[[BR]]This implies changes in all routines of both OPA and LIM_(2/3) that were using[[BR]]either ff or fcor.[[BR]]NB: the change of name for Coriolis parameter is quite useful. Indeed, with the [[BR]]old name (ff) it was impossible to find where coriolis was used as ‘ff’ appears in [[BR]]too many comments (nearly all modules !)[[BR]]NB: changes also include a small bug correction in ldftra.F90'''[[BR]][[BR]]'''Add in hgr_read and usr_def_hgr the read / calculation of ff_t, coriolis at [[BR]]T-point, and use it in LIM (nomore fcor calculation in limmsh(_2)[[BR]]==>> modification in dom_oce.F90, domhgr, hgr_read, usr_def_hgr, [[BR]]limmsh_2.F90 , and limmsh.F90 + others…[[BR]]including dyncor_c1d.F90'''[[BR]][[BR]]NEMO//OFF_SRC/domrea.F90 [[BR]]'''simply remove jphgr_msh from this routine and from the associated namelist
+The time evolution of ssh and scale factor are then computed as :
 
-'''NEMO//OPA_SRC/CRS/crsini.F90[[BR]]'''remove jphgr_msh from this routine. A deeper check is needed, since I don’t [[BR]]think we need a coriolis coarsened (perhaps yes to compute div coeff??)
+{{{
 
-'''NEMO//OPA_SRC/DOM/domngb.F90[[BR]]'''remove the shorter calculation for jphgr_msh = 2 or 3
+ssh_a = ssh_n - dt * ( div2D(DT) - emp(DT) ) where div2D is the vertically integrated divergence transport and DT is the frequency of dynamical fields
+e3t_a = e3t_0 * [ 1 + ssh_a / ht_0]
 
-'''NEMO//OPA_SRC/DOM/domzgr.F90[[BR]]'''remove the definition of a bump of topography in EEL case [[BR]]This should be implemented using usrdef.F90, therefore no more in the [[BR]]reference code'''[[BR]][[BR]]====>>>> '''run identical with both ln_read_cfg = T and F (with '''key_mpp_rep''' !)[[BR]]'''[[BR]]Not done : case C1D ==>>> '''the interface will have to be completely changed using the new user-defined interface…. (change to be done in domc1d.F90)[[BR]]'''[[BR]][[BR]]Step II : '''remove from namelist: jpiglo, jpjglo, jpk,[[BR]]jpidta, jpjdta, jpkdta[[BR]]remove from the code jpizoom, jpjzoom'''[[BR]][[BR]]removed from the namelist, not from the code at this stage as :[[BR]]'''jp.dta = jp.glo is set in nemo_init[[BR]]==>> namcfg changed, as well as nemogcm.F90'''[[BR]][[BR]]'''replace '''jpizoom by 1''' (idem for '''jpjzoom''') everywhere.[[BR]]==>> a lot of modules involved'''[[BR]][[BR]]domzgr.F90''', remove zgr_bat_zoom routine and its CALL'''[[BR]][[BR]]'''remove loom and lzoom_e,w,n,s everywhere'''[[BR]][[BR]]====>>>> '''run identical with both ln_read_cfg = T and F (with '''key_mpp_rep '''!)'''[[BR]][[BR]]Not done : case C1D ==>>> '''the interface will have to be completely changed using the new user-defined interface…. (change to be done in domc1d.F90)'''[[BR]][[BR]]Not done : DOC update… ===>>> '''this should be started after the definition of zgr interface '''[[BR]][[BR]][[BR]][[BR]]Step III :''' create '''domain_cfg.nc''' file '''[[BR]][[BR]]'''Modification from revision '''6596''' to next one (revision '''6624''')[[BR]]====>>>> run identical with both ln_read_cfg = T and F (with '''key_mpp_rep '''!)'''[[BR]][[BR]]'''- create '''cfg_wri''' (put in '''domain.F90)''' that will be used in old version to create the configuration input file (I name it domain_cfg.nc) [[BR]]This file is created if nn_msh = -1. When ln_read_cfg=T we now read domain_cfg.nc file (no more mesh_mask file)[[BR]]
 
- * add in this file all the information I think useful for a configuration[[BR]]in particular addition of '''jperio''' (read in dom_ or set usr_def )[[BR]]and also equivalent of''' ln_zco, lnzps, ln_sco, ln_isfcav'''[[BR]]
+}}}
+To be consistent with dynamics, we apply a leap-frog  scheme with asselin time-filter on ssh, when swapping the array
 
- * add in '''domzgr.F90''' a routine zgr_read to read the information [[BR]]'''===>>> CAUTION''' zgr_read has not been tested, and in not called[[BR]]- move jperio from par_oce to dom_oce (i.e. same place as nperio)'''[[BR]][[BR]]'''minor: '''[[BR]]'''- remove domstp.F90 together with atfp1 which is not used anymore[[BR]]- move “ocean domain parameters” print from phycst to domain.F90[[BR]]- remove jperio and cp_cfz from namelist (namcfg) (NB: cp_cfz remove from the whole code)[[BR]]'''[[BR]][[BR]]Ideas for future ( NOT strictly linked to SIMPLIF-2) :[[BR]][[BR]]1:'''
+{{{
 
-change nn_timing in ln_timing ==> it implies to change all :[[BR]]IF( nn_timing == 1 ) …[[BR]]en[[BR]]IF( ln_timing ) …[[BR]]'''[[BR]]2:[[BR]]'''remove key_netcdf4 key as this is done in xIOS ??? not sure (see Andrew: => Andrew says we keep it!!)[[BR]]'''[[BR]][[BR]]domvvl.F90 :[[BR]]'''- first change the name, sshdom ??? or other thing[[BR]]- second, separate (z/zps/s)* cases from z-tilde case[[BR]]- third, revisite z-tilde case in the light of depth being the sum of scale factors[[BR]]and vise versa ! this will notably change the interpolation of e3w from e3t'''[[BR]][[BR]]jperio : [[BR]]'''- change the jperio into nperio_glo, move it from par_ to dom_oce (like nperio)[[BR]]- define np_ parameters associated with jperio choice :'''[[BR]]'''jperio= 0, closed '''np_closed[[BR]]'''jperio= 1, cyclic east-west '''np_ew_cyclic or np_EWc[[BR]]'''jperio= 2, equatorial symmetric '''np_eq_symmetric or np_Eqs[[BR]]'''jperio= 3, north fold with T-point pivot '''np_Tnfd[[BR]]'''jperio= 4, cyclic east-west and north fold with T-point pivot '''np_ewc_Tnfd or np_EWc_Tnfd[[BR]]'''jperio= 5, north fold with F-point pivot''' np_Fnfd[[BR]]'''jperio= 6, cyclic east-west and north fold with F-point pivot''' np_ewc_Fnfd or np_EWc_Fnfd'''
+ssh_b = ssh_n + atfp * ( ssh_b -é * ssh_n + ssh_a  ) 
+ssh_n = ssh_a
 
-and replace all test of 0 to 6 by the corresponding np_….'''[[BR]][[BR]]URGENT '''(to be done before release): modification of '''dom_cfg'''
 
-'''[[BR]]DOM ZGR analyses[[BR]][[BR]]'''dom_zgr
+}}}
+=  =
+= Initial state : =
 
-  CALL '''zgr_z''' ! Reference z-coordinate system (always called)[[BR]]CALL '''zgr_bat''' ! Bathymetry fields (levels and meters)[[BR]]IF( lk_c1d ) CALL lbc_lnk( bathy , 'T', 1._wp ) ! 1D config.: same bathy value over the 3x3 domain
 
-IF( ln_zco ) CALL zgr_zco ! z-coordinate[[BR]]IF( ln_zps ) CALL zgr_zps ! Partial step z-coordinate[[BR]]IF( ln_sco ) CALL zgr_sco ! s-coordinate or hybrid z-s coordinate[[BR]]! [[BR]]! final adjustment of mbathy & check [[BR]]! -----------------------------------
+Ideally, the initial state of sea surface height ssh_0 comes from the restart of the last year of the simulation which produced the dynamics used.[[BR]]For example if one uses the dynamics from 1948 to 2009, the initial ssh comes from the restart of year 1947
 
-IF( lzoom ) CALL zgr_bat_zoom ! correct mbathy in case of zoom subdomain[[BR]]IF( .NOT.lk_c1d ) CALL zgr_bat_ctl ! check bathymetry (mbathy) and suppress isolated ocean points[[BR]]CALL zgr_bot_level ! deepest ocean level for t-, u- and v-points[[BR]]CALL zgr_top_level ! shallowest ocean level for T-, U-, V- points[[BR]][[BR]]——————[[BR]][[BR]]'''zgr_z'''[[BR]]gdept_1d, gdepw_1d[[BR]]e3t_1d , e3w_1d [[BR]]'''nlb10 [[BR]]nla10'''[[BR]][[BR]]'''>>>> : change nlb10 and nla10 from scalar field => to 2D field '''for s-coordinates[[BR]](if NOT the mixed layer is not really what we think to compute)[[BR]]idea: is good to open a ticket (so all people can see and fix it)[[BR]][[BR]]'''zgr_bat'''[[BR]]mbathy[[BR]]bathy >>>> = gdepw_1d(jpk) (flat bottom)[[BR]][[BR]]risfdep[[BR]]misfdep[[BR]][[BR]]'''zgr_zco >>>> from _1d values'''[[BR]]gdept_0 gdepw_0 '''gde3w_0(:,:,jk) '''[[BR]]e3t_0 (:,:,jk) e3u_0 (:,:,jk) e3v_0 (:,:,jk) e3f_0 (:,:,jk)[[BR]]e3w_0 (:,:,jk) e3uw_0 (:,:,jk) e3vw_0 (:,:,jk) [[BR]][[BR]]'''zgr_zps >>>> Idem zgr_zco'''[[BR]]gdept_0 gdepw_0 gde3w_0(:,:,jk) [[BR]]e3t_0 (:,:,jk) e3u_0 (:,:,jk) e3v_0 (:,:,jk) e3f_0 (:,:,jk)[[BR]]e3w_0 (:,:,jk) e3uw_0 (:,:,jk) e3vw_0 (:,:,jk) [[BR]][[BR]]'''zgr_isf'''[[BR]]risfdep[[BR]]misfdep[[BR]]mbathy[[BR]]bathy[[BR]][[BR]][[BR]]'''zgr_sco >>>> Idem zgr_zco'''[[BR]]gdept_0 gdepw_0 gde3w_0(:,:,jk) [[BR]]e3t_0 (:,:,jk) e3u_0 (:,:,jk) e3v_0 (:,:,jk) e3f_0 (:,:,jk)[[BR]]e3w_0 (:,:,jk) e3uw_0 (:,:,jk) e3vw_0 (:,:,jk) [[BR]][[BR]]'''URGENT:''' (urgent because dim_cfg changed)[[BR]]REMOVE gde3w and compte all e3T, e3w, e3uW, e3vw like:[[BR]]the sum of (delta) gdepT, gdepW, gdepUW, gdepVW [[BR]][[BR]]? but: are we sure that we want to remove all these ?[[BR]]? they can be useful for graphic use?[[BR]]? or we can output e3t,… optionally [[BR]][[BR]]'''=> simplification associated for dom_cfg because e3 output will be useless.'''[[BR]][[BR]][[BR]]zgr_bot_level[[BR]]mbkt, mbku, mbkv >>>> vertical indices of the deeptest ocean level[[BR]]mbku(ji,jj) = MIN( mbkt(ji+1,jj ) , mbkt(ji,jj) )[[BR]]mbkv(ji,jj) = MIN( mbkt(ji ,jj+1) , mbkt(ji,jj) )[[BR]][[BR]][[BR]][[BR]]zgr_top_level[[BR]]mikt, miku, mikv >>>> vertical indices of the shallowest ocean level
+= Simulations : =
+===  * Climatological run :  at each annual loop, restart from the ssh of the ocean restart file
+ * Interannual run      :  restart from ssh saved in passive tracers restart file. But when doing repeated cycle, restart from the 1st year of ocean restart file at the beginning of each cycle
 
- =
+ ===