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revision 1.837 by mlosch, Sun Jun 17 09:22:06 2007 UTC revision 1.927 by dimitri, Tue Dec 18 05:34:41 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint59l
8    o pkg/salt_plume: added various options for salt plume depth
9      criterion and for vertical distribution of the salt
10    o pkg/ptracers: new version of ptracers pickup:
11      read meta file and write only fields which are needed to restart.
12      ( same logic as main pickup file ; also using pickupStrictlyMatch )
13    o pkg/seaice:
14      - add timescale for melting due to warm mixed layer as a means of
15        setting SEAICE_availHeatFrac more conveniently
16      - add a CPP-flag/runtime parameter check for flooding algorithm
17      - reformulated availHeat in seaice_growth.F to be independent of AREA
18    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
19      unit changes
20    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
21    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
22      SX vector computer.
23    o pkg/seaice:
24      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
25        seaice forcing fields can now be read only through pkg/exf
26      - removed some unused halos
27    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
28    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
29      or U/VICE from U/VWIND before computing U/VSTRESS
30    
31    checkpoint59k
32    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
33      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
34    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
35      all experiments pass when compile with un-initialised var. checking option.
36    o added pkg/salt_plume
37    o script to test restart (for now, in MITgcm_contrib/jmc_script)
38    o pkg/seaice: new read/write pickup version.
39      read meta file and write only fields which are needed to restart.
40      ( same logic as main pickup file ; also using pickupStrictlyMatch )
41    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
42    o lab_sea.hb87: modify the domain & update output.hb87.txt :
43      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
44      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
45      process. Fixed here by closing the domain at the Northern boundary.
46    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
47    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
48      a set of consecutive levels in/from a 3-D array.
49    o pkg/ptracers:
50      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
51      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
52    
53    checkpoint59j
54    o in pkgs: dic, obcs, offline, rbcs:
55      standard way to compute coeff. for time interpolation between 2 time reccords
56      which retains full precision (& make results less dependent on compiler).
57      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
58    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
59      packages instead of reading ice cover and wind speed separately
60    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
61     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
62      to allow to compile customized code before the update)
63    o cleaning-up:
64      - fix CPP instruction syntax in pkg/obcs
65      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
66        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
67      - fix some threads issue in IO parts.
68    o pkg/dic:
69      - add tons of "_d 0" (--> much better testreports !)
70       and then update outputs of tutorial_global_oce_biogeo
71    o pkg/mom_fluxform:
72      add a special version of momentum advection intended to conserve momentum
73      next to a bathymetry step or a coastline edge. (default = off = #undef)
74    o new read/write pickup version:
75      - for now, only implemented for main (mdsio) pickup file.
76      - write out only what is needed to restart; merge pickup_nh , pickup_ph
77        and main pickup together.
78      - read meta file; read only what is needed to restart; stop if a field
79        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
80        if it make sense (even if the restart is not perfect).
81      - if no meta file, assume that pickup to read corresponds exactly to
82        a pickup that would currently be written.
83      - read pickup written in the old format (until checkpoint59i) if it
84        recognizes an old meta file (no field-list).
85      - add a meta file in exp. which starts from a pickup: 2 cases:
86        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
87         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
88        b) a meta file describing the content of the associated pickup file
89         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
90    o pkg/mdsio & pkg/rw:
91      - new routine to read a meta file ; new set of routine to read
92        Multiple-fields file (with meta file).
93    o added open boundary conditions capability for seaice
94        HSNOW, HSALT, UICE, and VICE
95    
96    checkpoint59i
97    o adjoint:
98      * fix multiDimAdvection adjoint
99        (partial recomputation problem by TAF for fVerT(:,:,kDown)
100        and comlev1 size definition (maxpass vs. max. number of tracers)
101      * verification/global_ocean.90x45x15 adjoint now tests
102        NLFS and multiDimAdvection using DST3 (=30)
103      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
104    o pkg/kpp: add "_d 0" to real constant (if missing);
105      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
106      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
107    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
108      for internal parameters related to restart process (formerly from PARAMS.h)
109      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
110    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
111      as argument. (only atm2d & obcs write_pickup have not yet been updated)
112    o pkg/monitor:
113      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
114      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
115      - account for deep Atmosphere factor and density factor (anelastic)
116    o added open boundary conditions capability for seaice HEFF and AREA
117    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
118      thermodynamics
119      - requires a little reorganization, which affects the testreport results
120        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
121        so that now the conservative form is tested
122      - add a few comments
123    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
124    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
125    o add new diagnostics to seaice: advective, diffusive fluxes (only for
126      multidim-advection, for scheme 2 they are not filled) and transports,
127      thermodynamic growth rates
128    o change units of EmPmR (inside the code, + within coupling interface)
129      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
130      Affects results @ truncation level (cg2d match) and update output of
131       experiments: lab_sea(6), global_ocean.90x40x15(10),
132      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
133      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
134      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
135      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
136    
137    checkpoint59h
138    o pkg/exf:
139      - improve vectorization by moving if-statement out of loops in
140        exf_mapfields, exf_radiation
141      - exf_bulkformulae.F: introduce 2D fields and vectorize code
142    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
143    o testreport:
144      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
145        monitor & update offline_exf_seaice exp. output.
146      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
147    o pkg/seaice:
148      - bug fix in the evp solver: boundary conditions were affected be
149        masking of zMax/zMin (changes results)
150      - minor bug fix in boundary conditions in seaice_calc_strainrates
151        (changes results for no_slip)
152      - seaice_lsr.F: make interpolation of eta dependent on boundaries
153      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
154      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
155        stress formulation and no-slip boundary conditions
156    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
157      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
158    o pkg/seaice: a first HSALT time stepping equation has been checked in
159    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
160      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
161      without requiring DO-IF statements
162    o pkg/thsice:
163      use continuous power-law function for partition of energy between lateral
164      melting/freezing and thinning/thickening ; old code using step function
165      still available with #undef THSICE_FRACEN_POWERLAW
166      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
167    o testreport: change AD testing : check against results/output_adm.txt
168      using same scripts as for forward test.
169    
170    checkpoint59g
171    o adjoint testing: in preparation for changing testreport:
172      - output format: cost and grad written on separated lines
173      - ad output results in directory "results" (instead of "results_ad")
174    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
175    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
176    o pkg/ecco: allow user defined cost function contributions
177    o testreport:
178      Allow to choose (per experiment) the list of tested output variables
179       and the main variable (used to issue a pass/FAIL ) ;
180      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
181      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
182      Also modify printing of summary:
183       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
184       b) echo the list of tested variables in the individual summary.txt of
185          each experiment.
186    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
187      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
188      (but still depend on the tile decompostion of the domain).
189    o pkg/seaice: change a discretization detail to make the B-grid code
190      "more symmetric". This change is likely to remove all "ridges/leads" that
191      where quasi-aligned with the grid in B-grid solutions. It may also be
192      the solution to the stress coupling issues with the B-grid.
193    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
194      remove .cvsignore from input dir. (since testreport no longer run here).
195    o pkg/thsice:
196     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
197     - fix reshaping of sea-ice just after advection:
198       melt all the ice only if ice-volume is too small.
199     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
200       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
201     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
202    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
203      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
204    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
205      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
206      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
207      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
208      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
209      -> update output.txt
210    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
211     this affects truncation error: -> update output.txt of exp:
212      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
213      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
214    
215    checkpoint59f
216    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
217    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
218      a bounded range (in forward mode)
219    o pkg/ecco, ctrl, autodiff and mom_common:
220     internal parameter controls, completements of implementations
221    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
222    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
223      (not seem any difference in testing results).
224    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
225       at face corners.
226    o pkg/generic_advdiff:
227     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
228      loop range indices for computing vertical advection tendency
229      and do the calculation in the interior only (no overlap) ;
230      for now, only implemented for SOM advection (to save CPU time).
231     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
232    o exch2 adjoint
233      First set of changes:
234      - add exch2 hand-written adjoint templates
235      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
236        This will require cleanup in pkg/autodiff/*.F
237        (changed routines currently kept separate in verif. code/)
238      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
239        that used to hide exch2 or cubed-sphere specific code
240        (commented via 'cph-exch2')
241    o pkg/seaice
242      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
243    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
244       output of global_ocean.cs32x15.thsice .
245    
246    checkpoint59e
247    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
248      for B-grid vector (not yet tested) and C-grid vector (<- only used
249      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
250    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
251      (#ifdef ALLOW_SALT_PLUME)
252    o gather_2d/scatter_2d: removed halo regions
253    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
254      scheme and the corresponding test case (under front_relax dir). For now,
255      only available with Skew-flux form and not yet tested in realistic set-up.
256      adjoint: store directives updated, but gradient checks deteriorated,
257      so maybe GM/Redi adjoint is now broken.
258    o seaice adjoint
259      * add AREA, HEFF, HSNOW as control variable
260        (should not change lab_sea results)
261      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
262    o pkg/seaice:
263      * added computation of saltFlux in seaice_growth;
264        For time being, sea ice salinity is assumed constant
265        contribution of snow flooding to freshening of sea ice is neglected.
266        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
267        defaults to 0.0 in order to maintain backward compatibility.
268        Typical values for SEAICE_salinity are 4 to 10 g/kg.
269      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
270      * added SEAICE_availHeatFrac, which specifies fraction of surface level
271        heat content used to melt or grow ice
272      * commented out cap of HICE: it helps keep ice thinner
273      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
274      * applied OBCS T/S mask to HEFFM sea ice mask
275    
276    checkpoint59d
277    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
278     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
279     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
280    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
281     and change default value of parameter "GM_Small_Number";
282     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
283       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
284       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
285    o pkg/ecco: cost function when applying pkg/smooth to controls
286    o pkg/ctrl: add forcingPrecond run time parameter
287    o pkg/seaice:
288     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
289     - fix bug in metric terms of u-equation in LSR solver (implicit part),
290       changes verification/lab_sea
291     - rearrange implicit part of u-equation in LSR solver to make it easier to
292       read, understand, and debug. This causes changes at the truncation level.
293     - fix (serious) bug in the boundary conditions (sign error in the implicit
294       part) of the LSR solver. Changes all LSR results.
295     - fixed problem with HSNOW initialization to avoid thick snow when AREA
296       is initilized with small values - does not change lab_sea results.
297     - added HsnowFile initialization capability
298    o pkg/smooth: addition to model/src and pkg/ctrl so allow
299     initialization of pkg/smooth and application to control vector
300  o pkg/seaice: fix another bug in the LSR no-slip boundary conditons  o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
301  o dependencies: pkg/profiles requires pkg/cal  o dependencies: pkg/profiles requires pkg/cal
302  o pkg/profiles:  o pkg/profiles:
# Line 15  o pkg/profiles: Line 308  o pkg/profiles:
308       that allow you to prepare netcdf input files.       that allow you to prepare netcdf input files.
309   - also modified: cleaner include statements, cleaner error print statements,   - also modified: cleaner include statements, cleaner error print statements,
310     cleaner stops when error, and more tests of the netcdf input files consistency.     cleaner stops when error, and more tests of the netcdf input files consistency.
   
311  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
312  o pkg/seaice:  o pkg/seaice:
313   - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this   - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
# Line 149  o in FFIELDS.h: Line 441  o in FFIELDS.h:
441       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
442  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
443  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
444      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
445        are no longer updating the vertical diffusivity array
446        (passed as argument) but are (re-) setting those arrays.
447  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
448    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
449      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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