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revision 1.835 by gforget, Fri Jun 15 05:09:24 2007 UTC revision 1.936 by dimitri, Fri Jan 11 19:59:28 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
8      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
9    o added verification/seaice_obcs both to test seaice open boundaries
10      and to provide an example matlab scrpt for generating them
11    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
12    o pkg/salt_plume: clean up salt_plume_frac.F to
13      remove redundancy in PlumeMethod 1 and 4
14    o pkg/kpp: added saltplume diagnostics
15    o pkg/obcs and pkg/seaice:
16      - do not set uice and vice to zero when OB*icefile are unspecified
17      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
18      - moved seaice tracer obcs after call to seaice_growth
19    o pkg/salt_plume: added various options for salt plume depth
20      criterion and for vertical distribution of the salt
21    
22    checkpoint59l
23    o pkg/ptracers: new version of ptracers pickup:
24      read meta file and write only fields which are needed to restart.
25      ( same logic as main pickup file ; also using pickupStrictlyMatch )
26    o pkg/seaice:
27      - add timescale for melting due to warm mixed layer as a means of
28        setting SEAICE_availHeatFrac more conveniently
29      - add a CPP-flag/runtime parameter check for flooding algorithm
30      - reformulated availHeat in seaice_growth.F to be independent of AREA
31    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
32      unit changes
33    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
34    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
35      SX vector computer.
36    o pkg/seaice:
37      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
38        seaice forcing fields can now be read only through pkg/exf
39      - removed some unused halos
40    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
41    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
42      or U/VICE from U/VWIND before computing U/VSTRESS
43    
44    checkpoint59k
45    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
46      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
47    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
48      all experiments pass when compile with un-initialised var. checking option.
49    o added pkg/salt_plume
50    o script to test restart (for now, in MITgcm_contrib/jmc_script)
51    o pkg/seaice: new read/write pickup version.
52      read meta file and write only fields which are needed to restart.
53      ( same logic as main pickup file ; also using pickupStrictlyMatch )
54    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
55    o lab_sea.hb87: modify the domain & update output.hb87.txt :
56      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
57      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
58      process. Fixed here by closing the domain at the Northern boundary.
59    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
60    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
61      a set of consecutive levels in/from a 3-D array.
62    o pkg/ptracers:
63      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
64      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
65    
66    checkpoint59j
67    o in pkgs: dic, obcs, offline, rbcs:
68      standard way to compute coeff. for time interpolation between 2 time reccords
69      which retains full precision (& make results less dependent on compiler).
70      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
71    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
72      packages instead of reading ice cover and wind speed separately
73    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
74     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
75      to allow to compile customized code before the update)
76    o cleaning-up:
77      - fix CPP instruction syntax in pkg/obcs
78      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
79        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
80      - fix some threads issue in IO parts.
81    o pkg/dic:
82      - add tons of "_d 0" (--> much better testreports !)
83       and then update outputs of tutorial_global_oce_biogeo
84    o pkg/mom_fluxform:
85      add a special version of momentum advection intended to conserve momentum
86      next to a bathymetry step or a coastline edge. (default = off = #undef)
87    o new read/write pickup version:
88      - for now, only implemented for main (mdsio) pickup file.
89      - write out only what is needed to restart; merge pickup_nh , pickup_ph
90        and main pickup together.
91      - read meta file; read only what is needed to restart; stop if a field
92        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
93        if it make sense (even if the restart is not perfect).
94      - if no meta file, assume that pickup to read corresponds exactly to
95        a pickup that would currently be written.
96      - read pickup written in the old format (until checkpoint59i) if it
97        recognizes an old meta file (no field-list).
98      - add a meta file in exp. which starts from a pickup: 2 cases:
99        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
100         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
101        b) a meta file describing the content of the associated pickup file
102         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
103    o pkg/mdsio & pkg/rw:
104      - new routine to read a meta file ; new set of routine to read
105        Multiple-fields file (with meta file).
106    o added open boundary conditions capability for seaice
107        HSNOW, HSALT, UICE, and VICE
108    
109    checkpoint59i
110    o adjoint:
111      * fix multiDimAdvection adjoint
112        (partial recomputation problem by TAF for fVerT(:,:,kDown)
113        and comlev1 size definition (maxpass vs. max. number of tracers)
114      * verification/global_ocean.90x45x15 adjoint now tests
115        NLFS and multiDimAdvection using DST3 (=30)
116      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
117    o pkg/kpp: add "_d 0" to real constant (if missing);
118      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
119      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
120    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
121      for internal parameters related to restart process (formerly from PARAMS.h)
122      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
123    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
124      as argument. (only atm2d & obcs write_pickup have not yet been updated)
125    o pkg/monitor:
126      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
127      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
128      - account for deep Atmosphere factor and density factor (anelastic)
129    o added open boundary conditions capability for seaice HEFF and AREA
130    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
131      thermodynamics
132      - requires a little reorganization, which affects the testreport results
133        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
134        so that now the conservative form is tested
135      - add a few comments
136    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
137    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
138    o add new diagnostics to seaice: advective, diffusive fluxes (only for
139      multidim-advection, for scheme 2 they are not filled) and transports,
140      thermodynamic growth rates
141    o change units of EmPmR (inside the code, + within coupling interface)
142      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
143      Affects results @ truncation level (cg2d match) and update output of
144       experiments: lab_sea(6), global_ocean.90x40x15(10),
145      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
146      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
147      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
148      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
149    
150    checkpoint59h
151    o pkg/exf:
152      - improve vectorization by moving if-statement out of loops in
153        exf_mapfields, exf_radiation
154      - exf_bulkformulae.F: introduce 2D fields and vectorize code
155    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
156    o testreport:
157      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
158        monitor & update offline_exf_seaice exp. output.
159      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
160    o pkg/seaice:
161      - bug fix in the evp solver: boundary conditions were affected be
162        masking of zMax/zMin (changes results)
163      - minor bug fix in boundary conditions in seaice_calc_strainrates
164        (changes results for no_slip)
165      - seaice_lsr.F: make interpolation of eta dependent on boundaries
166      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
167      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
168        stress formulation and no-slip boundary conditions
169    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
170      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
171    o pkg/seaice: a first HSALT time stepping equation has been checked in
172    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
173      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
174      without requiring DO-IF statements
175    o pkg/thsice:
176      use continuous power-law function for partition of energy between lateral
177      melting/freezing and thinning/thickening ; old code using step function
178      still available with #undef THSICE_FRACEN_POWERLAW
179      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
180    o testreport: change AD testing : check against results/output_adm.txt
181      using same scripts as for forward test.
182    
183    checkpoint59g
184    o adjoint testing: in preparation for changing testreport:
185      - output format: cost and grad written on separated lines
186      - ad output results in directory "results" (instead of "results_ad")
187    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
188    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
189    o pkg/ecco: allow user defined cost function contributions
190    o testreport:
191      Allow to choose (per experiment) the list of tested output variables
192       and the main variable (used to issue a pass/FAIL ) ;
193      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
194      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
195      Also modify printing of summary:
196       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
197       b) echo the list of tested variables in the individual summary.txt of
198          each experiment.
199    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
200      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
201      (but still depend on the tile decompostion of the domain).
202    o pkg/seaice: change a discretization detail to make the B-grid code
203      "more symmetric". This change is likely to remove all "ridges/leads" that
204      where quasi-aligned with the grid in B-grid solutions. It may also be
205      the solution to the stress coupling issues with the B-grid.
206    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
207      remove .cvsignore from input dir. (since testreport no longer run here).
208    o pkg/thsice:
209     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
210     - fix reshaping of sea-ice just after advection:
211       melt all the ice only if ice-volume is too small.
212     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
213       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
214     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
215    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
216      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
217    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
218      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
219      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
220      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
221      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
222      -> update output.txt
223    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
224     this affects truncation error: -> update output.txt of exp:
225      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
226      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
227    
228    checkpoint59f
229    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
230    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
231      a bounded range (in forward mode)
232    o pkg/ecco, ctrl, autodiff and mom_common:
233     internal parameter controls, completements of implementations
234    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
235    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
236      (not seem any difference in testing results).
237    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
238       at face corners.
239    o pkg/generic_advdiff:
240     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
241      loop range indices for computing vertical advection tendency
242      and do the calculation in the interior only (no overlap) ;
243      for now, only implemented for SOM advection (to save CPU time).
244     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
245    o exch2 adjoint
246      First set of changes:
247      - add exch2 hand-written adjoint templates
248      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
249        This will require cleanup in pkg/autodiff/*.F
250        (changed routines currently kept separate in verif. code/)
251      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
252        that used to hide exch2 or cubed-sphere specific code
253        (commented via 'cph-exch2')
254    o pkg/seaice
255      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
256    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
257       output of global_ocean.cs32x15.thsice .
258    
259    checkpoint59e
260    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
261      for B-grid vector (not yet tested) and C-grid vector (<- only used
262      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
263    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
264      (#ifdef ALLOW_SALT_PLUME)
265    o gather_2d/scatter_2d: removed halo regions
266    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
267      scheme and the corresponding test case (under front_relax dir). For now,
268      only available with Skew-flux form and not yet tested in realistic set-up.
269      adjoint: store directives updated, but gradient checks deteriorated,
270      so maybe GM/Redi adjoint is now broken.
271    o seaice adjoint
272      * add AREA, HEFF, HSNOW as control variable
273        (should not change lab_sea results)
274      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
275    o pkg/seaice:
276      * added computation of saltFlux in seaice_growth;
277        For time being, sea ice salinity is assumed constant
278        contribution of snow flooding to freshening of sea ice is neglected.
279        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
280        defaults to 0.0 in order to maintain backward compatibility.
281        Typical values for SEAICE_salinity are 4 to 10 g/kg.
282      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
283      * added SEAICE_availHeatFrac, which specifies fraction of surface level
284        heat content used to melt or grow ice
285      * commented out cap of HICE: it helps keep ice thinner
286      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
287      * applied OBCS T/S mask to HEFFM sea ice mask
288    
289    checkpoint59d
290    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
291     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
292     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
293    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
294     and change default value of parameter "GM_Small_Number";
295     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
296       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
297       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
298    o pkg/ecco: cost function when applying pkg/smooth to controls
299    o pkg/ctrl: add forcingPrecond run time parameter
300    o pkg/seaice:
301     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
302     - fix bug in metric terms of u-equation in LSR solver (implicit part),
303       changes verification/lab_sea
304     - rearrange implicit part of u-equation in LSR solver to make it easier to
305       read, understand, and debug. This causes changes at the truncation level.
306     - fix (serious) bug in the boundary conditions (sign error in the implicit
307       part) of the LSR solver. Changes all LSR results.
308     - fixed problem with HSNOW initialization to avoid thick snow when AREA
309       is initilized with small values - does not change lab_sea results.
310     - added HsnowFile initialization capability
311    o pkg/smooth: addition to model/src and pkg/ctrl so allow
312     initialization of pkg/smooth and application to control vector
313    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
314    o dependencies: pkg/profiles requires pkg/cal
315  o pkg/profiles:  o pkg/profiles:
316   - added option ALLOW_PROFILES_GENERICGRID   - added option ALLOW_PROFILES_GENERICGRID
317       -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming       -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
# Line 13  o pkg/profiles: Line 321  o pkg/profiles:
321       that allow you to prepare netcdf input files.       that allow you to prepare netcdf input files.
322   - also modified: cleaner include statements, cleaner error print statements,   - also modified: cleaner include statements, cleaner error print statements,
323     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.
   
324  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
325  o pkg/seaice:  o pkg/seaice:
326   - 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 147  o in FFIELDS.h: Line 454  o in FFIELDS.h:
454       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
455  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
456  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
457      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
458        are no longer updating the vertical diffusivity array
459        (passed as argument) but are (re-) setting those arrays.
460  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
461    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
462      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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