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revision 1.837 by mlosch, Sun Jun 17 09:22:06 2007 UTC revision 1.932 by dimitri, Sat Dec 22 17:44:49 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o added verification/lab_sea/input.salt_plume
8    o pkg/salt_plume: clean up salt_plume_frac.F to
9      remove redundancy in PlumeMethod 1 and 4
10    o pkg/kpp: added saltplume diagnostics
11    o pkg/obcs and pkg/seaice:
12      - do not set uice and vice to zero when OB*icefile are unspecified
13      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
14      - moved seaice tracer obcs after call to seaice_growth
15    o pkg/salt_plume: added various options for salt plume depth
16      criterion and for vertical distribution of the salt
17    
18    checkpoint59l
19    o pkg/ptracers: new version of ptracers pickup:
20      read meta file and write only fields which are needed to restart.
21      ( same logic as main pickup file ; also using pickupStrictlyMatch )
22    o pkg/seaice:
23      - add timescale for melting due to warm mixed layer as a means of
24        setting SEAICE_availHeatFrac more conveniently
25      - add a CPP-flag/runtime parameter check for flooding algorithm
26      - reformulated availHeat in seaice_growth.F to be independent of AREA
27    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
28      unit changes
29    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
30    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
31      SX vector computer.
32    o pkg/seaice:
33      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
34        seaice forcing fields can now be read only through pkg/exf
35      - removed some unused halos
36    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
37    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
38      or U/VICE from U/VWIND before computing U/VSTRESS
39    
40    checkpoint59k
41    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
42      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
43    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
44      all experiments pass when compile with un-initialised var. checking option.
45    o added pkg/salt_plume
46    o script to test restart (for now, in MITgcm_contrib/jmc_script)
47    o pkg/seaice: new read/write pickup version.
48      read meta file and write only fields which are needed to restart.
49      ( same logic as main pickup file ; also using pickupStrictlyMatch )
50    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
51    o lab_sea.hb87: modify the domain & update output.hb87.txt :
52      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
53      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
54      process. Fixed here by closing the domain at the Northern boundary.
55    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
56    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
57      a set of consecutive levels in/from a 3-D array.
58    o pkg/ptracers:
59      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
60      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
61    
62    checkpoint59j
63    o in pkgs: dic, obcs, offline, rbcs:
64      standard way to compute coeff. for time interpolation between 2 time reccords
65      which retains full precision (& make results less dependent on compiler).
66      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
67    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
68      packages instead of reading ice cover and wind speed separately
69    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
70     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
71      to allow to compile customized code before the update)
72    o cleaning-up:
73      - fix CPP instruction syntax in pkg/obcs
74      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
75        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
76      - fix some threads issue in IO parts.
77    o pkg/dic:
78      - add tons of "_d 0" (--> much better testreports !)
79       and then update outputs of tutorial_global_oce_biogeo
80    o pkg/mom_fluxform:
81      add a special version of momentum advection intended to conserve momentum
82      next to a bathymetry step or a coastline edge. (default = off = #undef)
83    o new read/write pickup version:
84      - for now, only implemented for main (mdsio) pickup file.
85      - write out only what is needed to restart; merge pickup_nh , pickup_ph
86        and main pickup together.
87      - read meta file; read only what is needed to restart; stop if a field
88        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
89        if it make sense (even if the restart is not perfect).
90      - if no meta file, assume that pickup to read corresponds exactly to
91        a pickup that would currently be written.
92      - read pickup written in the old format (until checkpoint59i) if it
93        recognizes an old meta file (no field-list).
94      - add a meta file in exp. which starts from a pickup: 2 cases:
95        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
96         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
97        b) a meta file describing the content of the associated pickup file
98         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
99    o pkg/mdsio & pkg/rw:
100      - new routine to read a meta file ; new set of routine to read
101        Multiple-fields file (with meta file).
102    o added open boundary conditions capability for seaice
103        HSNOW, HSALT, UICE, and VICE
104    
105    checkpoint59i
106    o adjoint:
107      * fix multiDimAdvection adjoint
108        (partial recomputation problem by TAF for fVerT(:,:,kDown)
109        and comlev1 size definition (maxpass vs. max. number of tracers)
110      * verification/global_ocean.90x45x15 adjoint now tests
111        NLFS and multiDimAdvection using DST3 (=30)
112      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
113    o pkg/kpp: add "_d 0" to real constant (if missing);
114      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
115      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
116    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
117      for internal parameters related to restart process (formerly from PARAMS.h)
118      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
119    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
120      as argument. (only atm2d & obcs write_pickup have not yet been updated)
121    o pkg/monitor:
122      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
123      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
124      - account for deep Atmosphere factor and density factor (anelastic)
125    o added open boundary conditions capability for seaice HEFF and AREA
126    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
127      thermodynamics
128      - requires a little reorganization, which affects the testreport results
129        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
130        so that now the conservative form is tested
131      - add a few comments
132    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
133    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
134    o add new diagnostics to seaice: advective, diffusive fluxes (only for
135      multidim-advection, for scheme 2 they are not filled) and transports,
136      thermodynamic growth rates
137    o change units of EmPmR (inside the code, + within coupling interface)
138      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
139      Affects results @ truncation level (cg2d match) and update output of
140       experiments: lab_sea(6), global_ocean.90x40x15(10),
141      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
142      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
143      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
144      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
145    
146    checkpoint59h
147    o pkg/exf:
148      - improve vectorization by moving if-statement out of loops in
149        exf_mapfields, exf_radiation
150      - exf_bulkformulae.F: introduce 2D fields and vectorize code
151    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
152    o testreport:
153      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
154        monitor & update offline_exf_seaice exp. output.
155      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
156    o pkg/seaice:
157      - bug fix in the evp solver: boundary conditions were affected be
158        masking of zMax/zMin (changes results)
159      - minor bug fix in boundary conditions in seaice_calc_strainrates
160        (changes results for no_slip)
161      - seaice_lsr.F: make interpolation of eta dependent on boundaries
162      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
163      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
164        stress formulation and no-slip boundary conditions
165    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
166      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
167    o pkg/seaice: a first HSALT time stepping equation has been checked in
168    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
169      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
170      without requiring DO-IF statements
171    o pkg/thsice:
172      use continuous power-law function for partition of energy between lateral
173      melting/freezing and thinning/thickening ; old code using step function
174      still available with #undef THSICE_FRACEN_POWERLAW
175      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
176    o testreport: change AD testing : check against results/output_adm.txt
177      using same scripts as for forward test.
178    
179    checkpoint59g
180    o adjoint testing: in preparation for changing testreport:
181      - output format: cost and grad written on separated lines
182      - ad output results in directory "results" (instead of "results_ad")
183    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
184    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
185    o pkg/ecco: allow user defined cost function contributions
186    o testreport:
187      Allow to choose (per experiment) the list of tested output variables
188       and the main variable (used to issue a pass/FAIL ) ;
189      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
190      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
191      Also modify printing of summary:
192       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
193       b) echo the list of tested variables in the individual summary.txt of
194          each experiment.
195    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
196      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
197      (but still depend on the tile decompostion of the domain).
198    o pkg/seaice: change a discretization detail to make the B-grid code
199      "more symmetric". This change is likely to remove all "ridges/leads" that
200      where quasi-aligned with the grid in B-grid solutions. It may also be
201      the solution to the stress coupling issues with the B-grid.
202    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
203      remove .cvsignore from input dir. (since testreport no longer run here).
204    o pkg/thsice:
205     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
206     - fix reshaping of sea-ice just after advection:
207       melt all the ice only if ice-volume is too small.
208     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
209       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
210     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
211    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
212      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
213    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
214      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
215      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
216      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
217      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
218      -> update output.txt
219    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
220     this affects truncation error: -> update output.txt of exp:
221      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
222      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
223    
224    checkpoint59f
225    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
226    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
227      a bounded range (in forward mode)
228    o pkg/ecco, ctrl, autodiff and mom_common:
229     internal parameter controls, completements of implementations
230    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
231    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
232      (not seem any difference in testing results).
233    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
234       at face corners.
235    o pkg/generic_advdiff:
236     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
237      loop range indices for computing vertical advection tendency
238      and do the calculation in the interior only (no overlap) ;
239      for now, only implemented for SOM advection (to save CPU time).
240     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
241    o exch2 adjoint
242      First set of changes:
243      - add exch2 hand-written adjoint templates
244      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
245        This will require cleanup in pkg/autodiff/*.F
246        (changed routines currently kept separate in verif. code/)
247      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
248        that used to hide exch2 or cubed-sphere specific code
249        (commented via 'cph-exch2')
250    o pkg/seaice
251      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
252    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
253       output of global_ocean.cs32x15.thsice .
254    
255    checkpoint59e
256    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
257      for B-grid vector (not yet tested) and C-grid vector (<- only used
258      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
259    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
260      (#ifdef ALLOW_SALT_PLUME)
261    o gather_2d/scatter_2d: removed halo regions
262    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
263      scheme and the corresponding test case (under front_relax dir). For now,
264      only available with Skew-flux form and not yet tested in realistic set-up.
265      adjoint: store directives updated, but gradient checks deteriorated,
266      so maybe GM/Redi adjoint is now broken.
267    o seaice adjoint
268      * add AREA, HEFF, HSNOW as control variable
269        (should not change lab_sea results)
270      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
271    o pkg/seaice:
272      * added computation of saltFlux in seaice_growth;
273        For time being, sea ice salinity is assumed constant
274        contribution of snow flooding to freshening of sea ice is neglected.
275        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
276        defaults to 0.0 in order to maintain backward compatibility.
277        Typical values for SEAICE_salinity are 4 to 10 g/kg.
278      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
279      * added SEAICE_availHeatFrac, which specifies fraction of surface level
280        heat content used to melt or grow ice
281      * commented out cap of HICE: it helps keep ice thinner
282      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
283      * applied OBCS T/S mask to HEFFM sea ice mask
284    
285    checkpoint59d
286    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
287     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
288     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
289    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
290     and change default value of parameter "GM_Small_Number";
291     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
292       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
293       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
294    o pkg/ecco: cost function when applying pkg/smooth to controls
295    o pkg/ctrl: add forcingPrecond run time parameter
296    o pkg/seaice:
297     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
298     - fix bug in metric terms of u-equation in LSR solver (implicit part),
299       changes verification/lab_sea
300     - rearrange implicit part of u-equation in LSR solver to make it easier to
301       read, understand, and debug. This causes changes at the truncation level.
302     - fix (serious) bug in the boundary conditions (sign error in the implicit
303       part) of the LSR solver. Changes all LSR results.
304     - fixed problem with HSNOW initialization to avoid thick snow when AREA
305       is initilized with small values - does not change lab_sea results.
306     - added HsnowFile initialization capability
307    o pkg/smooth: addition to model/src and pkg/ctrl so allow
308     initialization of pkg/smooth and application to control vector
309  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
310  o dependencies: pkg/profiles requires pkg/cal  o dependencies: pkg/profiles requires pkg/cal
311  o pkg/profiles:  o pkg/profiles:
# Line 15  o pkg/profiles: Line 317  o pkg/profiles:
317       that allow you to prepare netcdf input files.       that allow you to prepare netcdf input files.
318   - also modified: cleaner include statements, cleaner error print statements,   - also modified: cleaner include statements, cleaner error print statements,
319     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.
   
320  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
321  o pkg/seaice:  o pkg/seaice:
322   - 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 450  o in FFIELDS.h:
450       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
451  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
452  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
453      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
454        are no longer updating the vertical diffusivity array
455        (passed as argument) but are (re-) setting those arrays.
456  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
457    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
458      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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