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revision 1.837 by mlosch, Sun Jun 17 09:22:06 2007 UTC revision 1.938 by jmc, Mon Jan 14 02:29:20 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint59m
8    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
9      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
10    o gad_som : fix flux output (& diagnostics) to have same units as other  
11      advection scheme fluxes (was previously multiplied by deltaT).  
12    o added verification/seaice_obcs both to test seaice open boundaries
13      and to provide an example matlab scrpt for generating them
14    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
15    o pkg/salt_plume: clean up salt_plume_frac.F to
16      remove redundancy in PlumeMethod 1 and 4
17    o pkg/kpp: added saltplume diagnostics
18    o pkg/obcs and pkg/seaice:
19      - do not set uice and vice to zero when OB*icefile are unspecified
20      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
21      - moved seaice tracer obcs after call to seaice_growth
22    o pkg/salt_plume: added various options for salt plume depth
23      criterion and for vertical distribution of the salt
24    
25    checkpoint59l
26    o pkg/ptracers: new version of ptracers pickup:
27      read meta file and write only fields which are needed to restart.
28      ( same logic as main pickup file ; also using pickupStrictlyMatch )
29    o pkg/seaice:
30      - add timescale for melting due to warm mixed layer as a means of
31        setting SEAICE_availHeatFrac more conveniently
32      - add a CPP-flag/runtime parameter check for flooding algorithm
33      - reformulated availHeat in seaice_growth.F to be independent of AREA
34    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
35      unit changes
36    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
37    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
38      SX vector computer.
39    o pkg/seaice:
40      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
41        seaice forcing fields can now be read only through pkg/exf
42      - removed some unused halos
43    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
44    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
45      or U/VICE from U/VWIND before computing U/VSTRESS
46    
47    checkpoint59k
48    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
49      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
50    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
51      all experiments pass when compile with un-initialised var. checking option.
52    o added pkg/salt_plume
53    o script to test restart (for now, in MITgcm_contrib/jmc_script)
54    o pkg/seaice: new read/write pickup version.
55      read meta file and write only fields which are needed to restart.
56      ( same logic as main pickup file ; also using pickupStrictlyMatch )
57    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
58    o lab_sea.hb87: modify the domain & update output.hb87.txt :
59      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
60      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
61      process. Fixed here by closing the domain at the Northern boundary.
62    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
63    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
64      a set of consecutive levels in/from a 3-D array.
65    o pkg/ptracers:
66      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
67      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
68    
69    checkpoint59j
70    o in pkgs: dic, obcs, offline, rbcs:
71      standard way to compute coeff. for time interpolation between 2 time reccords
72      which retains full precision (& make results less dependent on compiler).
73      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
74    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
75      packages instead of reading ice cover and wind speed separately
76    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
77     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
78      to allow to compile customized code before the update)
79    o cleaning-up:
80      - fix CPP instruction syntax in pkg/obcs
81      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
82        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
83      - fix some threads issue in IO parts.
84    o pkg/dic:
85      - add tons of "_d 0" (--> much better testreports !)
86       and then update outputs of tutorial_global_oce_biogeo
87    o pkg/mom_fluxform:
88      add a special version of momentum advection intended to conserve momentum
89      next to a bathymetry step or a coastline edge. (default = off = #undef)
90    o new read/write pickup version:
91      - for now, only implemented for main (mdsio) pickup file.
92      - write out only what is needed to restart; merge pickup_nh , pickup_ph
93        and main pickup together.
94      - read meta file; read only what is needed to restart; stop if a field
95        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
96        if it make sense (even if the restart is not perfect).
97      - if no meta file, assume that pickup to read corresponds exactly to
98        a pickup that would currently be written.
99      - read pickup written in the old format (until checkpoint59i) if it
100        recognizes an old meta file (no field-list).
101      - add a meta file in exp. which starts from a pickup: 2 cases:
102        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
103         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
104        b) a meta file describing the content of the associated pickup file
105         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
106    o pkg/mdsio & pkg/rw:
107      - new routine to read a meta file ; new set of routine to read
108        Multiple-fields file (with meta file).
109    o added open boundary conditions capability for seaice
110        HSNOW, HSALT, UICE, and VICE
111    
112    checkpoint59i
113    o adjoint:
114      * fix multiDimAdvection adjoint
115        (partial recomputation problem by TAF for fVerT(:,:,kDown)
116        and comlev1 size definition (maxpass vs. max. number of tracers)
117      * verification/global_ocean.90x45x15 adjoint now tests
118        NLFS and multiDimAdvection using DST3 (=30)
119      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
120    o pkg/kpp: add "_d 0" to real constant (if missing);
121      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
122      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
123    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
124      for internal parameters related to restart process (formerly from PARAMS.h)
125      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
126    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
127      as argument. (only atm2d & obcs write_pickup have not yet been updated)
128    o pkg/monitor:
129      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
130      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
131      - account for deep Atmosphere factor and density factor (anelastic)
132    o added open boundary conditions capability for seaice HEFF and AREA
133    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
134      thermodynamics
135      - requires a little reorganization, which affects the testreport results
136        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
137        so that now the conservative form is tested
138      - add a few comments
139    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
140    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
141    o add new diagnostics to seaice: advective, diffusive fluxes (only for
142      multidim-advection, for scheme 2 they are not filled) and transports,
143      thermodynamic growth rates
144    o change units of EmPmR (inside the code, + within coupling interface)
145      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
146      Affects results @ truncation level (cg2d match) and update output of
147       experiments: lab_sea(6), global_ocean.90x40x15(10),
148      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
149      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
150      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
151      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
152    
153    checkpoint59h
154    o pkg/exf:
155      - improve vectorization by moving if-statement out of loops in
156        exf_mapfields, exf_radiation
157      - exf_bulkformulae.F: introduce 2D fields and vectorize code
158    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
159    o testreport:
160      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
161        monitor & update offline_exf_seaice exp. output.
162      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
163    o pkg/seaice:
164      - bug fix in the evp solver: boundary conditions were affected be
165        masking of zMax/zMin (changes results)
166      - minor bug fix in boundary conditions in seaice_calc_strainrates
167        (changes results for no_slip)
168      - seaice_lsr.F: make interpolation of eta dependent on boundaries
169      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
170      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
171        stress formulation and no-slip boundary conditions
172    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
173      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
174    o pkg/seaice: a first HSALT time stepping equation has been checked in
175    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
176      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
177      without requiring DO-IF statements
178    o pkg/thsice:
179      use continuous power-law function for partition of energy between lateral
180      melting/freezing and thinning/thickening ; old code using step function
181      still available with #undef THSICE_FRACEN_POWERLAW
182      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
183    o testreport: change AD testing : check against results/output_adm.txt
184      using same scripts as for forward test.
185    
186    checkpoint59g
187    o adjoint testing: in preparation for changing testreport:
188      - output format: cost and grad written on separated lines
189      - ad output results in directory "results" (instead of "results_ad")
190    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
191    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
192    o pkg/ecco: allow user defined cost function contributions
193    o testreport:
194      Allow to choose (per experiment) the list of tested output variables
195       and the main variable (used to issue a pass/FAIL ) ;
196      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
197      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
198      Also modify printing of summary:
199       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
200       b) echo the list of tested variables in the individual summary.txt of
201          each experiment.
202    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
203      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
204      (but still depend on the tile decompostion of the domain).
205    o pkg/seaice: change a discretization detail to make the B-grid code
206      "more symmetric". This change is likely to remove all "ridges/leads" that
207      where quasi-aligned with the grid in B-grid solutions. It may also be
208      the solution to the stress coupling issues with the B-grid.
209    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
210      remove .cvsignore from input dir. (since testreport no longer run here).
211    o pkg/thsice:
212     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
213     - fix reshaping of sea-ice just after advection:
214       melt all the ice only if ice-volume is too small.
215     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
216       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
217     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
218    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
219      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
220    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
221      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
222      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
223      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
224      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
225      -> update output.txt
226    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
227     this affects truncation error: -> update output.txt of exp:
228      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
229      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
230    
231    checkpoint59f
232    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
233    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
234      a bounded range (in forward mode)
235    o pkg/ecco, ctrl, autodiff and mom_common:
236     internal parameter controls, completements of implementations
237    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
238    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
239      (not seem any difference in testing results).
240    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
241       at face corners.
242    o pkg/generic_advdiff:
243     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
244      loop range indices for computing vertical advection tendency
245      and do the calculation in the interior only (no overlap) ;
246      for now, only implemented for SOM advection (to save CPU time).
247     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
248    o exch2 adjoint
249      First set of changes:
250      - add exch2 hand-written adjoint templates
251      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
252        This will require cleanup in pkg/autodiff/*.F
253        (changed routines currently kept separate in verif. code/)
254      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
255        that used to hide exch2 or cubed-sphere specific code
256        (commented via 'cph-exch2')
257    o pkg/seaice
258      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
259    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
260       output of global_ocean.cs32x15.thsice .
261    
262    checkpoint59e
263    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
264      for B-grid vector (not yet tested) and C-grid vector (<- only used
265      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
266    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
267      (#ifdef ALLOW_SALT_PLUME)
268    o gather_2d/scatter_2d: removed halo regions
269    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
270      scheme and the corresponding test case (under front_relax dir). For now,
271      only available with Skew-flux form and not yet tested in realistic set-up.
272      adjoint: store directives updated, but gradient checks deteriorated,
273      so maybe GM/Redi adjoint is now broken.
274    o seaice adjoint
275      * add AREA, HEFF, HSNOW as control variable
276        (should not change lab_sea results)
277      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
278    o pkg/seaice:
279      * added computation of saltFlux in seaice_growth;
280        For time being, sea ice salinity is assumed constant
281        contribution of snow flooding to freshening of sea ice is neglected.
282        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
283        defaults to 0.0 in order to maintain backward compatibility.
284        Typical values for SEAICE_salinity are 4 to 10 g/kg.
285      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
286      * added SEAICE_availHeatFrac, which specifies fraction of surface level
287        heat content used to melt or grow ice
288      * commented out cap of HICE: it helps keep ice thinner
289      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
290      * applied OBCS T/S mask to HEFFM sea ice mask
291    
292    checkpoint59d
293    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
294     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
295     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
296    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
297     and change default value of parameter "GM_Small_Number";
298     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
299       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
300       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
301    o pkg/ecco: cost function when applying pkg/smooth to controls
302    o pkg/ctrl: add forcingPrecond run time parameter
303    o pkg/seaice:
304     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
305     - fix bug in metric terms of u-equation in LSR solver (implicit part),
306       changes verification/lab_sea
307     - rearrange implicit part of u-equation in LSR solver to make it easier to
308       read, understand, and debug. This causes changes at the truncation level.
309     - fix (serious) bug in the boundary conditions (sign error in the implicit
310       part) of the LSR solver. Changes all LSR results.
311     - fixed problem with HSNOW initialization to avoid thick snow when AREA
312       is initilized with small values - does not change lab_sea results.
313     - added HsnowFile initialization capability
314    o pkg/smooth: addition to model/src and pkg/ctrl so allow
315     initialization of pkg/smooth and application to control vector
316  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
317  o dependencies: pkg/profiles requires pkg/cal  o dependencies: pkg/profiles requires pkg/cal
318  o pkg/profiles:  o pkg/profiles:
# Line 15  o pkg/profiles: Line 324  o pkg/profiles:
324       that allow you to prepare netcdf input files.       that allow you to prepare netcdf input files.
325   - also modified: cleaner include statements, cleaner error print statements,   - also modified: cleaner include statements, cleaner error print statements,
326     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.
   
327  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
328  o pkg/seaice:  o pkg/seaice:
329   - 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 457  o in FFIELDS.h:
457       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
458  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
459  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
460      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
461        are no longer updating the vertical diffusivity array
462        (passed as argument) but are (re-) setting those arrays.
463  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
464    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
465      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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