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revision 1.835 by gforget, Fri Jun 15 05:09:24 2007 UTC revision 1.935 by dimitri, Thu Jan 10 23:32:15 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/seaice_growth.F: use a different time constant for freezing
8      ice due to supercooled sea water, hardwired to SEAICE_deltaTtherm/0.1
9    o gad_som : fix flux output (& diagnostics) to have same units as other
10      advection scheme fluxes (was previously multiplied by deltaT).
11    o added verification/seaice_obcs both to test seaice open boundaries
12      and to provide an example matlab scrpt for generating them
13    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
14    o pkg/salt_plume: clean up salt_plume_frac.F to
15      remove redundancy in PlumeMethod 1 and 4
16    o pkg/kpp: added saltplume diagnostics
17    o pkg/obcs and pkg/seaice:
18      - do not set uice and vice to zero when OB*icefile are unspecified
19      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
20      - moved seaice tracer obcs after call to seaice_growth
21    o pkg/salt_plume: added various options for salt plume depth
22      criterion and for vertical distribution of the salt
23    
24    checkpoint59l
25    o pkg/ptracers: new version of ptracers pickup:
26      read meta file and write only fields which are needed to restart.
27      ( same logic as main pickup file ; also using pickupStrictlyMatch )
28    o pkg/seaice:
29      - add timescale for melting due to warm mixed layer as a means of
30        setting SEAICE_availHeatFrac more conveniently
31      - add a CPP-flag/runtime parameter check for flooding algorithm
32      - reformulated availHeat in seaice_growth.F to be independent of AREA
33    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
34      unit changes
35    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
36    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
37      SX vector computer.
38    o pkg/seaice:
39      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
40        seaice forcing fields can now be read only through pkg/exf
41      - removed some unused halos
42    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
43    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
44      or U/VICE from U/VWIND before computing U/VSTRESS
45    
46    checkpoint59k
47    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
48      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
49    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
50      all experiments pass when compile with un-initialised var. checking option.
51    o added pkg/salt_plume
52    o script to test restart (for now, in MITgcm_contrib/jmc_script)
53    o pkg/seaice: new read/write pickup version.
54      read meta file and write only fields which are needed to restart.
55      ( same logic as main pickup file ; also using pickupStrictlyMatch )
56    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
57    o lab_sea.hb87: modify the domain & update output.hb87.txt :
58      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
59      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
60      process. Fixed here by closing the domain at the Northern boundary.
61    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
62    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
63      a set of consecutive levels in/from a 3-D array.
64    o pkg/ptracers:
65      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
66      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
67    
68    checkpoint59j
69    o in pkgs: dic, obcs, offline, rbcs:
70      standard way to compute coeff. for time interpolation between 2 time reccords
71      which retains full precision (& make results less dependent on compiler).
72      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
73    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
74      packages instead of reading ice cover and wind speed separately
75    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
76     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
77      to allow to compile customized code before the update)
78    o cleaning-up:
79      - fix CPP instruction syntax in pkg/obcs
80      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
81        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
82      - fix some threads issue in IO parts.
83    o pkg/dic:
84      - add tons of "_d 0" (--> much better testreports !)
85       and then update outputs of tutorial_global_oce_biogeo
86    o pkg/mom_fluxform:
87      add a special version of momentum advection intended to conserve momentum
88      next to a bathymetry step or a coastline edge. (default = off = #undef)
89    o new read/write pickup version:
90      - for now, only implemented for main (mdsio) pickup file.
91      - write out only what is needed to restart; merge pickup_nh , pickup_ph
92        and main pickup together.
93      - read meta file; read only what is needed to restart; stop if a field
94        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
95        if it make sense (even if the restart is not perfect).
96      - if no meta file, assume that pickup to read corresponds exactly to
97        a pickup that would currently be written.
98      - read pickup written in the old format (until checkpoint59i) if it
99        recognizes an old meta file (no field-list).
100      - add a meta file in exp. which starts from a pickup: 2 cases:
101        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
102         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
103        b) a meta file describing the content of the associated pickup file
104         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
105    o pkg/mdsio & pkg/rw:
106      - new routine to read a meta file ; new set of routine to read
107        Multiple-fields file (with meta file).
108    o added open boundary conditions capability for seaice
109        HSNOW, HSALT, UICE, and VICE
110    
111    checkpoint59i
112    o adjoint:
113      * fix multiDimAdvection adjoint
114        (partial recomputation problem by TAF for fVerT(:,:,kDown)
115        and comlev1 size definition (maxpass vs. max. number of tracers)
116      * verification/global_ocean.90x45x15 adjoint now tests
117        NLFS and multiDimAdvection using DST3 (=30)
118      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
119    o pkg/kpp: add "_d 0" to real constant (if missing);
120      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
121      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
122    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
123      for internal parameters related to restart process (formerly from PARAMS.h)
124      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
125    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
126      as argument. (only atm2d & obcs write_pickup have not yet been updated)
127    o pkg/monitor:
128      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
129      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
130      - account for deep Atmosphere factor and density factor (anelastic)
131    o added open boundary conditions capability for seaice HEFF and AREA
132    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
133      thermodynamics
134      - requires a little reorganization, which affects the testreport results
135        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
136        so that now the conservative form is tested
137      - add a few comments
138    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
139    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
140    o add new diagnostics to seaice: advective, diffusive fluxes (only for
141      multidim-advection, for scheme 2 they are not filled) and transports,
142      thermodynamic growth rates
143    o change units of EmPmR (inside the code, + within coupling interface)
144      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
145      Affects results @ truncation level (cg2d match) and update output of
146       experiments: lab_sea(6), global_ocean.90x40x15(10),
147      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
148      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
149      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
150      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
151    
152    checkpoint59h
153    o pkg/exf:
154      - improve vectorization by moving if-statement out of loops in
155        exf_mapfields, exf_radiation
156      - exf_bulkformulae.F: introduce 2D fields and vectorize code
157    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
158    o testreport:
159      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
160        monitor & update offline_exf_seaice exp. output.
161      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
162    o pkg/seaice:
163      - bug fix in the evp solver: boundary conditions were affected be
164        masking of zMax/zMin (changes results)
165      - minor bug fix in boundary conditions in seaice_calc_strainrates
166        (changes results for no_slip)
167      - seaice_lsr.F: make interpolation of eta dependent on boundaries
168      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
169      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
170        stress formulation and no-slip boundary conditions
171    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
172      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
173    o pkg/seaice: a first HSALT time stepping equation has been checked in
174    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
175      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
176      without requiring DO-IF statements
177    o pkg/thsice:
178      use continuous power-law function for partition of energy between lateral
179      melting/freezing and thinning/thickening ; old code using step function
180      still available with #undef THSICE_FRACEN_POWERLAW
181      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
182    o testreport: change AD testing : check against results/output_adm.txt
183      using same scripts as for forward test.
184    
185    checkpoint59g
186    o adjoint testing: in preparation for changing testreport:
187      - output format: cost and grad written on separated lines
188      - ad output results in directory "results" (instead of "results_ad")
189    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
190    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
191    o pkg/ecco: allow user defined cost function contributions
192    o testreport:
193      Allow to choose (per experiment) the list of tested output variables
194       and the main variable (used to issue a pass/FAIL ) ;
195      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
196      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
197      Also modify printing of summary:
198       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
199       b) echo the list of tested variables in the individual summary.txt of
200          each experiment.
201    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
202      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
203      (but still depend on the tile decompostion of the domain).
204    o pkg/seaice: change a discretization detail to make the B-grid code
205      "more symmetric". This change is likely to remove all "ridges/leads" that
206      where quasi-aligned with the grid in B-grid solutions. It may also be
207      the solution to the stress coupling issues with the B-grid.
208    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
209      remove .cvsignore from input dir. (since testreport no longer run here).
210    o pkg/thsice:
211     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
212     - fix reshaping of sea-ice just after advection:
213       melt all the ice only if ice-volume is too small.
214     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
215       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
216     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
217    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
218      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
219    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
220      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
221      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
222      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
223      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
224      -> update output.txt
225    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
226     this affects truncation error: -> update output.txt of exp:
227      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
228      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
229    
230    checkpoint59f
231    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
232    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
233      a bounded range (in forward mode)
234    o pkg/ecco, ctrl, autodiff and mom_common:
235     internal parameter controls, completements of implementations
236    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
237    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
238      (not seem any difference in testing results).
239    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
240       at face corners.
241    o pkg/generic_advdiff:
242     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
243      loop range indices for computing vertical advection tendency
244      and do the calculation in the interior only (no overlap) ;
245      for now, only implemented for SOM advection (to save CPU time).
246     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
247    o exch2 adjoint
248      First set of changes:
249      - add exch2 hand-written adjoint templates
250      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
251        This will require cleanup in pkg/autodiff/*.F
252        (changed routines currently kept separate in verif. code/)
253      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
254        that used to hide exch2 or cubed-sphere specific code
255        (commented via 'cph-exch2')
256    o pkg/seaice
257      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
258    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
259       output of global_ocean.cs32x15.thsice .
260    
261    checkpoint59e
262    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
263      for B-grid vector (not yet tested) and C-grid vector (<- only used
264      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
265    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
266      (#ifdef ALLOW_SALT_PLUME)
267    o gather_2d/scatter_2d: removed halo regions
268    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
269      scheme and the corresponding test case (under front_relax dir). For now,
270      only available with Skew-flux form and not yet tested in realistic set-up.
271      adjoint: store directives updated, but gradient checks deteriorated,
272      so maybe GM/Redi adjoint is now broken.
273    o seaice adjoint
274      * add AREA, HEFF, HSNOW as control variable
275        (should not change lab_sea results)
276      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
277    o pkg/seaice:
278      * added computation of saltFlux in seaice_growth;
279        For time being, sea ice salinity is assumed constant
280        contribution of snow flooding to freshening of sea ice is neglected.
281        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
282        defaults to 0.0 in order to maintain backward compatibility.
283        Typical values for SEAICE_salinity are 4 to 10 g/kg.
284      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
285      * added SEAICE_availHeatFrac, which specifies fraction of surface level
286        heat content used to melt or grow ice
287      * commented out cap of HICE: it helps keep ice thinner
288      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
289      * applied OBCS T/S mask to HEFFM sea ice mask
290    
291    checkpoint59d
292    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
293     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
294     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
295    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
296     and change default value of parameter "GM_Small_Number";
297     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
298       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
299       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
300    o pkg/ecco: cost function when applying pkg/smooth to controls
301    o pkg/ctrl: add forcingPrecond run time parameter
302    o pkg/seaice:
303     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
304     - fix bug in metric terms of u-equation in LSR solver (implicit part),
305       changes verification/lab_sea
306     - rearrange implicit part of u-equation in LSR solver to make it easier to
307       read, understand, and debug. This causes changes at the truncation level.
308     - fix (serious) bug in the boundary conditions (sign error in the implicit
309       part) of the LSR solver. Changes all LSR results.
310     - fixed problem with HSNOW initialization to avoid thick snow when AREA
311       is initilized with small values - does not change lab_sea results.
312     - added HsnowFile initialization capability
313    o pkg/smooth: addition to model/src and pkg/ctrl so allow
314     initialization of pkg/smooth and application to control vector
315    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
316    o dependencies: pkg/profiles requires pkg/cal
317  o pkg/profiles:  o pkg/profiles:
318   - added option ALLOW_PROFILES_GENERICGRID   - added option ALLOW_PROFILES_GENERICGRID
319       -> 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 323  o pkg/profiles:
323       that allow you to prepare netcdf input files.       that allow you to prepare netcdf input files.
324   - also modified: cleaner include statements, cleaner error print statements,   - also modified: cleaner include statements, cleaner error print statements,
325     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.
   
326  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.  o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
327  o pkg/seaice:  o pkg/seaice:
328   - 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 456  o in FFIELDS.h:
456       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
457  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
458  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
459      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
460        are no longer updating the vertical diffusivity array
461        (passed as argument) but are (re-) setting those arrays.
462  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
463    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
464      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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