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revision 1.819 by jmc, Fri May 18 03:02:47 2007 UTC revision 1.908 by jmc, Sat Nov 10 22:17:09 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 pkg/ptracers:
8      use use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
9      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
10    
11    checkpoint59j
12    o in pkgs: dic, obcs, offline, rbcs:
13      standard way to compute coeff. for time interpolation between 2 time reccords
14      which retains full precision (& make results less dependent on compiler).
15      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
16    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
17      packages instead of reading ice cover and wind speed separately
18    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
19     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
20      to allow to compile customized code before the update)
21    o cleaning-up:
22      - fix CPP instruction syntax in pkg/obcs
23      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
24        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
25      - fix some threads issue in IO parts.
26    o pkg/dic:
27      - add tons of "_d 0" (--> much better testreports !)
28       and then update outputs of tutorial_global_oce_biogeo
29    o pkg/mom_fluxform:
30      add a special version of momentum advection intended to conserve momentum
31      next to a bathymetry step or a coastline edge. (default = off = #undef)
32    o new read/write pickup version:
33      - for now, only implemented for main (mdsio) pickup file.
34      - write out only what is needed to restart; merge pickup_nh , pickup_ph
35        and main pickup together.
36      - read meta file; read only what is needed to restart; stop if a field
37        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
38        if it make sense (even if the restart is not perfect).
39      - if no meta file, assume that pickup to read corresponds exactly to
40        a pickup that would currently be written.
41      - read pickup written in the old format (until checkpoint59i) if it
42        recognizes an old meta file (no field-list).
43      - add a meta file in exp. which starts from a pickup: 2 cases:
44        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
45         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
46        b) a meta file describing the content of the associated pickup file
47         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
48    o pkg/mdsio & pkg/rw:
49      - new routine to read a meta file ; new set of routine to read
50        Multiple-fields file (with meta file).
51    o added open boundary conditions capability for seaice
52        HSNOW, HSALT, UICE, and VICE
53    
54    checkpoint59i
55    o adjoint:
56      * fix multiDimAdvection adjoint
57        (partial recomputation problem by TAF for fVerT(:,:,kDown)
58        and comlev1 size definition (maxpass vs. max. number of tracers)
59      * verification/global_ocean.90x45x15 adjoint now tests
60        NLFS and multiDimAdvection using DST3 (=30)
61      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
62    o pkg/kpp: add "_d 0" to real constant (if missing);
63      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
64      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
65    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
66      for internal parameters related to restart process (formerly from PARAMS.h)
67      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
68    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
69      as argument. (only atm2d & obcs write_pickup have not yet been updated)
70    o pkg/monitor:
71      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
72      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
73      - account for deep Atmosphere factor and density factor (anelastic)
74    o added open boundary conditions capability for seaice HEFF and AREA
75    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
76      thermodynamics
77      - requires a little reorganization, which affects the testreport results
78        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
79        so that now the conservative form is tested
80      - add a few comments
81    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
82    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
83    o add new diagnostics to seaice: advective, diffusive fluxes (only for
84      multidim-advection, for scheme 2 they are not filled) and transports,
85      thermodynamic growth rates
86    o change units of EmPmR (inside the code, + within coupling interface)
87      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
88      Affects results @ truncation level (cg2d match) and update output of
89       experiments: lab_sea(6), global_ocean.90x40x15(10),
90      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
91      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
92      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
93      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
94    
95    checkpoint59h
96    o pkg/exf:
97      - improve vectorization by moving if-statement out of loops in
98        exf_mapfields, exf_radiation
99      - exf_bulkformulae.F: introduce 2D fields and vectorize code
100    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
101    o testreport:
102      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
103        monitor & update offline_exf_seaice exp. output.
104      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
105    o pkg/seaice:
106      - bug fix in the evp solver: boundary conditions were affected be
107        masking of zMax/zMin (changes results)
108      - minor bug fix in boundary conditions in seaice_calc_strainrates
109        (changes results for no_slip)
110      - seaice_lsr.F: make interpolation of eta dependent on boundaries
111      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
112      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
113        stress formulation and no-slip boundary conditions
114    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
115      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
116    o pkg/seaice: a first HSALT time stepping equation has been checked in
117    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
118      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
119      without requiring DO-IF statements
120    o pkg/thsice:
121      use continuous power-law function for partition of energy between lateral
122      melting/freezing and thinning/thickening ; old code using step function
123      still available with #undef THSICE_FRACEN_POWERLAW
124      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
125    o testreport: change AD testing : check against results/output_adm.txt
126      using same scripts as for forward test.
127    
128    checkpoint59g
129    o adjoint testing: in preparation for changing testreport:
130      - output format: cost and grad written on separated lines
131      - ad output results in directory "results" (instead of "results_ad")
132    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
133    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
134    o pkg/ecco: allow user defined cost function contributions
135    o testreport:
136      Allow to choose (per experiment) the list of tested output variables
137       and the main variable (used to issue a pass/FAIL ) ;
138      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
139      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
140      Also modify printing of summary:
141       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
142       b) echo the list of tested variables in the individual summary.txt of
143          each experiment.
144    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
145      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
146      (but still depend on the tile decompostion of the domain).
147    o pkg/seaice: change a discretization detail to make the B-grid code
148      "more symmetric". This change is likely to remove all "ridges/leads" that
149      where quasi-aligned with the grid in B-grid solutions. It may also be
150      the solution to the stress coupling issues with the B-grid.
151    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
152      remove .cvsignore from input dir. (since testreport no longer run here).
153    o pkg/thsice:
154     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
155     - fix reshaping of sea-ice just after advection:
156       melt all the ice only if ice-volume is too small.
157     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
158       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
159     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
160    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
161      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
162    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
163      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
164      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
165      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
166      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
167      -> update output.txt
168    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
169     this affects truncation error: -> update output.txt of exp:
170      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
171      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
172    
173    checkpoint59f
174    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
175    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
176      a bounded range (in forward mode)
177    o pkg/ecco, ctrl, autodiff and mom_common:
178     internal parameter controls, completements of implementations
179    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
180    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
181      (not seem any difference in testing results).
182    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
183       at face corners.
184    o pkg/generic_advdiff:
185     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
186      loop range indices for computing vertical advection tendency
187      and do the calculation in the interior only (no overlap) ;
188      for now, only implemented for SOM advection (to save CPU time).
189     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
190    o exch2 adjoint
191      First set of changes:
192      - add exch2 hand-written adjoint templates
193      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
194        This will require cleanup in pkg/autodiff/*.F
195        (changed routines currently kept separate in verif. code/)
196      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
197        that used to hide exch2 or cubed-sphere specific code
198        (commented via 'cph-exch2')
199    o pkg/seaice
200      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
201    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
202       output of global_ocean.cs32x15.thsice .
203    
204    checkpoint59e
205    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
206      for B-grid vector (not yet tested) and C-grid vector (<- only used
207      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
208    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
209      (#ifdef ALLOW_SALT_PLUME)
210    o gather_2d/scatter_2d: removed halo regions
211    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
212      scheme and the corresponding test case (under front_relax dir). For now,
213      only available with Skew-flux form and not yet tested in realistic set-up.
214      adjoint: store directives updated, but gradient checks deteriorated,
215      so maybe GM/Redi adjoint is now broken.
216    o seaice adjoint
217      * add AREA, HEFF, HSNOW as control variable
218        (should not change lab_sea results)
219      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
220    o pkg/seaice:
221      * added computation of saltFlux in seaice_growth;
222        For time being, sea ice salinity is assumed constant
223        contribution of snow flooding to freshening of sea ice is neglected.
224        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
225        defaults to 0.0 in order to maintain backward compatibility.
226        Typical values for SEAICE_salinity are 4 to 10 g/kg.
227      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
228      * added SEAICE_availHeatFrac, which specifies fraction of surface level
229        heat content used to melt or grow ice
230      * commented out cap of HICE: it helps keep ice thinner
231      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
232      * applied OBCS T/S mask to HEFFM sea ice mask
233    
234    checkpoint59d
235    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
236     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
237     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
238    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
239     and change default value of parameter "GM_Small_Number";
240     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
241       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
242       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
243    o pkg/ecco: cost function when applying pkg/smooth to controls
244    o pkg/ctrl: add forcingPrecond run time parameter
245    o pkg/seaice:
246     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
247     - fix bug in metric terms of u-equation in LSR solver (implicit part),
248       changes verification/lab_sea
249     - rearrange implicit part of u-equation in LSR solver to make it easier to
250       read, understand, and debug. This causes changes at the truncation level.
251     - fix (serious) bug in the boundary conditions (sign error in the implicit
252       part) of the LSR solver. Changes all LSR results.
253     - fixed problem with HSNOW initialization to avoid thick snow when AREA
254       is initilized with small values - does not change lab_sea results.
255     - added HsnowFile initialization capability
256    o pkg/smooth: addition to model/src and pkg/ctrl so allow
257     initialization of pkg/smooth and application to control vector
258    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
259    o dependencies: pkg/profiles requires pkg/cal
260    o pkg/profiles:
261     - added option ALLOW_PROFILES_GENERICGRID
262         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
263         that interpolation information (grid points and coefficients) is provided
264         within the netcdf input files.
265         -> sample matlab scripts can be found in MITgcm_contrib/gael
266         that allow you to prepare netcdf input files.
267     - also modified: cleaner include statements, cleaner error print statements,
268       cleaner stops when error, and more tests of the netcdf input files consistency.
269    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
270    o pkg/seaice:
271     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
272       requires a new routine: seaice_diagnostics_fill.F
273     - make sure that seaice does not move if not forced (pressure replacement
274       method, Hibler and Ip, 1995), changes results
275     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
276     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
277       It is turned off by default (=-1.), because it changes the results.
278     - make it possible to read AREA from a file, too.
279    
280    checkpoint59c
281    o add S/R and diagnostics for oceanic mixed-layer depth
282    o move GMRedi call after all vertical mixing schemes (including KPP)
283    o pkg/thsice:
284     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
285      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
286    o pkg/obcs:
287     - bug fix for balance code
288    o pkg/seaice:
289      - allow values of SEAICE_elasticParm > 1
290      - add new parameter SEAICE_evpTauRelax as an alternative
291        to SEAICE_elasticParm
292      - make lsr boundary conditions free slip (by default), changes result
293      - add code for no slip boundary conditions for lsr
294      - set minimum of zeta to zero (and not 4e8) (changes results)
295      - add a cap on AREA after advecting AREA if seaice_growth is not called
296    o change calculation of Visbeck K:
297      - no longer depend on tapering scheme; instead, compute slope (limited
298        by GM_maxSlope). this is equivalent to what was comuted before with
299        clipping or linear tappering.
300      - fix vertical averaging (wrong by 1/2 level)
301      - leave the old version (but will not be maintained) within
302        #ifdef OLD_VISBECK_CALC / #endif
303      - update output of exp. ideal_2D_oce
304    o change error catch in calc_r_star to improve vectorization
305  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
306    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
307    o adjoint:
308      Re-organized adjoint checkpointing according to Matt Mazloff
309      (but with modifs/completions/cleanups)
310      Storing is now bundled into large arrays to optimized I/O
311      (and second step in cleanup of the_main_loop)
312    
313  checkpoint59b  checkpoint59b
314  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
# Line 59  o pkg/exf: some cleaning-up: Line 362  o pkg/exf: some cleaning-up:
362  o pkg/thsice:  o pkg/thsice:
363   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
364    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
365    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
366    and in thsice_extend.F:    and in thsice_extend.F:
367    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
368    - start to form ice as soon as the minimum ice-volume is reachable.    - start to form ice as soon as the minimum ice-volume is reachable.
# Line 96  o in FFIELDS.h: Line 399  o in FFIELDS.h:
399       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
400  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
401  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
402      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
403        are no longer updating the vertical diffusivity array
404        (passed as argument) but are (re-) setting those arrays.
405  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
406    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
407      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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