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revision 1.802 by jmc, Mon Apr 30 16:03:40 2007 UTC revision 1.890 by mlosch, Wed Oct 10 12:25:20 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/shelfice: add option for convservative form of Hellmer&Olbers (1989)
8      thermodynamics
9      - requires a little reorganization, which affects the testreport results
10        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
11        so that now the conservative form is tested
12      - add a few comments
13    o add missing cvs $Header$ or $Name$ in eesupp/*, pkg/* & verification/code*
14    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
15    o add new diagnostics to seaice: advective, diffusive fluxes (only for
16      multidim-advection, for scheme 2 they are not filled) and transports,
17      thermodynamic growth rates
18    o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
19      leave input file unchanged. Affects results @ truncation level (cg2d match)
20      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
21      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
22      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
23      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
24    
25    checkpoint59h
26    o pkg/exf:
27      - improve vectorization by moving if-statement out of loops in
28        exf_mapfields, exf_radiation
29      - exf_bulkformulae.F: introduce 2D fields and vectorize code
30    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
31    o testreport:
32      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
33        monitor & update offline_exf_seaice exp. output.
34      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
35    o pkg/seaice:
36      - bug fix in the evp solver: boundary conditions were affected be
37        masking of zMax/zMin (changes results)
38      - minor bug fix in boundary conditions in seaice_calc_strainrates
39        (changes results for no_slip)
40      - seaice_lsr.F: make interpolation of eta dependent on boundaries
41      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
42      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
43        stress formulation and no-slip boundary conditions
44    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
45      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
46    o pkg/seaice: a first HSALT time stepping equation has been checked in
47    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
48      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
49      without requiring DO-IF statements
50    o pkg/thsice:
51      use continuous power-law function for partition of energy between lateral
52      melting/freezing and thinning/thickening ; old code using step function
53      still available with #undef THSICE_FRACEN_POWERLAW
54      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
55    o testreport: change AD testing : check against results/output_adm.txt
56      using same scripts as for forward test.
57    
58    checkpoint59g
59    o adjoint testing: in preparation for changing testreport:
60      - output format: cost and grad written on separated lines
61      - ad output results in directory "results" (instead of "results_ad")
62    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
63    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
64    o pkg/ecco: allow user defined cost function contributions
65    o testreport:
66      Allow to choose (per experiment) the list of tested output variables
67       and the main variable (used to issue a pass/FAIL ) ;
68      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
69      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
70      Also modify printing of summary:
71       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
72       b) echo the list of tested variables in the individual summary.txt of
73          each experiment.
74    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
75      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
76      (but still depend on the tile decompostion of the domain).
77    o pkg/seaice: change a discretization detail to make the B-grid code
78      "more symmetric". This change is likely to remove all "ridges/leads" that
79      where quasi-aligned with the grid in B-grid solutions. It may also be
80      the solution to the stress coupling issues with the B-grid.
81    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
82      remove .cvsignore from input dir. (since testreport no longer run here).
83    o pkg/thsice:
84     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
85     - fix reshaping of sea-ice just after advection:
86       melt all the ice only if ice-volume is too small.
87     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
88       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
89     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
90    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
91      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
92    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
93      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
94      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
95      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
96      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
97      -> update output.txt
98    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
99     this affects truncation error: -> update output.txt of exp:
100      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
101      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
102    
103    checkpoint59f
104    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
105    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
106      a bounded range (in forward mode)
107    o pkg/ecco, ctrl, autodiff and mom_common:
108     internal parameter controls, completements of implementations
109    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
110    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
111      (not seem any difference in testing results).
112    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
113       at face corners.
114    o pkg/generic_advdiff:
115     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
116      loop range indices for computing vertical advection tendency
117      and do the calculation in the interior only (no overlap) ;
118      for now, only implemented for SOM advection (to save CPU time).
119     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
120    o exch2 adjoint
121      First set of changes:
122      - add exch2 hand-written adjoint templates
123      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
124        This will require cleanup in pkg/autodiff/*.F
125        (changed routines currently kept separate in verif. code/)
126      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
127        that used to hide exch2 or cubed-sphere specific code
128        (commented via 'cph-exch2')
129    o pkg/seaice
130      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
131    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
132       output of global_ocean.cs32x15.thsice .
133    
134    checkpoint59e
135    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
136      for B-grid vector (not yet tested) and C-grid vector (<- only used
137      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
138    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
139      (#ifdef ALLOW_SALT_PLUME)
140    o gather_2d/scatter_2d: removed halo regions
141    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
142      scheme and the corresponding test case (under front_relax dir). For now,
143      only available with Skew-flux form and not yet tested in realistic set-up.
144      adjoint: store directives updated, but gradient checks deteriorated,
145      so maybe GM/Redi adjoint is now broken.
146    o seaice adjoint
147      * add AREA, HEFF, HSNOW as control variable
148        (should not change lab_sea results)
149      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
150    o pkg/seaice:
151      * added computation of saltFlux in seaice_growth;
152        For time being, sea ice salinity is assumed constant
153        contribution of snow flooding to freshening of sea ice is neglected.
154        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
155        defaults to 0.0 in order to maintain backward compatibility.
156        Typical values for SEAICE_salinity are 4 to 10 g/kg.
157      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
158      * added SEAICE_availHeatFrac, which specifies fraction of surface level
159        heat content used to melt or grow ice
160      * commented out cap of HICE: it helps keep ice thinner
161      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
162      * applied OBCS T/S mask to HEFFM sea ice mask
163    
164    checkpoint59d
165    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
166     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
167     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
168    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
169     and change default value of parameter "GM_Small_Number";
170     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
171       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
172       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
173    o pkg/ecco: cost function when applying pkg/smooth to controls
174    o pkg/ctrl: add forcingPrecond run time parameter
175    o pkg/seaice:
176     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
177     - fix bug in metric terms of u-equation in LSR solver (implicit part),
178       changes verification/lab_sea
179     - rearrange implicit part of u-equation in LSR solver to make it easier to
180       read, understand, and debug. This causes changes at the truncation level.
181     - fix (serious) bug in the boundary conditions (sign error in the implicit
182       part) of the LSR solver. Changes all LSR results.
183     - fixed problem with HSNOW initialization to avoid thick snow when AREA
184       is initilized with small values - does not change lab_sea results.
185     - added HsnowFile initialization capability
186    o pkg/smooth: addition to model/src and pkg/ctrl so allow
187     initialization of pkg/smooth and application to control vector
188    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
189    o dependencies: pkg/profiles requires pkg/cal
190    o pkg/profiles:
191     - added option ALLOW_PROFILES_GENERICGRID
192         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
193         that interpolation information (grid points and coefficients) is provided
194         within the netcdf input files.
195         -> sample matlab scripts can be found in MITgcm_contrib/gael
196         that allow you to prepare netcdf input files.
197     - also modified: cleaner include statements, cleaner error print statements,
198       cleaner stops when error, and more tests of the netcdf input files consistency.
199    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
200    o pkg/seaice:
201     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
202       requires a new routine: seaice_diagnostics_fill.F
203     - make sure that seaice does not move if not forced (pressure replacement
204       method, Hibler and Ip, 1995), changes results
205     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
206     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
207       It is turned off by default (=-1.), because it changes the results.
208     - make it possible to read AREA from a file, too.
209    
210    checkpoint59c
211    o add S/R and diagnostics for oceanic mixed-layer depth
212    o move GMRedi call after all vertical mixing schemes (including KPP)
213    o pkg/thsice:
214     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
215      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
216    o pkg/obcs:
217     - bug fix for balance code
218    o pkg/seaice:
219      - allow values of SEAICE_elasticParm > 1
220      - add new parameter SEAICE_evpTauRelax as an alternative
221        to SEAICE_elasticParm
222      - make lsr boundary conditions free slip (by default), changes result
223      - add code for no slip boundary conditions for lsr
224      - set minimum of zeta to zero (and not 4e8) (changes results)
225      - add a cap on AREA after advecting AREA if seaice_growth is not called
226    o change calculation of Visbeck K:
227      - no longer depend on tapering scheme; instead, compute slope (limited
228        by GM_maxSlope). this is equivalent to what was comuted before with
229        clipping or linear tappering.
230      - fix vertical averaging (wrong by 1/2 level)
231      - leave the old version (but will not be maintained) within
232        #ifdef OLD_VISBECK_CALC / #endif
233      - update output of exp. ideal_2D_oce
234    o change error catch in calc_r_star to improve vectorization
235    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
236      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
237    o adjoint:
238      Re-organized adjoint checkpointing according to Matt Mazloff
239      (but with modifs/completions/cleanups)
240      Storing is now bundled into large arrays to optimized I/O
241      (and second step in cleanup of the_main_loop)
242    
243    checkpoint59b
244    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
245      - export/import (between ocean & coupler) fields needed for ocean DIC.
246    o pkg/seaice:
247      - get rid of three more exchanges seaice_calc_viscosities (required
248        different loop boundaries in seaice_lsr and seaice_ocean_stress)
249      - bug fix in seaice_ocean_stress (update of lab_sea required)
250      - reduce loop boundaries to necessary minimum also in seaice_evp
251      - go back to the old way of computing deltaC/Z as the adjoint likes that
252        better
253    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
254      passive tracer to an Age Tracer) + update output.txt
255    o pkg/exf:
256      - implement A-grid / C-grid selection for wind-stress input files.
257      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
258      for now, in exf_bulk_largeyeager04.F only :
259      - change implementation for case where windspeed + 2. components wind-stress
260        are read-in. AND use rhoConstFresh to convert evap.
261    o pkg/seaice:
262      - use correct EXCH_UV for wind-forcing (on A-grid).
263      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
264        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
265    o pkg/exf:
266      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
267      EXF_INTERPOLATION:
268      - merge global_with_exf/code version of exf_interp_read.F
269        to the main code ;
270      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
271        reading the file ; Important: This options needs to be defined to recover
272        previous code.
273        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
274      - no longer loose real*8 precision along the way when using exf_iprec=64.
275    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
276      - change discretisation of evp-solver in order to avoid another exchange
277        (changes lab_sea) and clean up a little
278      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
279        help the adjoint (this also changes the results slightly)
280      - add a few "_d 0" where they had been missing in seaice_evp.F
281      - cleaning up: remove unused seaice_calc_rhs.F
282    o pkg/exf: some cleaning-up:
283      - change various "constants" into runtime parameters
284      - cleaned-up Large&Yeager04 routine which should eventually
285        replace exf_bulkformulae.F (changed names of S/R and CPP)
286        and merged various ALLOW_ATM_WIND options
287     only used with thsice pkg (in thsice_get_exf.F):
288      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
289        which are used when useStabilityFct_overIce=TRUE (= the default)
290      - change default values of ice & snow emissivity and scale downward LW
291        by ice & snow emissivity.
292    o pkg/thsice:
293     fix few little problems, in thsice_calc_thickn.F:
294      - growth vertically (and not laterally) if iceFrac == iceMaskMax
295      - melt only laterally if hIce < hThinIce (as the comments say)
296      and in thsice_extend.F:
297      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
298      - start to form ice as soon as the minimum ice-volume is reachable.
299     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
300      and cpl_aim+ocn
301    o pkg/kpp
302     - move computation of surface related input fields to KPP into a new
303       subroutine kpp_forcing_surf.F
304     - remove wrong (within bi,bj loops) EXCH calls.
305     - little cleaning (add argument myThid in last position, cvs header ...)
306     - for now, fix conservation problem by exchanging KPPviscAz (may not
307       be the best fix)
308    o pkg/seaice
309     - check for inconsistent evp parameter/cpp-flag combination
310     - remove leftover errIO flat for obsolete name list error handling
311    o OpenAD
312     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
313    
314    checkpoint59a
315    o pkg/seaice: some parameter clarifications and a little bit of clean up
316  o pkg/thsice: rename run-time parameters:  o pkg/thsice: rename run-time parameters:
317     himin       -> hIceMin     himin       -> hIceMin
318     himin0      -> hThinIce     himin0      -> hThinIce
# Line 20  o in FFIELDS.h: Line 329  o in FFIELDS.h:
329       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
330  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
331  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
332      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
333        are no longer updating the vertical diffusivity array
334        (passed as argument) but are (re-) setting those arrays.
335  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
336    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
337      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 40  o pkg/seaice: fix bug in evp solver, whi Line 351  o pkg/seaice: fix bug in evp solver, whi
351      of evp, complete rewrite for lsr case (latter is does not yet work      of evp, complete rewrite for lsr case (latter is does not yet work
352      in all cases)      in all cases)
353  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
354      - add myThid to all kpp routines (long overdue)
355    
356  checkpoint59  checkpoint59
357  o pkg/exf:  o pkg/exf:

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