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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1478 by mlosch, Thu Jul 21 13:45:55 2011 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: small changes that permit vectorizable
8      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
9      and should be avoided where possible.
10    o model/src (rStar):
11      - include r* effect on reference-state (PhiRef) in totPhiHyd
12        (so that it's really the potential anomaly at the cell center);
13        affect solution only if z* with full pressure in EOS.
14      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
15        update output (because of z* in totPhiHyd and viscA4 changes);
16      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
17        @ constant r) until interpolation at constant r is implemented.
18    o pkg/diagnostics
19      - fix RCENTER diagnostics in case cell center is not at interface middle
20    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
21      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
22      that THETA and SALT are "conservative temperature" and "absolute
23      salinity"
24    o pkg/ctrl
25      - fix computation of endrec in s/r ctrl_init_rec
26      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
27    o pkg/seaice/seaice_growth.F
28      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
29        remove then obsolete STORE directives
30      - fix STORE directives for tice and tices, so that only the
31        appropriate part of the fields are stored (and not the entire
32        field); update global_ocean.cs32x15.seaice AD output.
33      - cosmetic changes: adjust CPP flags and indentation for better
34        legibilty
35    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
36      Chris Wilson)
37    o pkg/gmredi:
38       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
39       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
40    
41    checkpoint63 (2011/07/11)
42    o pkg/exch2:
43     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
44     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
45       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
46       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
47    o pkg/diagnostics:
48     - deal with pairs of post-processed diags which are computed together; in
49       particular, re-order list of diags within 1 file to save 2nd computation.
50     - add S/R to compute velocity stream-function (called after velocity-potential
51       calculation) from divergence free transport -> new diagnostics "PsiVEL".
52     - add parameter to select grid-point location where PsiVEL == 0.
53    o eesupp/src:
54       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
55       (specific S/R needed with exch2 topology - for now, just print an error msg)
56    o pkg/shelfice
57     - Implement friction velocity-dependent transfer coefficients following
58       Holland and Jenkins, JPO, 1999
59       Original code by M. Losch with small modifs.
60       Enable with CPP option SHI_ALLOW_GAMMAFRICT
61       and runtime flag SHELFICEuseGammaFrict
62    o verification lab_sea & global_ocean.cs32x15:
63     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
64       does not miss some dependencies (but is slower) and also works with many files
65       (default makedepend limitation for AD built).
66     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
67    o pkg/diagnostics:
68     - add run-time parameter "useMissingValue" (def=False) to fill land-point
69        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
70       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
71     - Extend the use of "missing_value" setting from data.diagnostics for the case
72       of counter-diagnostics (where fraction-weight is zero). This applies both to
73       MNC and MDS output files.
74    o pkg/seaice/seaice_growth.F:
75      - add 'a priori' cap of latent heat flux based on actual mass considerations
76        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
77        non-legacy seaice_solve4temp.
78      - add diagnostic of the residual sublimation freshwater flux (the freshwater
79        flux taken from the ocean if the total actual latent heat fluxes exceed
80        the maximum)
81      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
82       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
83      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
84       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
85      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
86      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
87    o verification 1D_ocean_ice_column:
88       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
89       update results
90    o pkg/diagnostics:
91     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
92       which are not filled-up but computed from other diags ; In this case, the mate
93       diag points to the primary (filled-up) diag to used for post processing.
94     - Update Velocity-potential computation using post-processed diag framework.
95     ==> Change the ordering of fields and time-periods in MDS output file
96       when using periodic averaging: now writes one time record with the full set
97       of fields for this time period, then the next time reccord (it used to be
98       one field with the full set of time records then the next field).
99         Note: this is now similar to NetCDF (MNC) output file. <==
100    
101    checkpoint62z (2011/06/21)
102    o adjoint monitor:
103     - Add adjoint monitor output for packages exf, seaice
104       and update relevant testreport output
105    o pkg/seaice:
106     - re-order diags inits so that they appear in order in available_diagnostics.log
107     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
108       area/heff/hsnow preceeding thermodynamic growth/melt.
109     - modified diag: SIdA; output actual effect, as the description states.
110     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
111     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
112       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
113        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
114     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
115     - added diagnostics for seaice generic tracers (SItr*).
116     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
117     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
118     I. Fenty: 18-Jun-2011:
119     Minor changes to seaice package:
120     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
121        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
122       - Differentiated "regularization variables" from "floor variables"
123        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
124        * hiceMin became SEAICE_hice_reg (old hiceMin)
125          (with _reg meaning regularization variable)
126       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
127        so as to ensure energy conservation when going between phases
128      - A22 was not used anywhere
129     2) Changed regularization procedure for heffActual and hsnowActual to ensure
130        well-boundedness and smooth adjoint in seaice_growth.F
131     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
132        because the old regularization always set heffActual >= 0.05 cm
133     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
134        on AREA when HEFF > 0.
135      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
136        requiring that DISABLE_AREA_FLOOR *not* be defined
137     Affected verifications:
138      - 1D_ocean_ice_column (output.txt output_adm.txt)
139      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
140    o pkg/diagnostics:
141      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
142      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
143        (was _RL, now integer) with option = 0 to retrieve all levels.
144      - add pieces of code to compute velocity potential at each level (new diagnostics
145        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
146        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
147      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
148        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
149        and in diagnostics_fract_fill.F (do not need a valid pointer for the
150        diagnostics counter-mate); check that definition of counter-diagnostic
151        includes a valid counter-mate (in diagnostics_set_levels.F).
152    o model/src (rStar):
153      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
154        affect solution only if z* with full pressure in EOS;
155        update output of test-exp global_ocean.90x40x15.
156    o pkg/seaice:
157      - introduce siEps=1e-5 parameter
158      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
159      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
160      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
161        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
162        as well as ice cover age and ridging index (attached to AREA).
163        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
164        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
165        Up to SItrMaxNum=3 tracers can be used simultaneously.
166    o pkg/salt_plume:
167      -introduce SPsalFRAC run time parameter that sets the fraction of the
168       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
169       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
170    o model debug options:
171      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
172        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
173      - Refine debug-msg printing selection (3 new levels):
174        debugMode  : controls printing of debug messages (sequence of S/R calls).
175        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
176         debLevZero =  0 ; /* level of disabled aux. msg printing */
177         debLevA =  1 ; /* level of minimum  aux. msg printing */
178         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
179         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
180         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
181         debLevE =  5 ; /* level of extensive debug printing */
182        New debugLevel default: with default debugMode value (=F),
183          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
184          and if debugMode=T, default debugLevel = 4 (debLevD).
185        Relation with previous settings:
186         debLevB (=2) corresponds to former debLevA (=1)
187         debLevD (=4) corresponds to former debLevB (=2)
188        Note:
189         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
190         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
191            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
192      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
193        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
194    o pkg/obcs:
195      - change OBCSfixTopo default from True to False (should not change the results);
196        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
197    o pkg/thsice:
198      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
199        2nd layer seaice sublimation (unlikely to happen)
200      - use Interior mask for OBCS in thsice_advection.F (similar to what is
201        done in gad_advection & seaice_advection).
202    o adjoint:
203      bug fix spotted by Gael Forget:
204      seaice_advection and thsice_advection still had
205      legacy CPP options to avoid CS corner updates for adjoint
206    o pkg/seaice:
207      => Change some of the defaults (2011/05/29):
208         - change SEAICEuseFluxForm default (from False to True)
209         - change DIFF1 default (from 0.004 m/s to 0. m/s)
210         And print warnings if DIFF1 is not set in data.seaice and centered
211          avection scheme is used without any diffusion.
212      also:
213      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
214      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
215      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
216        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
217        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
218      update results of test exp.:
219         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
220             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
221             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
222         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
223         seaice_obcs: output (SEAICEuseFluxForm=T)
224      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
225          for standard fwd & AD lab_sea tests (to keep the same output).
226  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
227    - use Ian Fenty's capping formulas for actual ice    - use Ian Fenty's capping formulas for actual ice
228    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
229    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
230    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
231    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
232  o pkg/seaice:  o pkg/seaice:
233    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
234    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
235    also pass fac as a param, which can be 1. (to update the tendency    also pass fac as a param, which can be 1. (to update the tendency
236    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
237    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
238    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
239    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
240    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
241    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
   - note: if any of SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.  
   is specified to be >0, then DIFF1 is set to 0.  
242  o pkg/seaice:  o pkg/seaice:
243    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
244    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
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