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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1470 by jmc, Fri Jul 1 19:03:34 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/diagnostics:
8     - deal with pairs of post-processed diags which are computed together; in
9       particular, re-order list of diags within 1 file to save 2nd computation.
10     - add S/R to compute velocity stream-function (called after velocity-potential
11       calculation) from divergence free transport -> new diagnostics "PsiVEL".
12    o eesupp/src:
13       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
14       (specific S/R needed with exch2 topology - for now, just print an error msg)
15    o pkg/shelfice
16     - Implement friction velocity-dependent transfer coefficients following
17       Holland and Jenkins, JPO, 1999
18       Original code by M. Losch with small modifs.
19       Enable with CPP option SHI_ALLOW_GAMMAFRICT
20       and runtime flag SHELFICEuseGammaFrict
21    o verification lab_sea & global_ocean.cs32x15:
22     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
23       does not miss some dependencies (but is slower) and also works with many files
24       (default makedepend limitation for AD built).
25     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
26    o pkg/diagnostics:
27     - add run-time parameter "useMissingValue" (def=False) to fill land-point
28        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
29       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
30     - Extend the use of "missing_value" setting from data.diagnostics for the case
31       of counter-diagnostics (where fraction-weight is zero). This applies both to
32       MNC and MDS output files.
33  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
34    - use Ian Fenty's capping formulas for actual ice    - add 'a priori' cap of latent heat flux based on actual mass considerations
35        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
36        non-legacy seaice_solve4temp.
37      - add diagnostic of the residual sublimation freshwater flux (the freshwater
38        flux taken from the ocean if the total actual latent heat fluxes exceed
39        the maximum)
40      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
41       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
42      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
43       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
44      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
45      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
46    o verification 1D_ocean_ice_column:
47       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
48       update results
49    o pkg/diagnostics:
50     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
51       which are not filled-up but computed from other diags ; In this case, the mate
52       diag points to the primary (filled-up) diag to used for post processing.
53     - Update Velocity-potential computation using post-processed diag framework.
54     ==> Change the ordering of fields and time-periods in MDS output file
55       when using periodic averaging: now writes one time record with the full set
56       of fields for this time period, then the next time reccord (it used to be
57       one field with the full set of time records then the next field).
58         Note: this is now similar to NetCDF (MNC) output file. <==
59    
60    checkpoint62z (2011/06/21)
61    o adjoint monitor:
62     - Add adjoint monitor output for packages exf, seaice
63       and update relevant testreport output
64    o pkg/seaice:
65     - re-order diags inits so that they appear in order in available_diagnostics.log
66     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
67       area/heff/hsnow preceeding thermodynamic growth/melt.
68     - modified diag: SIdA; output actual effect, as the description states.
69     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
70     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
71       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
72        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
73     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
74     - added diagnostics for seaice generic tracers (SItr*).
75     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
76     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
77     I. Fenty: 18-Jun-2011:
78     Minor changes to seaice package:
79     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
80        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
81       - Differentiated "regularization variables" from "floor variables"
82        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
83        * hiceMin became SEAICE_hice_reg (old hiceMin)
84          (with _reg meaning regularization variable)
85       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
86        so as to ensure energy conservation when going between phases
87      - A22 was not used anywhere
88     2) Changed regularization procedure for heffActual and hsnowActual to ensure
89        well-boundedness and smooth adjoint in seaice_growth.F
90     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
91        because the old regularization always set heffActual >= 0.05 cm
92     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
93        on AREA when HEFF > 0.
94      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
95        requiring that DISABLE_AREA_FLOOR *not* be defined
96     Affected verifications:
97      - 1D_ocean_ice_column (output.txt output_adm.txt)
98      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
99    o pkg/diagnostics:
100      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
101      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
102        (was _RL, now integer) with option = 0 to retrieve all levels.
103      - add pieces of code to compute velocity potential at each level (new diagnostics
104        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
105        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
106      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
107        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
108        and in diagnostics_fract_fill.F (do not need a valid pointer for the
109        diagnostics counter-mate); check that definition of counter-diagnostic
110        includes a valid counter-mate (in diagnostics_set_levels.F).
111    o model/src (rStar):
112      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
113        affect solution only if z* with full pressure in EOS;
114        update output of test-exp global_ocean.90x40x15.
115    o pkg/seaice:
116      - introduce siEps=1e-5 parameter
117      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
118      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
119      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
120        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
121        as well as ice cover age and ridging index (attached to AREA).
122        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
123        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
124        Up to SItrMaxNum=3 tracers can be used simultaneously.
125    o pkg/salt_plume:
126      -introduce SPsalFRAC run time parameter that sets the fraction of the
127       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
128       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
129    o model debug options:
130      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
131        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
132      - Refine debug-msg printing selection (3 new levels):
133        debugMode  : controls printing of debug messages (sequence of S/R calls).
134        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
135         debLevZero =  0 ; /* level of disabled aux. msg printing */
136         debLevA =  1 ; /* level of minimum  aux. msg printing */
137         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
138         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
139         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
140         debLevE =  5 ; /* level of extensive debug printing */
141        New debugLevel default: with default debugMode value (=F),
142          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
143          and if debugMode=T, default debugLevel = 4 (debLevD).
144        Relation with previous settings:
145         debLevB (=2) corresponds to former debLevA (=1)
146         debLevD (=4) corresponds to former debLevB (=2)
147        Note:
148         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
149         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
150            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
151      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
152        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
153    o pkg/obcs:
154      - change OBCSfixTopo default from True to False (should not change the results);
155        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
156    o pkg/thsice:
157      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
158        2nd layer seaice sublimation (unlikely to happen)
159      - use Interior mask for OBCS in thsice_advection.F (similar to what is
160        done in gad_advection & seaice_advection).
161    o adjoint:
162      bug fix spotted by Gael Forget:
163      seaice_advection and thsice_advection still had
164      legacy CPP options to avoid CS corner updates for adjoint
165    o pkg/seaice:
166      => Change some of the defaults (2011/05/29):
167         - change SEAICEuseFluxForm default (from False to True)
168         - change DIFF1 default (from 0.004 m/s to 0. m/s)
169         And print warnings if DIFF1 is not set in data.seaice and centered
170          avection scheme is used without any diffusion.
171      also:
172      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
173      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
174      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
175        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
176        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
177      update results of test exp.:
178         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
179             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
180             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
181         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
182         seaice_obcs: output (SEAICEuseFluxForm=T)
183      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
184          for standard fwd & AD lab_sea tests (to keep the same output).
185    o pkg/seaice/seaice_growth.F:
186      - use Ian Fenty's capping formulas for actual ice
187    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
188    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
189    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
190    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
191  o pkg/seaice:  o pkg/seaice:
192    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
193    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
194    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
195    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
196    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
197    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
198    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
199    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
200    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.  
201  o pkg/seaice:  o pkg/seaice:
202    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
203    - 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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