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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1465 by gforget, Mon Jun 27 16:00:08 2011 UTC
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5      ==============================      ==============================
6    
7  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
8    - use Ian Fenty's capping formulas for actual ice    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
9       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
10      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
11       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
12      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
13      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
14    o verification 1D_ocean_ice_column:
15       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
16       update results
17    o pkg/diagnostics:
18     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
19       which are not filled-up but computed from other diags ; In this case, the mate
20       diag points to the primary (filled-up) diag to used for post processing.
21     - Update Velocity-potential computation using post-processed diag framework.
22     ==> Change the ordering of fields and time-periods in MDS output file
23       when using periodic averaging: now writes one time record with the full set
24       of fields for this time period, then the next time reccord (it used to be
25       one field with the full set of time records then the next field).
26         Note: this is now similar to NetCDF (MNC) output file. <==
27     - Extend the use of "missing_value" setting from data.diagnostics for the case
28       of counter-diagnostics (where fraction-weight is zero). This applies both to
29       MNC and MDS output files.
30    
31    checkpoint62z (2011/06/21)
32    o adjoint monitor:
33     - Add adjoint monitor output for packages exf, seaice
34       and update relevant testreport output
35    o pkg/seaice:
36     - re-order diags inits so that they appear in order in available_diagnostics.log
37     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
38       area/heff/hsnow preceeding thermodynamic growth/melt.
39     - modified diag: SIdA; output actual effect, as the description states.
40     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
41     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
42       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
43        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
44     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
45     - added diagnostics for seaice generic tracers (SItr*).
46     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
47     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
48     I. Fenty: 18-Jun-2011:
49     Minor changes to seaice package:
50     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
51        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
52       - Differentiated "regularization variables" from "floor variables"
53        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
54        * hiceMin became SEAICE_hice_reg (old hiceMin)
55          (with _reg meaning regularization variable)
56       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
57        so as to ensure energy conservation when going between phases
58      - A22 was not used anywhere
59     2) Changed regularization procedure for heffActual and hsnowActual to ensure
60        well-boundedness and smooth adjoint in seaice_growth.F
61     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
62        because the old regularization always set heffActual >= 0.05 cm
63     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
64        on AREA when HEFF > 0.
65      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
66        requiring that DISABLE_AREA_FLOOR *not* be defined
67     Affected verifications:
68      - 1D_ocean_ice_column (output.txt output_adm.txt)
69      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
70    o pkg/diagnostics:
71      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
72      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
73        (was _RL, now integer) with option = 0 to retrieve all levels.
74      - add pieces of code to compute velocity potential at each level (new diagnostics
75        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
76        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
77      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
78        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
79        and in diagnostics_fract_fill.F (do not need a valid pointer for the
80        diagnostics counter-mate); check that definition of counter-diagnostic
81        includes a valid counter-mate (in diagnostics_set_levels.F).
82    o model/src (rStar):
83      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
84        affect solution only if z* with full pressure in EOS;
85        update output of test-exp global_ocean.90x40x15.
86    o pkg/seaice:
87      - introduce siEps=1e-5 parameter
88      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
89      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
90      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
91        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
92        as well as ice cover age and ridging index (attached to AREA).
93        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
94        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
95        Up to SItrMaxNum=3 tracers can be used simultaneously.
96    o pkg/salt_plume:
97      -introduce SPsalFRAC run time parameter that sets the fraction of the
98       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
99       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
100    o model debug options:
101      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
102        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
103      - Refine debug-msg printing selection (3 new levels):
104        debugMode  : controls printing of debug messages (sequence of S/R calls).
105        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
106         debLevZero =  0 ; /* level of disabled aux. msg printing */
107         debLevA =  1 ; /* level of minimum  aux. msg printing */
108         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
109         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
110         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
111         debLevE =  5 ; /* level of extensive debug printing */
112        New debugLevel default: with default debugMode value (=F),
113          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
114          and if debugMode=T, default debugLevel = 4 (debLevD).
115        Relation with previous settings:
116         debLevB (=2) corresponds to former debLevA (=1)
117         debLevD (=4) corresponds to former debLevB (=2)
118        Note:
119         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
120         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
121            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
122      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
123        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
124    o pkg/obcs:
125      - change OBCSfixTopo default from True to False (should not change the results);
126        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
127    o pkg/thsice:
128      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
129        2nd layer seaice sublimation (unlikely to happen)
130      - use Interior mask for OBCS in thsice_advection.F (similar to what is
131        done in gad_advection & seaice_advection).
132    o adjoint:
133      bug fix spotted by Gael Forget:
134      seaice_advection and thsice_advection still had
135      legacy CPP options to avoid CS corner updates for adjoint
136    o pkg/seaice:
137      => Change some of the defaults (2011/05/29):
138         - change SEAICEuseFluxForm default (from False to True)
139         - change DIFF1 default (from 0.004 m/s to 0. m/s)
140         And print warnings if DIFF1 is not set in data.seaice and centered
141          avection scheme is used without any diffusion.
142      also:
143      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
144      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
145      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
146        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
147        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
148      update results of test exp.:
149         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
150             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
151             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
152         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
153         seaice_obcs: output (SEAICEuseFluxForm=T)
154      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
155          for standard fwd & AD lab_sea tests (to keep the same output).
156    o pkg/seaice/seaice_growth.F:
157      - use Ian Fenty's capping formulas for actual ice
158    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
159    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
160    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
161    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
162  o pkg/seaice:  o pkg/seaice:
163    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
164    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
165    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
166    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
167    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
168    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
169    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
170    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
171    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.  
172  o pkg/seaice:  o pkg/seaice:
173    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
174    - 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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