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revision 1.1454 by jmc, Tue Jun 14 16:52:22 2011 UTC revision 1.1490 by jmc, Sun Aug 7 19:53:51 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 adding package bbl (Bottom Boundary Layer)
8      description in MITgcm/pkg/bbl/bbl_description.tex
9      example/test experiment in MITgcm_contrib/bbl
10    o adjoint verifications
11      - changed 5 experiments to multi-tiles
12        * global_ocean.90x40x15
13        * obcs_ctrl
14        * offline_exf_seaice
15        * tutorial_dic_adjoffline
16        * tutorial_tracer_adjsens
17        changed reference output for those that crossed tile boundaries
18        (changed choices of gradient check positions)
19      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
20      - temporary bug fix in grdchk_loc.F for obcs
21    o genmake2 & testreport
22      - add target "obj" (just for OBJFILES files) to Makefile;
23      - add option to specify FEXTRAFLAGS on command line.
24    o pkg/mypackage:
25      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
26    
27    checkpoint63a (2011/08/02)
28    o pkg/diagnostics (velocity potential):
29      - fix velocity-potential calculation when using OBCS: balance net inflow
30        at each level (new S/R OBCS_DIAG_BALANCE).
31      - fix some of the problems with OBCS in stream-function calculation.
32    o pkg/exf/exf_readparms.F
33      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
34        EXF_NML_OBCS) more consistent, so that you need not have these lists
35        in data.exf when they are not used.
36    o optim/optim_readdata.F:
37      - add some output about obcs variables that might help debugging
38      - add a check about nvarlength
39    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
40    o pkg/diagnostics (velocity potential):
41      - fix mask for OBCS (still problems in stream-function with OBCS);
42      - add specific parameter (default = main code CG2D params) for solver;
43      - in case of poor convergence, use solution corresponding to lowest residual.
44    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
45      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
46      and should be avoided where possible.
47    o model/src (rStar):
48      - include r* effect on reference-state (PhiRef) in totPhiHyd
49        (so that it's really the potential anomaly at the cell center);
50        affect solution only if z* with full pressure in EOS.
51      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
52        update output (because of z* in totPhiHyd and viscA4 changes);
53      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
54        @ constant r) until interpolation at constant r is implemented.
55    o pkg/diagnostics
56      - fix RCENTER diagnostics in case cell center is not at interface middle
57    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
58      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
59      that THETA and SALT are "conservative temperature" and "absolute
60      salinity"
61    o pkg/ctrl
62      - fix computation of endrec in s/r ctrl_init_rec
63      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
64    o pkg/seaice/seaice_growth.F
65      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
66        remove then obsolete STORE directives
67      - fix STORE directives for tice and tices, so that only the
68        appropriate part of the fields are stored (and not the entire
69        field); update global_ocean.cs32x15.seaice AD output.
70      - cosmetic changes: adjust CPP flags and indentation for better
71        legibilty
72    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
73      Chris Wilson)
74    o pkg/gmredi:
75       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
76       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
77    
78    checkpoint63  (2011/07/11)
79    o pkg/exch2:
80     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
81     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
82       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
83       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
84    o pkg/diagnostics:
85     - deal with pairs of post-processed diags which are computed together; in
86       particular, re-order list of diags within 1 file to save 2nd computation.
87     - add S/R to compute velocity stream-function (called after velocity-potential
88       calculation) from divergence free transport -> new diagnostics "PsiVEL".
89     - add parameter to select grid-point location where PsiVEL == 0.
90    o eesupp/src:
91       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
92       (specific S/R needed with exch2 topology - for now, just print an error msg)
93    o pkg/shelfice
94     - Implement friction velocity-dependent transfer coefficients following
95       Holland and Jenkins, JPO, 1999
96       Original code by M. Losch with small modifs.
97       Enable with CPP option SHI_ALLOW_GAMMAFRICT
98       and runtime flag SHELFICEuseGammaFrict
99    o verification lab_sea & global_ocean.cs32x15:
100     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
101       does not miss some dependencies (but is slower) and also works with many files
102       (default makedepend limitation for AD built).
103     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
104    o pkg/diagnostics:
105     - add run-time parameter "useMissingValue" (def=False) to fill land-point
106        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
107       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
108     - Extend the use of "missing_value" setting from data.diagnostics for the case
109       of counter-diagnostics (where fraction-weight is zero). This applies both to
110       MNC and MDS output files.
111    o pkg/seaice/seaice_growth.F:
112      - add 'a priori' cap of latent heat flux based on actual mass considerations
113        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
114        non-legacy seaice_solve4temp.
115      - add diagnostic of the residual sublimation freshwater flux (the freshwater
116        flux taken from the ocean if the total actual latent heat fluxes exceed
117        the maximum)
118      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
119       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
120      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
121       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
122      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
123      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
124    o verification 1D_ocean_ice_column:
125       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
126       update results
127    o pkg/diagnostics:
128     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
129       which are not filled-up but computed from other diags ; In this case, the mate
130       diag points to the primary (filled-up) diag to used for post processing.
131     - Update Velocity-potential computation using post-processed diag framework.
132     ==> Change the ordering of fields and time-periods in MDS output file
133       when using periodic averaging: now writes one time record with the full set
134       of fields for this time period, then the next time reccord (it used to be
135       one field with the full set of time records then the next field).
136         Note: this is now similar to NetCDF (MNC) output file. <==
137    
138    checkpoint62z (2011/06/21)
139    o adjoint monitor:
140     - Add adjoint monitor output for packages exf, seaice
141       and update relevant testreport output
142    o pkg/seaice:
143     - re-order diags inits so that they appear in order in available_diagnostics.log
144     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
145       area/heff/hsnow preceeding thermodynamic growth/melt.
146     - modified diag: SIdA; output actual effect, as the description states.
147     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
148     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
149       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
150        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
151     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
152     - added diagnostics for seaice generic tracers (SItr*).
153     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
154     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
155     I. Fenty: 18-Jun-2011:
156     Minor changes to seaice package:
157     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
158        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
159       - Differentiated "regularization variables" from "floor variables"
160        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
161        * hiceMin became SEAICE_hice_reg (old hiceMin)
162          (with _reg meaning regularization variable)
163       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
164        so as to ensure energy conservation when going between phases
165      - A22 was not used anywhere
166     2) Changed regularization procedure for heffActual and hsnowActual to ensure
167        well-boundedness and smooth adjoint in seaice_growth.F
168     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
169        because the old regularization always set heffActual >= 0.05 cm
170     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
171        on AREA when HEFF > 0.
172      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
173        requiring that DISABLE_AREA_FLOOR *not* be defined
174     Affected verifications:
175      - 1D_ocean_ice_column (output.txt output_adm.txt)
176      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
177  o pkg/diagnostics:  o pkg/diagnostics:
178    - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).    - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
179    - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument    - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
# Line 11  o pkg/diagnostics: Line 181  o pkg/diagnostics:
181    - add pieces of code to compute velocity potential at each level (new diagnostics    - add pieces of code to compute velocity potential at each level (new diagnostics
182      PhiVEL, works only when UVELMASS & VVELMASS are also turned on);      PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
183      for now, using same params as CG2D (target-resisual, max Nb of iter ...).      for now, using same params as CG2D (target-resisual, max Nb of iter ...).
184      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
185        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
186        and in diagnostics_fract_fill.F (do not need a valid pointer for the
187        diagnostics counter-mate); check that definition of counter-diagnostic
188        includes a valid counter-mate (in diagnostics_set_levels.F).
189  o model/src (rStar):  o model/src (rStar):
190    - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);    - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
191      affect solution only if z* with full pressure in EOS;      affect solution only if z* with full pressure in EOS;
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