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revision 1.1435 by jmc, Wed May 18 02:21:49 2011 UTC revision 1.1481 by mlosch, Mon Jul 25 08:26:46 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 optim/optim_readdata.F:
8      - add some output about obcs variables that might help debugging
9    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
10    o pkg/diagnostics (velocity potential):
11      - fix mask for OBCS (still problems in stream-function with OBCS);
12      - add specific parameter (default = main code CG2D params) for solver;
13      - in case of poor convergence, use solution corresponding to lowest residual.
14    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
15      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
16      and should be avoided where possible.
17    o model/src (rStar):
18      - include r* effect on reference-state (PhiRef) in totPhiHyd
19        (so that it's really the potential anomaly at the cell center);
20        affect solution only if z* with full pressure in EOS.
21      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
22        update output (because of z* in totPhiHyd and viscA4 changes);
23      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
24        @ constant r) until interpolation at constant r is implemented.
25    o pkg/diagnostics
26      - fix RCENTER diagnostics in case cell center is not at interface middle
27    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
28      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
29      that THETA and SALT are "conservative temperature" and "absolute
30      salinity"
31    o pkg/ctrl
32      - fix computation of endrec in s/r ctrl_init_rec
33      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
34    o pkg/seaice/seaice_growth.F
35      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
36        remove then obsolete STORE directives
37      - fix STORE directives for tice and tices, so that only the
38        appropriate part of the fields are stored (and not the entire
39        field); update global_ocean.cs32x15.seaice AD output.
40      - cosmetic changes: adjust CPP flags and indentation for better
41        legibilty
42    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
43      Chris Wilson)
44    o pkg/gmredi:
45       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
46       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
47    
48    checkpoint63 (2011/07/11)
49    o pkg/exch2:
50     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
51     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
52       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
53       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
54    o pkg/diagnostics:
55     - deal with pairs of post-processed diags which are computed together; in
56       particular, re-order list of diags within 1 file to save 2nd computation.
57     - add S/R to compute velocity stream-function (called after velocity-potential
58       calculation) from divergence free transport -> new diagnostics "PsiVEL".
59     - add parameter to select grid-point location where PsiVEL == 0.
60    o eesupp/src:
61       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
62       (specific S/R needed with exch2 topology - for now, just print an error msg)
63    o pkg/shelfice
64     - Implement friction velocity-dependent transfer coefficients following
65       Holland and Jenkins, JPO, 1999
66       Original code by M. Losch with small modifs.
67       Enable with CPP option SHI_ALLOW_GAMMAFRICT
68       and runtime flag SHELFICEuseGammaFrict
69    o verification lab_sea & global_ocean.cs32x15:
70     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
71       does not miss some dependencies (but is slower) and also works with many files
72       (default makedepend limitation for AD built).
73     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
74    o pkg/diagnostics:
75     - add run-time parameter "useMissingValue" (def=False) to fill land-point
76        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
77       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
78     - Extend the use of "missing_value" setting from data.diagnostics for the case
79       of counter-diagnostics (where fraction-weight is zero). This applies both to
80       MNC and MDS output files.
81    o pkg/seaice/seaice_growth.F:
82      - add 'a priori' cap of latent heat flux based on actual mass considerations
83        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
84        non-legacy seaice_solve4temp.
85      - add diagnostic of the residual sublimation freshwater flux (the freshwater
86        flux taken from the ocean if the total actual latent heat fluxes exceed
87        the maximum)
88      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
89       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
90      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
91       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
92      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
93      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
94    o verification 1D_ocean_ice_column:
95       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
96       update results
97    o pkg/diagnostics:
98     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
99       which are not filled-up but computed from other diags ; In this case, the mate
100       diag points to the primary (filled-up) diag to used for post processing.
101     - Update Velocity-potential computation using post-processed diag framework.
102     ==> Change the ordering of fields and time-periods in MDS output file
103       when using periodic averaging: now writes one time record with the full set
104       of fields for this time period, then the next time reccord (it used to be
105       one field with the full set of time records then the next field).
106         Note: this is now similar to NetCDF (MNC) output file. <==
107    
108    checkpoint62z (2011/06/21)
109    o adjoint monitor:
110     - Add adjoint monitor output for packages exf, seaice
111       and update relevant testreport output
112    o pkg/seaice:
113     - re-order diags inits so that they appear in order in available_diagnostics.log
114     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
115       area/heff/hsnow preceeding thermodynamic growth/melt.
116     - modified diag: SIdA; output actual effect, as the description states.
117     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
118     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
119       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
120        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
121     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
122     - added diagnostics for seaice generic tracers (SItr*).
123     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
124     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
125     I. Fenty: 18-Jun-2011:
126     Minor changes to seaice package:
127     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
128        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
129       - Differentiated "regularization variables" from "floor variables"
130        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
131        * hiceMin became SEAICE_hice_reg (old hiceMin)
132          (with _reg meaning regularization variable)
133       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
134        so as to ensure energy conservation when going between phases
135      - A22 was not used anywhere
136     2) Changed regularization procedure for heffActual and hsnowActual to ensure
137        well-boundedness and smooth adjoint in seaice_growth.F
138     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
139        because the old regularization always set heffActual >= 0.05 cm
140     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
141        on AREA when HEFF > 0.
142      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
143        requiring that DISABLE_AREA_FLOOR *not* be defined
144     Affected verifications:
145      - 1D_ocean_ice_column (output.txt output_adm.txt)
146      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
147    o pkg/diagnostics:
148      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
149      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
150        (was _RL, now integer) with option = 0 to retrieve all levels.
151      - add pieces of code to compute velocity potential at each level (new diagnostics
152        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
153        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
154      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
155        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
156        and in diagnostics_fract_fill.F (do not need a valid pointer for the
157        diagnostics counter-mate); check that definition of counter-diagnostic
158        includes a valid counter-mate (in diagnostics_set_levels.F).
159    o model/src (rStar):
160      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
161        affect solution only if z* with full pressure in EOS;
162        update output of test-exp global_ocean.90x40x15.
163    o pkg/seaice:
164      - introduce siEps=1e-5 parameter
165      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
166      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
167      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
168        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
169        as well as ice cover age and ridging index (attached to AREA).
170        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
171        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
172        Up to SItrMaxNum=3 tracers can be used simultaneously.
173    o pkg/salt_plume:
174      -introduce SPsalFRAC run time parameter that sets the fraction of the
175       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
176       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
177    o model debug options:
178      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
179        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
180      - Refine debug-msg printing selection (3 new levels):
181        debugMode  : controls printing of debug messages (sequence of S/R calls).
182        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
183         debLevZero =  0 ; /* level of disabled aux. msg printing */
184         debLevA =  1 ; /* level of minimum  aux. msg printing */
185         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
186         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
187         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
188         debLevE =  5 ; /* level of extensive debug printing */
189        New debugLevel default: with default debugMode value (=F),
190          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
191          and if debugMode=T, default debugLevel = 4 (debLevD).
192        Relation with previous settings:
193         debLevB (=2) corresponds to former debLevA (=1)
194         debLevD (=4) corresponds to former debLevB (=2)
195        Note:
196         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
197         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
198            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
199      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
200        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
201    o pkg/obcs:
202      - change OBCSfixTopo default from True to False (should not change the results);
203        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
204    o pkg/thsice:
205      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
206        2nd layer seaice sublimation (unlikely to happen)
207      - use Interior mask for OBCS in thsice_advection.F (similar to what is
208        done in gad_advection & seaice_advection).
209    o adjoint:
210      bug fix spotted by Gael Forget:
211      seaice_advection and thsice_advection still had
212      legacy CPP options to avoid CS corner updates for adjoint
213    o pkg/seaice:
214      => Change some of the defaults (2011/05/29):
215         - change SEAICEuseFluxForm default (from False to True)
216         - change DIFF1 default (from 0.004 m/s to 0. m/s)
217         And print warnings if DIFF1 is not set in data.seaice and centered
218          avection scheme is used without any diffusion.
219      also:
220      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
221      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
222      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
223        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
224        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
225      update results of test exp.:
226         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
227             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
228             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
229         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
230         seaice_obcs: output (SEAICEuseFluxForm=T)
231      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
232          for standard fwd & AD lab_sea tests (to keep the same output).
233    o pkg/seaice/seaice_growth.F:
234      - use Ian Fenty's capping formulas for actual ice
235      thickness thoughout EVOLUTION branch.
236      - put treatment pathological case #2) in CPP brackets
237      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
238      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
239    o pkg/seaice:
240      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
241      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
242      also pass fac as a param, which can be 1. (to update the tendency
243      field) or the time step (to update the field itself).
244      - seaice_advdiff.F: for multidim, call seaice_diffusion with
245      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
246      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
247      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
248      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
249    o pkg/seaice:
250      diffusion with centered advection scheme (diffus.F & advect.F):
251      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
252        to just compute the laplacian of input-field.
253      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
254      - fix flux-form version in diffus.F to conserve tracer.
255      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
256       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
257    
258    checkpoint62y (2011/05/26)
259    o pkg/seaice:
260     - seaice_growth.F : in EVOLUTION branch, always include
261       a_QSWbyATM_cover in qnet (as it should be).
262     - verification/global_ocean.cs32x15 : update results accordingly
263       (output.seaice.txt output_adm.seaice.txt).
264    o pkg/seaice + obcs:
265     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
266       equivalent of assuming no tracer gradient outside the OB region.
267       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
268     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
269       after changes above);
270     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
271       only at OB location (instead of over a band of OLx width).
272    o pkg/seaice:
273     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
274       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
275    o pkg/obcs:
276      - split header file "OBCS.h" into 4 separated files:
277        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
278       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
279         (contain no conditional statement which depends on OBCS options).
280      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
281        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
282    o ctrl, cost, grdchk & autodiff pkgs:
283      - make options file more standard (like other {PKG}_OPTIONS.h file but
284        with AD_CONFIG.h); clean-up some of the included header files.
285    o pkg/obcs:
286      - do not mask tracer when applying OB (tracer == 0 could generate problems)
287      - apply tracer OB values to tracer field only at OB location (instead of
288        over a band of OLx width)
289      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
290      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
291        obcs_apply_tloc.F & obcs_apply_sloc.F
292    o obcs in model/src:
293      - call OBCS_APPLY_W only if NonHydrostatic.
294      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
295      - reset dEtaHdt and wVel to zero outside OB interior region ;
296      - leave tracer unchanged outside OB interior region: This has no effect
297        on the solution but just to prevent unrealistic tracer value outside OB.
298      - zero out velocity outside OB interior region: This has no effect on
299        the solution but just to prevent unrealistic velocity outside OB.
300    o obcs and non-lin free-surf:
301       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
302       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
303       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
304       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
305       update results of test-exp. exp4(nlfs).
306    o exp4 (nlfs) test-exp:
307       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
308       with NonLin-FreeSurf); update output.nlfs.txt
309  o obcs and 2d/3d solver norm:  o obcs and 2d/3d solver norm:
310     use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB     use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
311     and outside OB interior region (will allow to place OB further inside the     and outside OB interior region (will allow to place OB further inside the
312     domain). Depending on the domain, can affects cg2d-Norm (previous     domain). Depending on the domain, can affects cg2d-Norm (previous
313     cancelation outside OB was only partial), e.g. in exp4 & obcs_ctrl,     cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
314     and cg3d-Norm (previous Norm was computed before canceling OB terms),     and cg3d-Norm (previous Norm was computed before canceling OB terms),
315     e.g. in tutorial_plume_on_slope.     e.g. in tutorial_plume_on_slope.
316    - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.    - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
# Line 20  o pkg/shelfice/shelfice_init_fixed.F Line 322  o pkg/shelfice/shelfice_init_fixed.F
322    fix CPP-flag combinations    fix CPP-flag combinations
323  o pkg/seaice: Merge iceage code of Pierre Rampal  o pkg/seaice: Merge iceage code of Pierre Rampal
324    * update/change/correct ice age calculations    * update/change/correct ice age calculations
325    * add age updates for pathological cases    * add age updates for pathological cases
326    Probably needs more testing...    Probably needs more testing...
327    
328  checkpoint62x (2011/05/13)  checkpoint62x (2011/05/13)

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