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revision 1.1424 by mlosch, Thu May 5 09:24:44 2011 UTC revision 1.1485 by jmc, Tue Aug 2 14:04:56 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/ctrl:  checkpoint63a (2011/08/02)
8    o pkg/diagnostics (velocity potential):
9      - fix velocity-potential calculation when using OBCS: balance net inflow
10        at each level (new S/R OBCS_DIAG_BALANCE).
11      - fix some of the problems with OBCS in stream-function calculation.
12    o pkg/exf/exf_readparms.F
13      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
14        EXF_NML_OBCS) more consistent, so that you need not have these lists
15        in data.exf when they are not used.
16    o optim/optim_readdata.F:
17      - add some output about obcs variables that might help debugging
18      - add a check about nvarlength
19    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
20    o pkg/diagnostics (velocity potential):
21      - fix mask for OBCS (still problems in stream-function with OBCS);
22      - add specific parameter (default = main code CG2D params) for solver;
23      - in case of poor convergence, use solution corresponding to lowest residual.
24    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
25      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
26      and should be avoided where possible.
27    o model/src (rStar):
28      - include r* effect on reference-state (PhiRef) in totPhiHyd
29        (so that it's really the potential anomaly at the cell center);
30        affect solution only if z* with full pressure in EOS.
31      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
32        update output (because of z* in totPhiHyd and viscA4 changes);
33      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
34        @ constant r) until interpolation at constant r is implemented.
35    o pkg/diagnostics
36      - fix RCENTER diagnostics in case cell center is not at interface middle
37    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
38      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
39      that THETA and SALT are "conservative temperature" and "absolute
40      salinity"
41    o pkg/ctrl
42      - fix computation of endrec in s/r ctrl_init_rec
43      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
44    o pkg/seaice/seaice_growth.F
45      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
46        remove then obsolete STORE directives
47      - fix STORE directives for tice and tices, so that only the
48        appropriate part of the fields are stored (and not the entire
49        field); update global_ocean.cs32x15.seaice AD output.
50      - cosmetic changes: adjust CPP flags and indentation for better
51        legibilty
52    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
53      Chris Wilson)
54    o pkg/gmredi:
55       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
56       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
57    
58    checkpoint63  (2011/07/11)
59    o pkg/exch2:
60     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
61     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
62       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
63       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
64    o pkg/diagnostics:
65     - deal with pairs of post-processed diags which are computed together; in
66       particular, re-order list of diags within 1 file to save 2nd computation.
67     - add S/R to compute velocity stream-function (called after velocity-potential
68       calculation) from divergence free transport -> new diagnostics "PsiVEL".
69     - add parameter to select grid-point location where PsiVEL == 0.
70    o eesupp/src:
71       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
72       (specific S/R needed with exch2 topology - for now, just print an error msg)
73    o pkg/shelfice
74     - Implement friction velocity-dependent transfer coefficients following
75       Holland and Jenkins, JPO, 1999
76       Original code by M. Losch with small modifs.
77       Enable with CPP option SHI_ALLOW_GAMMAFRICT
78       and runtime flag SHELFICEuseGammaFrict
79    o verification lab_sea & global_ocean.cs32x15:
80     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
81       does not miss some dependencies (but is slower) and also works with many files
82       (default makedepend limitation for AD built).
83     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
84    o pkg/diagnostics:
85     - add run-time parameter "useMissingValue" (def=False) to fill land-point
86        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
87       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
88     - Extend the use of "missing_value" setting from data.diagnostics for the case
89       of counter-diagnostics (where fraction-weight is zero). This applies both to
90       MNC and MDS output files.
91    o pkg/seaice/seaice_growth.F:
92      - add 'a priori' cap of latent heat flux based on actual mass considerations
93        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
94        non-legacy seaice_solve4temp.
95      - add diagnostic of the residual sublimation freshwater flux (the freshwater
96        flux taken from the ocean if the total actual latent heat fluxes exceed
97        the maximum)
98      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
99       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
100      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
101       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
102      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
103      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
104    o verification 1D_ocean_ice_column:
105       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
106       update results
107    o pkg/diagnostics:
108     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
109       which are not filled-up but computed from other diags ; In this case, the mate
110       diag points to the primary (filled-up) diag to used for post processing.
111     - Update Velocity-potential computation using post-processed diag framework.
112     ==> Change the ordering of fields and time-periods in MDS output file
113       when using periodic averaging: now writes one time record with the full set
114       of fields for this time period, then the next time reccord (it used to be
115       one field with the full set of time records then the next field).
116         Note: this is now similar to NetCDF (MNC) output file. <==
117    
118    checkpoint62z (2011/06/21)
119    o adjoint monitor:
120     - Add adjoint monitor output for packages exf, seaice
121       and update relevant testreport output
122    o pkg/seaice:
123     - re-order diags inits so that they appear in order in available_diagnostics.log
124     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
125       area/heff/hsnow preceeding thermodynamic growth/melt.
126     - modified diag: SIdA; output actual effect, as the description states.
127     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
128     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
129       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
130        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
131     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
132     - added diagnostics for seaice generic tracers (SItr*).
133     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
134     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
135     I. Fenty: 18-Jun-2011:
136     Minor changes to seaice package:
137     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
138        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
139       - Differentiated "regularization variables" from "floor variables"
140        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
141        * hiceMin became SEAICE_hice_reg (old hiceMin)
142          (with _reg meaning regularization variable)
143       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
144        so as to ensure energy conservation when going between phases
145      - A22 was not used anywhere
146     2) Changed regularization procedure for heffActual and hsnowActual to ensure
147        well-boundedness and smooth adjoint in seaice_growth.F
148     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
149        because the old regularization always set heffActual >= 0.05 cm
150     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
151        on AREA when HEFF > 0.
152      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
153        requiring that DISABLE_AREA_FLOOR *not* be defined
154     Affected verifications:
155      - 1D_ocean_ice_column (output.txt output_adm.txt)
156      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
157    o pkg/diagnostics:
158      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
159      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
160        (was _RL, now integer) with option = 0 to retrieve all levels.
161      - add pieces of code to compute velocity potential at each level (new diagnostics
162        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
163        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
164      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
165        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
166        and in diagnostics_fract_fill.F (do not need a valid pointer for the
167        diagnostics counter-mate); check that definition of counter-diagnostic
168        includes a valid counter-mate (in diagnostics_set_levels.F).
169    o model/src (rStar):
170      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
171        affect solution only if z* with full pressure in EOS;
172        update output of test-exp global_ocean.90x40x15.
173    o pkg/seaice:
174      - introduce siEps=1e-5 parameter
175      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
176      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
177      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
178        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
179        as well as ice cover age and ridging index (attached to AREA).
180        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
181        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
182        Up to SItrMaxNum=3 tracers can be used simultaneously.
183    o pkg/salt_plume:
184      -introduce SPsalFRAC run time parameter that sets the fraction of the
185       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
186       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
187    o model debug options:
188      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
189        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
190      - Refine debug-msg printing selection (3 new levels):
191        debugMode  : controls printing of debug messages (sequence of S/R calls).
192        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
193         debLevZero =  0 ; /* level of disabled aux. msg printing */
194         debLevA =  1 ; /* level of minimum  aux. msg printing */
195         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
196         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
197         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
198         debLevE =  5 ; /* level of extensive debug printing */
199        New debugLevel default: with default debugMode value (=F),
200          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
201          and if debugMode=T, default debugLevel = 4 (debLevD).
202        Relation with previous settings:
203         debLevB (=2) corresponds to former debLevA (=1)
204         debLevD (=4) corresponds to former debLevB (=2)
205        Note:
206         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
207         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
208            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
209      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
210        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
211    o pkg/obcs:
212      - change OBCSfixTopo default from True to False (should not change the results);
213        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
214    o pkg/thsice:
215      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
216        2nd layer seaice sublimation (unlikely to happen)
217      - use Interior mask for OBCS in thsice_advection.F (similar to what is
218        done in gad_advection & seaice_advection).
219    o adjoint:
220      bug fix spotted by Gael Forget:
221      seaice_advection and thsice_advection still had
222      legacy CPP options to avoid CS corner updates for adjoint
223    o pkg/seaice:
224      => Change some of the defaults (2011/05/29):
225         - change SEAICEuseFluxForm default (from False to True)
226         - change DIFF1 default (from 0.004 m/s to 0. m/s)
227         And print warnings if DIFF1 is not set in data.seaice and centered
228          avection scheme is used without any diffusion.
229      also:
230      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
231      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
232      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
233        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
234        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
235      update results of test exp.:
236         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
237             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
238             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
239         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
240         seaice_obcs: output (SEAICEuseFluxForm=T)
241      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
242          for standard fwd & AD lab_sea tests (to keep the same output).
243    o pkg/seaice/seaice_growth.F:
244      - use Ian Fenty's capping formulas for actual ice
245      thickness thoughout EVOLUTION branch.
246      - put treatment pathological case #2) in CPP brackets
247      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
248      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
249    o pkg/seaice:
250      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
251      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
252      also pass fac as a param, which can be 1. (to update the tendency
253      field) or the time step (to update the field itself).
254      - seaice_advdiff.F: for multidim, call seaice_diffusion with
255      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
256      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
257      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
258      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
259    o pkg/seaice:
260      diffusion with centered advection scheme (diffus.F & advect.F):
261      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
262        to just compute the laplacian of input-field.
263      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
264      - fix flux-form version in diffus.F to conserve tracer.
265      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
266       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
267    
268    checkpoint62y (2011/05/26)
269    o pkg/seaice:
270     - seaice_growth.F : in EVOLUTION branch, always include
271       a_QSWbyATM_cover in qnet (as it should be).
272     - verification/global_ocean.cs32x15 : update results accordingly
273       (output.seaice.txt output_adm.seaice.txt).
274    o pkg/seaice + obcs:
275     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
276       equivalent of assuming no tracer gradient outside the OB region.
277       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
278     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
279       after changes above);
280     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
281       only at OB location (instead of over a band of OLx width).
282    o pkg/seaice:
283     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
284       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
285    o pkg/obcs:
286      - split header file "OBCS.h" into 4 separated files:
287        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
288       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
289         (contain no conditional statement which depends on OBCS options).
290      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
291        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
292    o ctrl, cost, grdchk & autodiff pkgs:
293      - make options file more standard (like other {PKG}_OPTIONS.h file but
294        with AD_CONFIG.h); clean-up some of the included header files.
295    o pkg/obcs:
296      - do not mask tracer when applying OB (tracer == 0 could generate problems)
297      - apply tracer OB values to tracer field only at OB location (instead of
298        over a band of OLx width)
299      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
300      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
301        obcs_apply_tloc.F & obcs_apply_sloc.F
302    o obcs in model/src:
303      - call OBCS_APPLY_W only if NonHydrostatic.
304      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
305      - reset dEtaHdt and wVel to zero outside OB interior region ;
306      - leave tracer unchanged outside OB interior region: This has no effect
307        on the solution but just to prevent unrealistic tracer value outside OB.
308      - zero out velocity outside OB interior region: This has no effect on
309        the solution but just to prevent unrealistic velocity outside OB.
310    o obcs and non-lin free-surf:
311       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
312       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
313       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
314       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
315       update results of test-exp. exp4(nlfs).
316    o exp4 (nlfs) test-exp:
317       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
318       with NonLin-FreeSurf); update output.nlfs.txt
319    o obcs and 2d/3d solver norm:
320       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
321       and outside OB interior region (will allow to place OB further inside the
322       domain). Depending on the domain, can affects cg2d-Norm (previous
323       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
324       and cg3d-Norm (previous Norm was computed before canceling OB terms),
325       e.g. in tutorial_plume_on_slope.
326      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
327    o pkg rbcs:
328      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
329      - add capability to apply relaxation to horizontal velocity uVel & vVel.
330    o pkg/grdchk: add gradient check for control variable xx_shifwflx
331    o pkg/shelfice/shelfice_init_fixed.F
332      fix CPP-flag combinations
333    o pkg/seaice: Merge iceage code of Pierre Rampal
334      * update/change/correct ice age calculations
335      * add age updates for pathological cases
336      Probably needs more testing...
337    
338    checkpoint62x (2011/05/13)
339    o pkg/mom_vecinv:
340       high-order vorticity scheme: use interior masks (maskInW & S)
341       to zero-out (outside OB) gradient of vorticity.
342    o verification exp.:
343       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
344       hs94.128x64x5 and seaice_obcs ; update results.
345    o pkg/obcs:
346      fix bug in OBeta for YZ sections in obcs_exf_load.F
347    o pkg/ctrl, pkg/shelfice, and optim:
348      - add new control variable xx_shifwflx (fresh water flux underneath ice
349        shelves). This is almost as tedious as obcs-ctrl, because the
350        variables needs its own mask.
351      - add a cost function term that penalizes the deviation of xx_shifwflx
352        from the first guess (zero) in analogy to other control variables
353    o pkg/shelfice:
354      - start basic adjoint
355    o pkg/ctrl:
356      - remove extra 2D field "for good measure" when initializing in
357        ctrl_set_globfld_[xy/xz/yz].F
358    - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec    - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
359    - improve error messages in ctrl_set_unpack_*    - improve error messages in ctrl_set_unpack_*
360  o OBC implementation in momentum:  o OBC implementation in momentum:

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