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revision 1.1367 by mlosch, Wed Jan 19 13:52:14 2011 UTC revision 1.1467 by jmc, Tue Jun 28 20:49:13 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 verification lab_sea & global_ocean.cs32x15:
8     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
9       does not miss some dependencies (but is slower) and also works with many files
10       (default makedepend limitation for AD built).
11     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
12    o pkg/diagnostics:
13     - add run-time parameter "useMissingValue" (def=False) to fill land-point
14        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
15       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
16     - Extend the use of "missing_value" setting from data.diagnostics for the case
17       of counter-diagnostics (where fraction-weight is zero). This applies both to
18       MNC and MDS output files.
19    o pkg/seaice/seaice_growth.F:
20      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
21       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
22      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
23       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
24      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
25      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
26    o verification 1D_ocean_ice_column:
27       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
28       update results
29    o pkg/diagnostics:
30     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
31       which are not filled-up but computed from other diags ; In this case, the mate
32       diag points to the primary (filled-up) diag to used for post processing.
33     - Update Velocity-potential computation using post-processed diag framework.
34     ==> Change the ordering of fields and time-periods in MDS output file
35       when using periodic averaging: now writes one time record with the full set
36       of fields for this time period, then the next time reccord (it used to be
37       one field with the full set of time records then the next field).
38         Note: this is now similar to NetCDF (MNC) output file. <==
39    
40    checkpoint62z (2011/06/21)
41    o adjoint monitor:
42     - Add adjoint monitor output for packages exf, seaice
43       and update relevant testreport output
44    o pkg/seaice:
45     - re-order diags inits so that they appear in order in available_diagnostics.log
46     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
47       area/heff/hsnow preceeding thermodynamic growth/melt.
48     - modified diag: SIdA; output actual effect, as the description states.
49     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
50     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
51       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
52        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
53     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
54     - added diagnostics for seaice generic tracers (SItr*).
55     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
56     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
57     I. Fenty: 18-Jun-2011:
58     Minor changes to seaice package:
59     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
60        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
61       - Differentiated "regularization variables" from "floor variables"
62        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
63        * hiceMin became SEAICE_hice_reg (old hiceMin)
64          (with _reg meaning regularization variable)
65       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
66        so as to ensure energy conservation when going between phases
67      - A22 was not used anywhere
68     2) Changed regularization procedure for heffActual and hsnowActual to ensure
69        well-boundedness and smooth adjoint in seaice_growth.F
70     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
71        because the old regularization always set heffActual >= 0.05 cm
72     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
73        on AREA when HEFF > 0.
74      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
75        requiring that DISABLE_AREA_FLOOR *not* be defined
76     Affected verifications:
77      - 1D_ocean_ice_column (output.txt output_adm.txt)
78      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
79    o pkg/diagnostics:
80      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
81      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
82        (was _RL, now integer) with option = 0 to retrieve all levels.
83      - add pieces of code to compute velocity potential at each level (new diagnostics
84        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
85        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
86      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
87        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
88        and in diagnostics_fract_fill.F (do not need a valid pointer for the
89        diagnostics counter-mate); check that definition of counter-diagnostic
90        includes a valid counter-mate (in diagnostics_set_levels.F).
91    o model/src (rStar):
92      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
93        affect solution only if z* with full pressure in EOS;
94        update output of test-exp global_ocean.90x40x15.
95    o pkg/seaice:
96      - introduce siEps=1e-5 parameter
97      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
98      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
99      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
100        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
101        as well as ice cover age and ridging index (attached to AREA).
102        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
103        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
104        Up to SItrMaxNum=3 tracers can be used simultaneously.
105    o pkg/salt_plume:
106      -introduce SPsalFRAC run time parameter that sets the fraction of the
107       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
108       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
109    o model debug options:
110      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
111        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
112      - Refine debug-msg printing selection (3 new levels):
113        debugMode  : controls printing of debug messages (sequence of S/R calls).
114        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
115         debLevZero =  0 ; /* level of disabled aux. msg printing */
116         debLevA =  1 ; /* level of minimum  aux. msg printing */
117         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
118         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
119         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
120         debLevE =  5 ; /* level of extensive debug printing */
121        New debugLevel default: with default debugMode value (=F),
122          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
123          and if debugMode=T, default debugLevel = 4 (debLevD).
124        Relation with previous settings:
125         debLevB (=2) corresponds to former debLevA (=1)
126         debLevD (=4) corresponds to former debLevB (=2)
127        Note:
128         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
129         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
130            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
131      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
132        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
133    o pkg/obcs:
134      - change OBCSfixTopo default from True to False (should not change the results);
135        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
136    o pkg/thsice:
137      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
138        2nd layer seaice sublimation (unlikely to happen)
139      - use Interior mask for OBCS in thsice_advection.F (similar to what is
140        done in gad_advection & seaice_advection).
141    o adjoint:
142      bug fix spotted by Gael Forget:
143      seaice_advection and thsice_advection still had
144      legacy CPP options to avoid CS corner updates for adjoint
145    o pkg/seaice:
146      => Change some of the defaults (2011/05/29):
147         - change SEAICEuseFluxForm default (from False to True)
148         - change DIFF1 default (from 0.004 m/s to 0. m/s)
149         And print warnings if DIFF1 is not set in data.seaice and centered
150          avection scheme is used without any diffusion.
151      also:
152      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
153      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
154      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
155        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
156        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
157      update results of test exp.:
158         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
159             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
160             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
161         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
162         seaice_obcs: output (SEAICEuseFluxForm=T)
163      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
164          for standard fwd & AD lab_sea tests (to keep the same output).
165    o pkg/seaice/seaice_growth.F:
166      - use Ian Fenty's capping formulas for actual ice
167      thickness thoughout EVOLUTION branch.
168      - put treatment pathological case #2) in CPP brackets
169      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
170      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
171    o pkg/seaice:
172      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
173      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
174      also pass fac as a param, which can be 1. (to update the tendency
175      field) or the time step (to update the field itself).
176      - seaice_advdiff.F: for multidim, call seaice_diffusion with
177      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
178      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
179      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
180      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
181    o pkg/seaice:
182      diffusion with centered advection scheme (diffus.F & advect.F):
183      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
184        to just compute the laplacian of input-field.
185      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
186      - fix flux-form version in diffus.F to conserve tracer.
187      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
188       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
189    
190    checkpoint62y (2011/05/26)
191    o pkg/seaice:
192     - seaice_growth.F : in EVOLUTION branch, always include
193       a_QSWbyATM_cover in qnet (as it should be).
194     - verification/global_ocean.cs32x15 : update results accordingly
195       (output.seaice.txt output_adm.seaice.txt).
196    o pkg/seaice + obcs:
197     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
198       equivalent of assuming no tracer gradient outside the OB region.
199       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
200     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
201       after changes above);
202     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
203       only at OB location (instead of over a band of OLx width).
204    o pkg/seaice:
205     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
206       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
207    o pkg/obcs:
208      - split header file "OBCS.h" into 4 separated files:
209        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
210       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
211         (contain no conditional statement which depends on OBCS options).
212      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
213        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
214    o ctrl, cost, grdchk & autodiff pkgs:
215      - make options file more standard (like other {PKG}_OPTIONS.h file but
216        with AD_CONFIG.h); clean-up some of the included header files.
217    o pkg/obcs:
218      - do not mask tracer when applying OB (tracer == 0 could generate problems)
219      - apply tracer OB values to tracer field only at OB location (instead of
220        over a band of OLx width)
221      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
222      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
223        obcs_apply_tloc.F & obcs_apply_sloc.F
224    o obcs in model/src:
225      - call OBCS_APPLY_W only if NonHydrostatic.
226      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
227      - reset dEtaHdt and wVel to zero outside OB interior region ;
228      - leave tracer unchanged outside OB interior region: This has no effect
229        on the solution but just to prevent unrealistic tracer value outside OB.
230      - zero out velocity outside OB interior region: This has no effect on
231        the solution but just to prevent unrealistic velocity outside OB.
232    o obcs and non-lin free-surf:
233       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
234       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
235       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
236       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
237       update results of test-exp. exp4(nlfs).
238    o exp4 (nlfs) test-exp:
239       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
240       with NonLin-FreeSurf); update output.nlfs.txt
241    o obcs and 2d/3d solver norm:
242       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
243       and outside OB interior region (will allow to place OB further inside the
244       domain). Depending on the domain, can affects cg2d-Norm (previous
245       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
246       and cg3d-Norm (previous Norm was computed before canceling OB terms),
247       e.g. in tutorial_plume_on_slope.
248      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
249    o pkg rbcs:
250      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
251      - add capability to apply relaxation to horizontal velocity uVel & vVel.
252    o pkg/grdchk: add gradient check for control variable xx_shifwflx
253    o pkg/shelfice/shelfice_init_fixed.F
254      fix CPP-flag combinations
255    o pkg/seaice: Merge iceage code of Pierre Rampal
256      * update/change/correct ice age calculations
257      * add age updates for pathological cases
258      Probably needs more testing...
259    
260    checkpoint62x (2011/05/13)
261    o pkg/mom_vecinv:
262       high-order vorticity scheme: use interior masks (maskInW & S)
263       to zero-out (outside OB) gradient of vorticity.
264    o verification exp.:
265       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
266       hs94.128x64x5 and seaice_obcs ; update results.
267    o pkg/obcs:
268      fix bug in OBeta for YZ sections in obcs_exf_load.F
269    o pkg/ctrl, pkg/shelfice, and optim:
270      - add new control variable xx_shifwflx (fresh water flux underneath ice
271        shelves). This is almost as tedious as obcs-ctrl, because the
272        variables needs its own mask.
273      - add a cost function term that penalizes the deviation of xx_shifwflx
274        from the first guess (zero) in analogy to other control variables
275    o pkg/shelfice:
276      - start basic adjoint
277    o pkg/ctrl:
278      - remove extra 2D field "for good measure" when initializing in
279        ctrl_set_globfld_[xy/xz/yz].F
280      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
281      - improve error messages in ctrl_set_unpack_*
282    o OBC implementation in momentum:
283       use interior masks (maskInC,W & S) in momentum S/R:
284       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
285       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
286       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
287       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
288       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
289        (and also with Leith/Smagorinsky harmonic-viscosity).
290       Update output of experiment dome and exp4 (+nlfs).
291    o exp4 test-exp:
292      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
293        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
294        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
295        time-varying OB at Western-side for wVel (NonHyd); update output.
296      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
297        and biharmonic-viscosity ; also use prescribed time varying OB.
298    o pkg/obcs:
299      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
300    o model/src:
301      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
302      - initialise startTime & nIter0 with unlikely values: allows to set one
303        from the other without ambiguity.
304    o seaice_obcs test-exp.:
305      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
306    o pkg/obcs:
307      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
308        no longer needed with maskInC,W,S in pkg/generic_advdiff.
309    o pkg/seaice:
310      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
311        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
312      - fixed bug in the initialization of sea ice salinity variable HSALT
313        in seaice_init_varia.F  (removed dependence on ICE2WATR)
314    o fizhi-cs test exp.:
315       switch reference output convention for these 2 non-standard test-exp,
316        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
317          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
318       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
319    o model/inc:
320      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
321        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
322    o pkg/seaice:
323      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
324    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
325      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
326        and initial HSALT
327    
328    checkpoint62w (2011/04/26)
329    o pkg/mom_fluxform:
330      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
331      - use parameter "sideDragFactor" in no-slip BC side-drag part.
332      - update output of exp. global_ocean.90x40x15
333    o pkg/mom_vecinv:
334      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
335    o update seaice exp.:
336      use more consistent parameter values (remove "backward compatability only":
337       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
338      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
339       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
340    o update test-exp global_ocean.90x40x15:
341      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
342      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
343      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
344      o turn on zStar & viscA4 in standard set-up (dir input/)
345        and update output files: output.txt & output.dwnslp.txt
346    o new AD-test experiment: obcs_ctrl
347      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
348    o pkg/dic:
349      fix two bugs in handling water vapour pressure in carbonate chemistry
350      and air-sea fluxes. Found by Val Bennington and Galen McKinley
351      (add DIC Option = WATERVAP_BUG to recover old results)
352      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
353    o adding allowInteriorFreezing option to check for water below freezing point
354      at depth and bring the negative heat anomaly to the surface level
355    o pkgs _fields_load:
356      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
357      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
358        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
359        rbcs to get interpolation weights and time reccord number.
360      - fix multi-threading in aim_fields_load.F
361      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
362    o external_fields_load:
363      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
364       interpolation weights) to use in a periodic time-series ; do not divide by
365       time-step to convert to integer:
366       - this fixes case where externForcingPeriod is not multiple of time-step
367          (Thanks to Christopher L. Wolfe)
368       - this fixes case where externForcingPeriod is an odd multiple of time-step
369         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
370      store index of time-record which is currently loaded:
371       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
372       - needed for the adjoint but not yet used because of extensive recomputations;
373         (to be fixed soon)
374    
375    checkpoint62v (2011/04/02)
376    o verification/1D_ocean_ice_column added to test Ian Fenty's
377      pkg/seaice_growth.F modifications for improving sea ice code differentiability
378    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
379      (new velocity statistics after changing maskInW & maskInS definition)
380    o pkg/generic_advdiff with OBCS:
381      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
382      equivalent to assumption of no tracer gradient outside the OB region.
383      This will affect the results if using obcs+biharmonic diffusion.
384      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
385    o pkg/obcs:
386      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
387      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
388      in Interior region. No impact on solution but affects Velocity monitor stats.
389    o pkg/ptracers (adjoint)
390      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
391      tape file for each tracer
392    o model/inc/src and pkg/autodiff: add parameters that allow to turn
393      of parts of the adjoint code at run time. For now, there are only
394      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
395      parameters are set in data.pkg.
396      This is the lazy coward's version of doing this, but still useful for
397      debugging. In order to do it right, everything needs to be moved to
398      pkg/autodiff.
399    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
400      the end; this fixes the adjoint balancing code for open boundaries.
401    o pkg/ctrl:
402      - change behavior of xx_${varname}period to be analogous to exf-conventions:
403        xx_${varname}period =   0.,  means time-independent control part
404        xx_${varname}period = -12., means one-year-periodic monthly control part
405      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
406        clean up ctrl_init a little, remove unused variables
407      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
408      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
409    
410    checkpoint62u (2011/03/15)
411    o model/src:
412      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
413        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
414      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
415        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
416    o pkg/ctrl/obcs/ecco:
417      - remove obsolete, unused, and partially broken code:
418        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
419        ALLOW_CTRL_OBCS_BALANCE
420      - put a stop statement into ecco/cost_obcsvol.F, but also add
421        cost_obcsvol to ecco_ad_diff.list
422    o pkg/ecco: fix counting cost function contributions for obcs (code
423      by Matt M.) and diffkr for diagnostics
424    o pkg/ecco, pkg/ctrl, pkg/grdchk:
425      add cost penalty terms for initial uvel, vvel, eta controls
426      and I/O for prior error files
427    o pkg/mdsio:
428       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
429       (new argument) to check for tiled file in mdsioLocalDir : this fix the
430       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
431    o pkg/ctrl:
432     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
433       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
434       unused and superfluous variables
435     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
436    o pkg/ecco
437     - enable adjoint of Stevens OB
438    o pkg/ctrl/ecco/grdchk:
439      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
440        Fortunately, we do not have any tests for the numerous cpp-flagged
441        option of "obcs as control parameters" so we will never know
442        if this is an improvement (but at least now things compile).
443      - remove an obsolete initialization from ecco_cost_init_barfiles.F
444      - fix some problems within never used ifdefs to make the code compile
445    o pkg/obcs:
446     - Refine Interior mask definition to work with more complex OB (e.g.
447       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
448       read in Interior mask from file. Check if Interior mask is consistent
449       with OB list of indices.
450    o pkg/seaice
451     - beginning code for a seaice tracer package,
452       but currently only used for seaice age: SEAICE_AGE
453       SEAICE_num = 4
454       iTracer = 1: area-weighted ice age
455               = 2: volume-weighted ice age
456               = 3, 4: template for one-year vs. multi-year ice
457       data.seaice has new namelist SEAICE_PARM03 for arrays related to
458       SEAICE_num
459    
460    checkpoint62t (2011/03/05)
461    o pkg/obcs:
462     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
463       then normal component. This ensures that the normal component is set
464       correctly even when it conficts with tangential setting from an other OB.
465       Affects results of test-experiment seaice_obcs: update the output.txt
466    o pkg/obcs:
467     - add code to monitor statistics of dynamical fields at OB.
468     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
469       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
470       - change default: balance the Net inflow through all OB (instead of balancing
471         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
472     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
473       to match Nortern OB inflow (OBCS_balanceFacN=0).
474    o pkg/seaice:
475     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
476    o pkg/seaice (seaice_growth v 1.113):
477     - reverting seaice_growth to v 1.111 in order to have code with exact bit
478       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
479       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
480       runtime flag SEAICEareaFormula is kept but is inactive
481    o model/src:
482     - add new param to scale curvilinear grid distance and area when using
483       a different sphere radius from the grid-files.
484     - test/check multi-threads EXCH applied to local variable (cg2d_x)
485    o adjoint:
486     - enable adjoint of Stevens OB
487     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
488       (a bit delicate because of potentially modified adj. common block structure;
489       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
490    
491    checkpoint62s (2011/02/15)
492    o pkg/seaice (seaice_growth v 1.112):
493     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
494       computing the ice cover tendency from effective thickness tendencies. Include
495       Ian Fenty's formula.
496     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
497       SEAICEareaFormula.
498     - simplify notations for the various d_HEFF/d_AREA terms.
499    o pkg/gmredi:
500     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
501       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
502       add a verification test-run (front_relax.bvp) to test GM_useBVP.
503    o pkg/seaice (seaice_growth v 1.111):
504     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
505     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
506       also melt ice.
507    o pkg/seaice:
508     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
509     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
510    o pkg/cheapaml:
511     - from Nico Wienders: New version of this package.
512    o pkg/flt:
513     - add CPP options to prevent floats to re-enter the opposite side of
514       a periodic domain (default: keep periodicity)
515    o pkg/gmredi:
516     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
517       (needed for multi-dim advection).
518     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
519    o model/src:
520     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
521    o tutorial_tracer_adjsens
522     - extend to NLFS and replace maskC by hFacC
523       (change reference output accordingly)
524    
525    checkpoint62r (2011/01/24)
526    o testreport:
527     - add option -deloutp (-do) to remove output file after successful run
528     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
529       extract exact list of procs from this file ; adjust COMMAND by
530       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
531  o pkg/ecco: replace old ineffective way of penalizing deviations from  o pkg/ecco: replace old ineffective way of penalizing deviations from
532    first guess (of obcs) with code by Matt Mazloff    first guess (of obcs) with code by Matt Mazloff
533  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
534    exf/cal    exf/cal
535    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
536      and handle case of obcs?period == 0      and handle case of obcs?period == 0
537      Not affected by these changes: There is still an inconsistency in      Not affected by these changes: There is still an inconsistency in
538      the computation of start/endrec for the obcs variables for ALLOW_CAL      the computation of start/endrec for the obcs variables for ALLOW_CAL
539      defined (see comment by Menemenlis, 7-Mar-2003)      defined (see comment by Menemenlis, 7-Mar-2003)
540    - make S/R ctrl_get_gen_rec return something meaningful even if    - make S/R ctrl_get_gen_rec return something meaningful even if
541      ALLOW_CAL is not defined      ALLOW_CAL is not defined
542    - ctrl_getobcs?: simplify code so that it does not need to use    - ctrl_getobcs?: simplify code so that it does not need to use
543                     S/R exf_swapfields                     S/R exf_swapfields
544  o testreport:  o testreport:
545     allow to test MPI with different number of processors for each experiment:     allow to test MPI with different number of processors for each experiment:
# Line 24  o testreport: Line 548  o testreport:
548  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
549    alleviate the need for additional 3D tapes when using    alleviate the need for additional 3D tapes when using
550    the non-inear free surface in the adjoint. This is done    the non-inear free surface in the adjoint. This is done
551    by adding an 'update' of hfacc etc. to their current    by adding an 'update' of hfacc etc. to their current
552    value at the beginning of forward_step.F.    value at the beginning of forward_step.F.
553  o pkg/seaice  o pkg/seaice
554    seaice_lsr: move stress-divergence computations out of outer pseudo-    seaice_lsr: move stress-divergence computations out of outer pseudo-
555    timestepping loop    timestepping loop
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