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revision 1.1374 by jmc, Sun Feb 6 00:24:40 2011 UTC revision 1.1474 by jmc, Thu Jul 14 17:06:12 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/gmredi:
8       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
9       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
10    
11    checkpoint63 (2011/07/11)
12    o pkg/exch2:
13     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
14     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
15       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
16       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
17    o pkg/diagnostics:
18     - deal with pairs of post-processed diags which are computed together; in
19       particular, re-order list of diags within 1 file to save 2nd computation.
20     - add S/R to compute velocity stream-function (called after velocity-potential
21       calculation) from divergence free transport -> new diagnostics "PsiVEL".
22     - add parameter to select grid-point location where PsiVEL == 0.
23    o eesupp/src:
24       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
25       (specific S/R needed with exch2 topology - for now, just print an error msg)
26    o pkg/shelfice
27     - Implement friction velocity-dependent transfer coefficients following
28       Holland and Jenkins, JPO, 1999
29       Original code by M. Losch with small modifs.
30       Enable with CPP option SHI_ALLOW_GAMMAFRICT
31       and runtime flag SHELFICEuseGammaFrict
32    o verification lab_sea & global_ocean.cs32x15:
33     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
34       does not miss some dependencies (but is slower) and also works with many files
35       (default makedepend limitation for AD built).
36     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
37    o pkg/diagnostics:
38     - add run-time parameter "useMissingValue" (def=False) to fill land-point
39        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
40       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
41     - Extend the use of "missing_value" setting from data.diagnostics for the case
42       of counter-diagnostics (where fraction-weight is zero). This applies both to
43       MNC and MDS output files.
44    o pkg/seaice/seaice_growth.F:
45      - add 'a priori' cap of latent heat flux based on actual mass considerations
46        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
47        non-legacy seaice_solve4temp.
48      - add diagnostic of the residual sublimation freshwater flux (the freshwater
49        flux taken from the ocean if the total actual latent heat fluxes exceed
50        the maximum)
51      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
52       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
53      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
54       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
55      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
56      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
57    o verification 1D_ocean_ice_column:
58       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
59       update results
60    o pkg/diagnostics:
61     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
62       which are not filled-up but computed from other diags ; In this case, the mate
63       diag points to the primary (filled-up) diag to used for post processing.
64     - Update Velocity-potential computation using post-processed diag framework.
65     ==> Change the ordering of fields and time-periods in MDS output file
66       when using periodic averaging: now writes one time record with the full set
67       of fields for this time period, then the next time reccord (it used to be
68       one field with the full set of time records then the next field).
69         Note: this is now similar to NetCDF (MNC) output file. <==
70    
71    checkpoint62z (2011/06/21)
72    o adjoint monitor:
73     - Add adjoint monitor output for packages exf, seaice
74       and update relevant testreport output
75    o pkg/seaice:
76     - re-order diags inits so that they appear in order in available_diagnostics.log
77     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
78       area/heff/hsnow preceeding thermodynamic growth/melt.
79     - modified diag: SIdA; output actual effect, as the description states.
80     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
81     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
82       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
83        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
84     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
85     - added diagnostics for seaice generic tracers (SItr*).
86     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
87     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
88     I. Fenty: 18-Jun-2011:
89     Minor changes to seaice package:
90     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
91        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
92       - Differentiated "regularization variables" from "floor variables"
93        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
94        * hiceMin became SEAICE_hice_reg (old hiceMin)
95          (with _reg meaning regularization variable)
96       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
97        so as to ensure energy conservation when going between phases
98      - A22 was not used anywhere
99     2) Changed regularization procedure for heffActual and hsnowActual to ensure
100        well-boundedness and smooth adjoint in seaice_growth.F
101     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
102        because the old regularization always set heffActual >= 0.05 cm
103     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
104        on AREA when HEFF > 0.
105      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
106        requiring that DISABLE_AREA_FLOOR *not* be defined
107     Affected verifications:
108      - 1D_ocean_ice_column (output.txt output_adm.txt)
109      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
110    o pkg/diagnostics:
111      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
112      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
113        (was _RL, now integer) with option = 0 to retrieve all levels.
114      - add pieces of code to compute velocity potential at each level (new diagnostics
115        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
116        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
117      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
118        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
119        and in diagnostics_fract_fill.F (do not need a valid pointer for the
120        diagnostics counter-mate); check that definition of counter-diagnostic
121        includes a valid counter-mate (in diagnostics_set_levels.F).
122    o model/src (rStar):
123      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
124        affect solution only if z* with full pressure in EOS;
125        update output of test-exp global_ocean.90x40x15.
126    o pkg/seaice:
127      - introduce siEps=1e-5 parameter
128      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
129      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
130      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
131        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
132        as well as ice cover age and ridging index (attached to AREA).
133        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
134        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
135        Up to SItrMaxNum=3 tracers can be used simultaneously.
136    o pkg/salt_plume:
137      -introduce SPsalFRAC run time parameter that sets the fraction of the
138       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
139       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
140    o model debug options:
141      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
142        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
143      - Refine debug-msg printing selection (3 new levels):
144        debugMode  : controls printing of debug messages (sequence of S/R calls).
145        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
146         debLevZero =  0 ; /* level of disabled aux. msg printing */
147         debLevA =  1 ; /* level of minimum  aux. msg printing */
148         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
149         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
150         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
151         debLevE =  5 ; /* level of extensive debug printing */
152        New debugLevel default: with default debugMode value (=F),
153          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
154          and if debugMode=T, default debugLevel = 4 (debLevD).
155        Relation with previous settings:
156         debLevB (=2) corresponds to former debLevA (=1)
157         debLevD (=4) corresponds to former debLevB (=2)
158        Note:
159         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
160         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
161            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
162      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
163        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
164    o pkg/obcs:
165      - change OBCSfixTopo default from True to False (should not change the results);
166        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
167    o pkg/thsice:
168      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
169        2nd layer seaice sublimation (unlikely to happen)
170      - use Interior mask for OBCS in thsice_advection.F (similar to what is
171        done in gad_advection & seaice_advection).
172    o adjoint:
173      bug fix spotted by Gael Forget:
174      seaice_advection and thsice_advection still had
175      legacy CPP options to avoid CS corner updates for adjoint
176    o pkg/seaice:
177      => Change some of the defaults (2011/05/29):
178         - change SEAICEuseFluxForm default (from False to True)
179         - change DIFF1 default (from 0.004 m/s to 0. m/s)
180         And print warnings if DIFF1 is not set in data.seaice and centered
181          avection scheme is used without any diffusion.
182      also:
183      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
184      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
185      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
186        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
187        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
188      update results of test exp.:
189         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
190             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
191             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
192         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
193         seaice_obcs: output (SEAICEuseFluxForm=T)
194      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
195          for standard fwd & AD lab_sea tests (to keep the same output).
196    o pkg/seaice/seaice_growth.F:
197      - use Ian Fenty's capping formulas for actual ice
198      thickness thoughout EVOLUTION branch.
199      - put treatment pathological case #2) in CPP brackets
200      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
201      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
202    o pkg/seaice:
203      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
204      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
205      also pass fac as a param, which can be 1. (to update the tendency
206      field) or the time step (to update the field itself).
207      - seaice_advdiff.F: for multidim, call seaice_diffusion with
208      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
209      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
210      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
211      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
212    o pkg/seaice:
213      diffusion with centered advection scheme (diffus.F & advect.F):
214      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
215        to just compute the laplacian of input-field.
216      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
217      - fix flux-form version in diffus.F to conserve tracer.
218      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
219       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
220    
221    checkpoint62y (2011/05/26)
222    o pkg/seaice:
223     - seaice_growth.F : in EVOLUTION branch, always include
224       a_QSWbyATM_cover in qnet (as it should be).
225     - verification/global_ocean.cs32x15 : update results accordingly
226       (output.seaice.txt output_adm.seaice.txt).
227    o pkg/seaice + obcs:
228     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
229       equivalent of assuming no tracer gradient outside the OB region.
230       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
231     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
232       after changes above);
233     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
234       only at OB location (instead of over a band of OLx width).
235    o pkg/seaice:
236     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
237       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
238    o pkg/obcs:
239      - split header file "OBCS.h" into 4 separated files:
240        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
241       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
242         (contain no conditional statement which depends on OBCS options).
243      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
244        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
245    o ctrl, cost, grdchk & autodiff pkgs:
246      - make options file more standard (like other {PKG}_OPTIONS.h file but
247        with AD_CONFIG.h); clean-up some of the included header files.
248    o pkg/obcs:
249      - do not mask tracer when applying OB (tracer == 0 could generate problems)
250      - apply tracer OB values to tracer field only at OB location (instead of
251        over a band of OLx width)
252      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
253      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
254        obcs_apply_tloc.F & obcs_apply_sloc.F
255    o obcs in model/src:
256      - call OBCS_APPLY_W only if NonHydrostatic.
257      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
258      - reset dEtaHdt and wVel to zero outside OB interior region ;
259      - leave tracer unchanged outside OB interior region: This has no effect
260        on the solution but just to prevent unrealistic tracer value outside OB.
261      - zero out velocity outside OB interior region: This has no effect on
262        the solution but just to prevent unrealistic velocity outside OB.
263    o obcs and non-lin free-surf:
264       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
265       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
266       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
267       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
268       update results of test-exp. exp4(nlfs).
269    o exp4 (nlfs) test-exp:
270       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
271       with NonLin-FreeSurf); update output.nlfs.txt
272    o obcs and 2d/3d solver norm:
273       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
274       and outside OB interior region (will allow to place OB further inside the
275       domain). Depending on the domain, can affects cg2d-Norm (previous
276       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
277       and cg3d-Norm (previous Norm was computed before canceling OB terms),
278       e.g. in tutorial_plume_on_slope.
279      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
280    o pkg rbcs:
281      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
282      - add capability to apply relaxation to horizontal velocity uVel & vVel.
283    o pkg/grdchk: add gradient check for control variable xx_shifwflx
284    o pkg/shelfice/shelfice_init_fixed.F
285      fix CPP-flag combinations
286    o pkg/seaice: Merge iceage code of Pierre Rampal
287      * update/change/correct ice age calculations
288      * add age updates for pathological cases
289      Probably needs more testing...
290    
291    checkpoint62x (2011/05/13)
292    o pkg/mom_vecinv:
293       high-order vorticity scheme: use interior masks (maskInW & S)
294       to zero-out (outside OB) gradient of vorticity.
295    o verification exp.:
296       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
297       hs94.128x64x5 and seaice_obcs ; update results.
298    o pkg/obcs:
299      fix bug in OBeta for YZ sections in obcs_exf_load.F
300    o pkg/ctrl, pkg/shelfice, and optim:
301      - add new control variable xx_shifwflx (fresh water flux underneath ice
302        shelves). This is almost as tedious as obcs-ctrl, because the
303        variables needs its own mask.
304      - add a cost function term that penalizes the deviation of xx_shifwflx
305        from the first guess (zero) in analogy to other control variables
306    o pkg/shelfice:
307      - start basic adjoint
308    o pkg/ctrl:
309      - remove extra 2D field "for good measure" when initializing in
310        ctrl_set_globfld_[xy/xz/yz].F
311      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
312      - improve error messages in ctrl_set_unpack_*
313    o OBC implementation in momentum:
314       use interior masks (maskInC,W & S) in momentum S/R:
315       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
316       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
317       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
318       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
319       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
320        (and also with Leith/Smagorinsky harmonic-viscosity).
321       Update output of experiment dome and exp4 (+nlfs).
322    o exp4 test-exp:
323      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
324        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
325        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
326        time-varying OB at Western-side for wVel (NonHyd); update output.
327      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
328        and biharmonic-viscosity ; also use prescribed time varying OB.
329    o pkg/obcs:
330      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
331    o model/src:
332      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
333      - initialise startTime & nIter0 with unlikely values: allows to set one
334        from the other without ambiguity.
335    o seaice_obcs test-exp.:
336      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
337    o pkg/obcs:
338      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
339        no longer needed with maskInC,W,S in pkg/generic_advdiff.
340    o pkg/seaice:
341      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
342        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
343      - fixed bug in the initialization of sea ice salinity variable HSALT
344        in seaice_init_varia.F  (removed dependence on ICE2WATR)
345    o fizhi-cs test exp.:
346       switch reference output convention for these 2 non-standard test-exp,
347        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
348          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
349       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
350    o model/inc:
351      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
352        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
353    o pkg/seaice:
354      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
355    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
356      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
357        and initial HSALT
358    
359    checkpoint62w (2011/04/26)
360    o pkg/mom_fluxform:
361      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
362      - use parameter "sideDragFactor" in no-slip BC side-drag part.
363      - update output of exp. global_ocean.90x40x15
364    o pkg/mom_vecinv:
365      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
366    o update seaice exp.:
367      use more consistent parameter values (remove "backward compatability only":
368       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
369      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
370       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
371    o update test-exp global_ocean.90x40x15:
372      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
373      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
374      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
375      o turn on zStar & viscA4 in standard set-up (dir input/)
376        and update output files: output.txt & output.dwnslp.txt
377    o new AD-test experiment: obcs_ctrl
378      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
379    o pkg/dic:
380      fix two bugs in handling water vapour pressure in carbonate chemistry
381      and air-sea fluxes. Found by Val Bennington and Galen McKinley
382      (add DIC Option = WATERVAP_BUG to recover old results)
383      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
384    o adding allowInteriorFreezing option to check for water below freezing point
385      at depth and bring the negative heat anomaly to the surface level
386    o pkgs _fields_load:
387      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
388      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
389        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
390        rbcs to get interpolation weights and time reccord number.
391      - fix multi-threading in aim_fields_load.F
392      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
393    o external_fields_load:
394      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
395       interpolation weights) to use in a periodic time-series ; do not divide by
396       time-step to convert to integer:
397       - this fixes case where externForcingPeriod is not multiple of time-step
398          (Thanks to Christopher L. Wolfe)
399       - this fixes case where externForcingPeriod is an odd multiple of time-step
400         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
401      store index of time-record which is currently loaded:
402       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
403       - needed for the adjoint but not yet used because of extensive recomputations;
404         (to be fixed soon)
405    
406    checkpoint62v (2011/04/02)
407    o verification/1D_ocean_ice_column added to test Ian Fenty's
408      pkg/seaice_growth.F modifications for improving sea ice code differentiability
409    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
410      (new velocity statistics after changing maskInW & maskInS definition)
411    o pkg/generic_advdiff with OBCS:
412      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
413      equivalent to assumption of no tracer gradient outside the OB region.
414      This will affect the results if using obcs+biharmonic diffusion.
415      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
416    o pkg/obcs:
417      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
418      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
419      in Interior region. No impact on solution but affects Velocity monitor stats.
420    o pkg/ptracers (adjoint)
421      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
422      tape file for each tracer
423    o model/inc/src and pkg/autodiff: add parameters that allow to turn
424      of parts of the adjoint code at run time. For now, there are only
425      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
426      parameters are set in data.pkg.
427      This is the lazy coward's version of doing this, but still useful for
428      debugging. In order to do it right, everything needs to be moved to
429      pkg/autodiff.
430    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
431      the end; this fixes the adjoint balancing code for open boundaries.
432    o pkg/ctrl:
433      - change behavior of xx_${varname}period to be analogous to exf-conventions:
434        xx_${varname}period =   0.,  means time-independent control part
435        xx_${varname}period = -12., means one-year-periodic monthly control part
436      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
437        clean up ctrl_init a little, remove unused variables
438      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
439      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
440    
441    checkpoint62u (2011/03/15)
442    o model/src:
443      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
444        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
445      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
446        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
447    o pkg/ctrl/obcs/ecco:
448      - remove obsolete, unused, and partially broken code:
449        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
450        ALLOW_CTRL_OBCS_BALANCE
451      - put a stop statement into ecco/cost_obcsvol.F, but also add
452        cost_obcsvol to ecco_ad_diff.list
453    o pkg/ecco: fix counting cost function contributions for obcs (code
454      by Matt M.) and diffkr for diagnostics
455    o pkg/ecco, pkg/ctrl, pkg/grdchk:
456      add cost penalty terms for initial uvel, vvel, eta controls
457      and I/O for prior error files
458    o pkg/mdsio:
459       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
460       (new argument) to check for tiled file in mdsioLocalDir : this fix the
461       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
462    o pkg/ctrl:
463     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
464       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
465       unused and superfluous variables
466     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
467    o pkg/ecco
468     - enable adjoint of Stevens OB
469    o pkg/ctrl/ecco/grdchk:
470      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
471        Fortunately, we do not have any tests for the numerous cpp-flagged
472        option of "obcs as control parameters" so we will never know
473        if this is an improvement (but at least now things compile).
474      - remove an obsolete initialization from ecco_cost_init_barfiles.F
475      - fix some problems within never used ifdefs to make the code compile
476    o pkg/obcs:
477     - Refine Interior mask definition to work with more complex OB (e.g.
478       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
479       read in Interior mask from file. Check if Interior mask is consistent
480       with OB list of indices.
481    o pkg/seaice
482     - beginning code for a seaice tracer package,
483       but currently only used for seaice age: SEAICE_AGE
484       SEAICE_num = 4
485       iTracer = 1: area-weighted ice age
486               = 2: volume-weighted ice age
487               = 3, 4: template for one-year vs. multi-year ice
488       data.seaice has new namelist SEAICE_PARM03 for arrays related to
489       SEAICE_num
490    
491    checkpoint62t (2011/03/05)
492    o pkg/obcs:
493     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
494       then normal component. This ensures that the normal component is set
495       correctly even when it conficts with tangential setting from an other OB.
496       Affects results of test-experiment seaice_obcs: update the output.txt
497    o pkg/obcs:
498     - add code to monitor statistics of dynamical fields at OB.
499     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
500       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
501       - change default: balance the Net inflow through all OB (instead of balancing
502         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
503     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
504       to match Nortern OB inflow (OBCS_balanceFacN=0).
505    o pkg/seaice:
506     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
507    o pkg/seaice (seaice_growth v 1.113):
508     - reverting seaice_growth to v 1.111 in order to have code with exact bit
509       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
510       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
511       runtime flag SEAICEareaFormula is kept but is inactive
512    o model/src:
513     - add new param to scale curvilinear grid distance and area when using
514       a different sphere radius from the grid-files.
515     - test/check multi-threads EXCH applied to local variable (cg2d_x)
516    o adjoint:
517     - enable adjoint of Stevens OB
518     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
519       (a bit delicate because of potentially modified adj. common block structure;
520       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
521    
522    checkpoint62s (2011/02/15)
523    o pkg/seaice (seaice_growth v 1.112):
524     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
525       computing the ice cover tendency from effective thickness tendencies. Include
526       Ian Fenty's formula.
527     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
528       SEAICEareaFormula.
529     - simplify notations for the various d_HEFF/d_AREA terms.
530    o pkg/gmredi:
531     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
532       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
533       add a verification test-run (front_relax.bvp) to test GM_useBVP.
534    o pkg/seaice (seaice_growth v 1.111):
535     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
536     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
537       also melt ice.
538    o pkg/seaice:
539     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
540     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
541  o pkg/cheapaml:  o pkg/cheapaml:
542   - from Nico Wienders: New version of this package.   - from Nico Wienders: New version of this package.
543  o pkg/flt:  o pkg/flt:
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