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revision 1.1295 by jmc, Sat Sep 11 21:39:13 2010 UTC revision 1.1472 by jmc, Sat Jul 9 22:17:28 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/exch2:
8     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
9     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
10       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
11       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
12    o pkg/diagnostics:
13     - deal with pairs of post-processed diags which are computed together; in
14       particular, re-order list of diags within 1 file to save 2nd computation.
15     - add S/R to compute velocity stream-function (called after velocity-potential
16       calculation) from divergence free transport -> new diagnostics "PsiVEL".
17     - add parameter to select grid-point location where PsiVEL == 0.
18    o eesupp/src:
19       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
20       (specific S/R needed with exch2 topology - for now, just print an error msg)
21    o pkg/shelfice
22     - Implement friction velocity-dependent transfer coefficients following
23       Holland and Jenkins, JPO, 1999
24       Original code by M. Losch with small modifs.
25       Enable with CPP option SHI_ALLOW_GAMMAFRICT
26       and runtime flag SHELFICEuseGammaFrict
27    o verification lab_sea & global_ocean.cs32x15:
28     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
29       does not miss some dependencies (but is slower) and also works with many files
30       (default makedepend limitation for AD built).
31     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
32    o pkg/diagnostics:
33     - add run-time parameter "useMissingValue" (def=False) to fill land-point
34        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
35       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
36     - Extend the use of "missing_value" setting from data.diagnostics for the case
37       of counter-diagnostics (where fraction-weight is zero). This applies both to
38       MNC and MDS output files.
39    o pkg/seaice/seaice_growth.F:
40      - add 'a priori' cap of latent heat flux based on actual mass considerations
41        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
42        non-legacy seaice_solve4temp.
43      - add diagnostic of the residual sublimation freshwater flux (the freshwater
44        flux taken from the ocean if the total actual latent heat fluxes exceed
45        the maximum)
46      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
47       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
48      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
49       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
50      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
51      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
52    o verification 1D_ocean_ice_column:
53       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
54       update results
55    o pkg/diagnostics:
56     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
57       which are not filled-up but computed from other diags ; In this case, the mate
58       diag points to the primary (filled-up) diag to used for post processing.
59     - Update Velocity-potential computation using post-processed diag framework.
60     ==> Change the ordering of fields and time-periods in MDS output file
61       when using periodic averaging: now writes one time record with the full set
62       of fields for this time period, then the next time reccord (it used to be
63       one field with the full set of time records then the next field).
64         Note: this is now similar to NetCDF (MNC) output file. <==
65    
66    checkpoint62z (2011/06/21)
67    o adjoint monitor:
68     - Add adjoint monitor output for packages exf, seaice
69       and update relevant testreport output
70    o pkg/seaice:
71     - re-order diags inits so that they appear in order in available_diagnostics.log
72     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
73       area/heff/hsnow preceeding thermodynamic growth/melt.
74     - modified diag: SIdA; output actual effect, as the description states.
75     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
76     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
77       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
78        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
79     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
80     - added diagnostics for seaice generic tracers (SItr*).
81     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
82     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
83     I. Fenty: 18-Jun-2011:
84     Minor changes to seaice package:
85     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
86        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
87       - Differentiated "regularization variables" from "floor variables"
88        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
89        * hiceMin became SEAICE_hice_reg (old hiceMin)
90          (with _reg meaning regularization variable)
91       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
92        so as to ensure energy conservation when going between phases
93      - A22 was not used anywhere
94     2) Changed regularization procedure for heffActual and hsnowActual to ensure
95        well-boundedness and smooth adjoint in seaice_growth.F
96     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
97        because the old regularization always set heffActual >= 0.05 cm
98     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
99        on AREA when HEFF > 0.
100      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
101        requiring that DISABLE_AREA_FLOOR *not* be defined
102     Affected verifications:
103      - 1D_ocean_ice_column (output.txt output_adm.txt)
104      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
105    o pkg/diagnostics:
106      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
107      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
108        (was _RL, now integer) with option = 0 to retrieve all levels.
109      - add pieces of code to compute velocity potential at each level (new diagnostics
110        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
111        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
112      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
113        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
114        and in diagnostics_fract_fill.F (do not need a valid pointer for the
115        diagnostics counter-mate); check that definition of counter-diagnostic
116        includes a valid counter-mate (in diagnostics_set_levels.F).
117    o model/src (rStar):
118      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
119        affect solution only if z* with full pressure in EOS;
120        update output of test-exp global_ocean.90x40x15.
121    o pkg/seaice:
122      - introduce siEps=1e-5 parameter
123      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
124      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
125      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
126        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
127        as well as ice cover age and ridging index (attached to AREA).
128        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
129        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
130        Up to SItrMaxNum=3 tracers can be used simultaneously.
131    o pkg/salt_plume:
132      -introduce SPsalFRAC run time parameter that sets the fraction of the
133       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
134       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
135    o model debug options:
136      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
137        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
138      - Refine debug-msg printing selection (3 new levels):
139        debugMode  : controls printing of debug messages (sequence of S/R calls).
140        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
141         debLevZero =  0 ; /* level of disabled aux. msg printing */
142         debLevA =  1 ; /* level of minimum  aux. msg printing */
143         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
144         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
145         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
146         debLevE =  5 ; /* level of extensive debug printing */
147        New debugLevel default: with default debugMode value (=F),
148          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
149          and if debugMode=T, default debugLevel = 4 (debLevD).
150        Relation with previous settings:
151         debLevB (=2) corresponds to former debLevA (=1)
152         debLevD (=4) corresponds to former debLevB (=2)
153        Note:
154         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
155         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
156            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
157      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
158        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
159    o pkg/obcs:
160      - change OBCSfixTopo default from True to False (should not change the results);
161        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
162    o pkg/thsice:
163      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
164        2nd layer seaice sublimation (unlikely to happen)
165      - use Interior mask for OBCS in thsice_advection.F (similar to what is
166        done in gad_advection & seaice_advection).
167    o adjoint:
168      bug fix spotted by Gael Forget:
169      seaice_advection and thsice_advection still had
170      legacy CPP options to avoid CS corner updates for adjoint
171    o pkg/seaice:
172      => Change some of the defaults (2011/05/29):
173         - change SEAICEuseFluxForm default (from False to True)
174         - change DIFF1 default (from 0.004 m/s to 0. m/s)
175         And print warnings if DIFF1 is not set in data.seaice and centered
176          avection scheme is used without any diffusion.
177      also:
178      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
179      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
180      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
181        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
182        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
183      update results of test exp.:
184         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
185             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
186             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
187         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
188         seaice_obcs: output (SEAICEuseFluxForm=T)
189      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
190          for standard fwd & AD lab_sea tests (to keep the same output).
191    o pkg/seaice/seaice_growth.F:
192      - use Ian Fenty's capping formulas for actual ice
193      thickness thoughout EVOLUTION branch.
194      - put treatment pathological case #2) in CPP brackets
195      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
196      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
197    o pkg/seaice:
198      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
199      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
200      also pass fac as a param, which can be 1. (to update the tendency
201      field) or the time step (to update the field itself).
202      - seaice_advdiff.F: for multidim, call seaice_diffusion with
203      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
204      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
205      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
206      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
207    o pkg/seaice:
208      diffusion with centered advection scheme (diffus.F & advect.F):
209      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
210        to just compute the laplacian of input-field.
211      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
212      - fix flux-form version in diffus.F to conserve tracer.
213      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
214       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
215    
216    checkpoint62y (2011/05/26)
217    o pkg/seaice:
218     - seaice_growth.F : in EVOLUTION branch, always include
219       a_QSWbyATM_cover in qnet (as it should be).
220     - verification/global_ocean.cs32x15 : update results accordingly
221       (output.seaice.txt output_adm.seaice.txt).
222    o pkg/seaice + obcs:
223     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
224       equivalent of assuming no tracer gradient outside the OB region.
225       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
226     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
227       after changes above);
228     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
229       only at OB location (instead of over a band of OLx width).
230    o pkg/seaice:
231     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
232       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
233    o pkg/obcs:
234      - split header file "OBCS.h" into 4 separated files:
235        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
236       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
237         (contain no conditional statement which depends on OBCS options).
238      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
239        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
240    o ctrl, cost, grdchk & autodiff pkgs:
241      - make options file more standard (like other {PKG}_OPTIONS.h file but
242        with AD_CONFIG.h); clean-up some of the included header files.
243    o pkg/obcs:
244      - do not mask tracer when applying OB (tracer == 0 could generate problems)
245      - apply tracer OB values to tracer field only at OB location (instead of
246        over a band of OLx width)
247      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
248      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
249        obcs_apply_tloc.F & obcs_apply_sloc.F
250    o obcs in model/src:
251      - call OBCS_APPLY_W only if NonHydrostatic.
252      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
253      - reset dEtaHdt and wVel to zero outside OB interior region ;
254      - leave tracer unchanged outside OB interior region: This has no effect
255        on the solution but just to prevent unrealistic tracer value outside OB.
256      - zero out velocity outside OB interior region: This has no effect on
257        the solution but just to prevent unrealistic velocity outside OB.
258    o obcs and non-lin free-surf:
259       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
260       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
261       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
262       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
263       update results of test-exp. exp4(nlfs).
264    o exp4 (nlfs) test-exp:
265       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
266       with NonLin-FreeSurf); update output.nlfs.txt
267    o obcs and 2d/3d solver norm:
268       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
269       and outside OB interior region (will allow to place OB further inside the
270       domain). Depending on the domain, can affects cg2d-Norm (previous
271       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
272       and cg3d-Norm (previous Norm was computed before canceling OB terms),
273       e.g. in tutorial_plume_on_slope.
274      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
275    o pkg rbcs:
276      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
277      - add capability to apply relaxation to horizontal velocity uVel & vVel.
278    o pkg/grdchk: add gradient check for control variable xx_shifwflx
279    o pkg/shelfice/shelfice_init_fixed.F
280      fix CPP-flag combinations
281    o pkg/seaice: Merge iceage code of Pierre Rampal
282      * update/change/correct ice age calculations
283      * add age updates for pathological cases
284      Probably needs more testing...
285    
286    checkpoint62x (2011/05/13)
287    o pkg/mom_vecinv:
288       high-order vorticity scheme: use interior masks (maskInW & S)
289       to zero-out (outside OB) gradient of vorticity.
290    o verification exp.:
291       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
292       hs94.128x64x5 and seaice_obcs ; update results.
293    o pkg/obcs:
294      fix bug in OBeta for YZ sections in obcs_exf_load.F
295    o pkg/ctrl, pkg/shelfice, and optim:
296      - add new control variable xx_shifwflx (fresh water flux underneath ice
297        shelves). This is almost as tedious as obcs-ctrl, because the
298        variables needs its own mask.
299      - add a cost function term that penalizes the deviation of xx_shifwflx
300        from the first guess (zero) in analogy to other control variables
301    o pkg/shelfice:
302      - start basic adjoint
303    o pkg/ctrl:
304      - remove extra 2D field "for good measure" when initializing in
305        ctrl_set_globfld_[xy/xz/yz].F
306      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
307      - improve error messages in ctrl_set_unpack_*
308    o OBC implementation in momentum:
309       use interior masks (maskInC,W & S) in momentum S/R:
310       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
311       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
312       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
313       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
314       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
315        (and also with Leith/Smagorinsky harmonic-viscosity).
316       Update output of experiment dome and exp4 (+nlfs).
317    o exp4 test-exp:
318      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
319        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
320        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
321        time-varying OB at Western-side for wVel (NonHyd); update output.
322      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
323        and biharmonic-viscosity ; also use prescribed time varying OB.
324    o pkg/obcs:
325      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
326    o model/src:
327      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
328      - initialise startTime & nIter0 with unlikely values: allows to set one
329        from the other without ambiguity.
330    o seaice_obcs test-exp.:
331      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
332    o pkg/obcs:
333      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
334        no longer needed with maskInC,W,S in pkg/generic_advdiff.
335    o pkg/seaice:
336      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
337        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
338      - fixed bug in the initialization of sea ice salinity variable HSALT
339        in seaice_init_varia.F  (removed dependence on ICE2WATR)
340    o fizhi-cs test exp.:
341       switch reference output convention for these 2 non-standard test-exp,
342        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
343          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
344       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
345    o model/inc:
346      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
347        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
348    o pkg/seaice:
349      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
350    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
351      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
352        and initial HSALT
353    
354    checkpoint62w (2011/04/26)
355    o pkg/mom_fluxform:
356      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
357      - use parameter "sideDragFactor" in no-slip BC side-drag part.
358      - update output of exp. global_ocean.90x40x15
359    o pkg/mom_vecinv:
360      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
361    o update seaice exp.:
362      use more consistent parameter values (remove "backward compatability only":
363       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
364      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
365       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
366    o update test-exp global_ocean.90x40x15:
367      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
368      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
369      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
370      o turn on zStar & viscA4 in standard set-up (dir input/)
371        and update output files: output.txt & output.dwnslp.txt
372    o new AD-test experiment: obcs_ctrl
373      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
374    o pkg/dic:
375      fix two bugs in handling water vapour pressure in carbonate chemistry
376      and air-sea fluxes. Found by Val Bennington and Galen McKinley
377      (add DIC Option = WATERVAP_BUG to recover old results)
378      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
379    o adding allowInteriorFreezing option to check for water below freezing point
380      at depth and bring the negative heat anomaly to the surface level
381    o pkgs _fields_load:
382      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
383      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
384        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
385        rbcs to get interpolation weights and time reccord number.
386      - fix multi-threading in aim_fields_load.F
387      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
388    o external_fields_load:
389      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
390       interpolation weights) to use in a periodic time-series ; do not divide by
391       time-step to convert to integer:
392       - this fixes case where externForcingPeriod is not multiple of time-step
393          (Thanks to Christopher L. Wolfe)
394       - this fixes case where externForcingPeriod is an odd multiple of time-step
395         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
396      store index of time-record which is currently loaded:
397       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
398       - needed for the adjoint but not yet used because of extensive recomputations;
399         (to be fixed soon)
400    
401    checkpoint62v (2011/04/02)
402    o verification/1D_ocean_ice_column added to test Ian Fenty's
403      pkg/seaice_growth.F modifications for improving sea ice code differentiability
404    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
405      (new velocity statistics after changing maskInW & maskInS definition)
406    o pkg/generic_advdiff with OBCS:
407      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
408      equivalent to assumption of no tracer gradient outside the OB region.
409      This will affect the results if using obcs+biharmonic diffusion.
410      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
411    o pkg/obcs:
412      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
413      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
414      in Interior region. No impact on solution but affects Velocity monitor stats.
415    o pkg/ptracers (adjoint)
416      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
417      tape file for each tracer
418    o model/inc/src and pkg/autodiff: add parameters that allow to turn
419      of parts of the adjoint code at run time. For now, there are only
420      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
421      parameters are set in data.pkg.
422      This is the lazy coward's version of doing this, but still useful for
423      debugging. In order to do it right, everything needs to be moved to
424      pkg/autodiff.
425    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
426      the end; this fixes the adjoint balancing code for open boundaries.
427    o pkg/ctrl:
428      - change behavior of xx_${varname}period to be analogous to exf-conventions:
429        xx_${varname}period =   0.,  means time-independent control part
430        xx_${varname}period = -12., means one-year-periodic monthly control part
431      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
432        clean up ctrl_init a little, remove unused variables
433      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
434      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
435    
436    checkpoint62u (2011/03/15)
437    o model/src:
438      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
439        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
440      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
441        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
442    o pkg/ctrl/obcs/ecco:
443      - remove obsolete, unused, and partially broken code:
444        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
445        ALLOW_CTRL_OBCS_BALANCE
446      - put a stop statement into ecco/cost_obcsvol.F, but also add
447        cost_obcsvol to ecco_ad_diff.list
448    o pkg/ecco: fix counting cost function contributions for obcs (code
449      by Matt M.) and diffkr for diagnostics
450    o pkg/ecco, pkg/ctrl, pkg/grdchk:
451      add cost penalty terms for initial uvel, vvel, eta controls
452      and I/O for prior error files
453    o pkg/mdsio:
454       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
455       (new argument) to check for tiled file in mdsioLocalDir : this fix the
456       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
457    o pkg/ctrl:
458     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
459       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
460       unused and superfluous variables
461     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
462    o pkg/ecco
463     - enable adjoint of Stevens OB
464    o pkg/ctrl/ecco/grdchk:
465      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
466        Fortunately, we do not have any tests for the numerous cpp-flagged
467        option of "obcs as control parameters" so we will never know
468        if this is an improvement (but at least now things compile).
469      - remove an obsolete initialization from ecco_cost_init_barfiles.F
470      - fix some problems within never used ifdefs to make the code compile
471    o pkg/obcs:
472     - Refine Interior mask definition to work with more complex OB (e.g.
473       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
474       read in Interior mask from file. Check if Interior mask is consistent
475       with OB list of indices.
476    o pkg/seaice
477     - beginning code for a seaice tracer package,
478       but currently only used for seaice age: SEAICE_AGE
479       SEAICE_num = 4
480       iTracer = 1: area-weighted ice age
481               = 2: volume-weighted ice age
482               = 3, 4: template for one-year vs. multi-year ice
483       data.seaice has new namelist SEAICE_PARM03 for arrays related to
484       SEAICE_num
485    
486    checkpoint62t (2011/03/05)
487    o pkg/obcs:
488     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
489       then normal component. This ensures that the normal component is set
490       correctly even when it conficts with tangential setting from an other OB.
491       Affects results of test-experiment seaice_obcs: update the output.txt
492    o pkg/obcs:
493     - add code to monitor statistics of dynamical fields at OB.
494     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
495       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
496       - change default: balance the Net inflow through all OB (instead of balancing
497         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
498     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
499       to match Nortern OB inflow (OBCS_balanceFacN=0).
500    o pkg/seaice:
501     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
502    o pkg/seaice (seaice_growth v 1.113):
503     - reverting seaice_growth to v 1.111 in order to have code with exact bit
504       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
505       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
506       runtime flag SEAICEareaFormula is kept but is inactive
507    o model/src:
508     - add new param to scale curvilinear grid distance and area when using
509       a different sphere radius from the grid-files.
510     - test/check multi-threads EXCH applied to local variable (cg2d_x)
511    o adjoint:
512     - enable adjoint of Stevens OB
513     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
514       (a bit delicate because of potentially modified adj. common block structure;
515       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
516    
517    checkpoint62s (2011/02/15)
518    o pkg/seaice (seaice_growth v 1.112):
519     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
520       computing the ice cover tendency from effective thickness tendencies. Include
521       Ian Fenty's formula.
522     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
523       SEAICEareaFormula.
524     - simplify notations for the various d_HEFF/d_AREA terms.
525    o pkg/gmredi:
526     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
527       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
528       add a verification test-run (front_relax.bvp) to test GM_useBVP.
529    o pkg/seaice (seaice_growth v 1.111):
530     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
531     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
532       also melt ice.
533    o pkg/seaice:
534     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
535     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
536    o pkg/cheapaml:
537     - from Nico Wienders: New version of this package.
538    o pkg/flt:
539     - add CPP options to prevent floats to re-enter the opposite side of
540       a periodic domain (default: keep periodicity)
541    o pkg/gmredi:
542     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
543       (needed for multi-dim advection).
544     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
545    o model/src:
546     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
547    o tutorial_tracer_adjsens
548     - extend to NLFS and replace maskC by hFacC
549       (change reference output accordingly)
550    
551    checkpoint62r (2011/01/24)
552    o testreport:
553     - add option -deloutp (-do) to remove output file after successful run
554     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
555       extract exact list of procs from this file ; adjust COMMAND by
556       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
557    o pkg/ecco: replace old ineffective way of penalizing deviations from
558      first guess (of obcs) with code by Matt Mazloff
559    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
560      exf/cal
561      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
562        and handle case of obcs?period == 0
563        Not affected by these changes: There is still an inconsistency in
564        the computation of start/endrec for the obcs variables for ALLOW_CAL
565        defined (see comment by Menemenlis, 7-Mar-2003)
566      - make S/R ctrl_get_gen_rec return something meaningful even if
567        ALLOW_CAL is not defined
568      - ctrl_getobcs?: simplify code so that it does not need to use
569                       S/R exf_swapfields
570    o testreport:
571       allow to test MPI with different number of processors for each experiment:
572       create file "SIZE.h.mpi" in each build dir.
573       Note: update of "-command" argument not yet implemented.
574    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
575      alleviate the need for additional 3D tapes when using
576      the non-inear free surface in the adjoint. This is done
577      by adding an 'update' of hfacc etc. to their current
578      value at the beginning of forward_step.F.
579    o pkg/seaice
580      seaice_lsr: move stress-divergence computations out of outer pseudo-
581      timestepping loop
582    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
583      up, so that the calls of the ctrl_* subroutines are really at the end
584      of the routine.
585    o pkg/gmredi:
586      allow to specify a 2-D horizontal map and a 1-D vertical profil
587      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
588    o pkg/seaice:
589      move lsr iterations from seaice_dynsolver to seaice_lsr.
590    o pkg/seaice:
591      reduce memory footprint of seaice mutldim advection tapes,
592      by using a 2D tape independent of the generic_advdiff ones,
593      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
594    
595    checkpoint62q (2010/12/29)
596    o model/src:
597      - check horizontal grid-spacing for unset or zero/negative values.
598      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
599    o pkg/flt:
600      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
601      - precision of input and output files set according to readBinaryPrec
602        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
603      - initial float position from tiled file was not converted to index space
604        (looks like a bug): fixed to make it similar to initial pos. global file.
605    o global_ocean.cs32x15:
606       change SIZE.h of AD set-up to get same tiling as with MPI.
607       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
608    o model/src:
609       add flag to control printing of domain fields (bathymetry, hFac ...) in
610       ini_mask_etc (call to plot_fieds_xy*).
611    o pkg/thsice:
612       if useEXF, some forcing fields are not valid in overlap: fixed by computing
613       over the interior only + apply EXCH at the end (like with SEAICE advection).
614    o pkg/mdsio:
615      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
616        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
617      - change barrier call for safe multi-threads access to 3-D shared buffer.
618      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
619      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
620        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
621    o pkg/flt:
622      - add fourth-order Runge-Kutta integration
623      - add basic exch2 support (only 1 facet supported so far!)
624    o pkg/mdsio+rw:
625      new S/R to read local (or tile independent) vector (read counterpart of
626       mds_writevec_loc, and front-end write_glvec_rl/rs).
627    o global_ocean.cs32x15: additional input_ad.seaice experiment
628        that uses pkg/seaice rather than pkg/thsice.
629        (using multidim advection for seaice)
630    o towards more F95 syntax for array specification in namelist:
631      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
632        of all verification experiments.
633           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
634          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
635      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
636    o global_ocean.cs32x15: additional input.seaice experiment
637        that uses pkg/seaice rather than pkg/thsice.
638    
639    checkpoint62p (2010/12/17)
640    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
641        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
642    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
643        allow for use of multim. advection in seaice adjoint.
644    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
645      - first attempt to close budgets by taking into account the freshwater
646        flux implied by the sublimation of snow and ice. So far only the
647        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
648        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
649    o eesupp/src:
650      new S/R with new option (NML_EXTENDED_F77) to change array specification
651      from F95 standard to commonly accepted extended F77 form.
652      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
653      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
654      for less tolerant f77 compiler (e.g., pgf77, g77).
655    o globalFiles:
656      commented out in parameter file "data" since it's not safe with MPI
657      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
658      in this case); no longer commented out in restart test (tst_2+2).
659    o add adTapeDir to specify a special directory where adjoint tapes are
660      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
661      and cannot be used together with mdsioLocalDir.
662    o nesting pkgs:
663      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
664      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
665      - add parameter files + utils dir + output from short run on beagle.
666    o pkg/seaice:
667        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
668    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
669      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
670    
671    checkpoint62o (2010/11/25)
672    o pkg/exf:
673      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
674    o pkg/seaice:
675      - seaice_ocean_stress: split a loop for better vectorization of the
676        adjoint code
677      - seaice_growth.F: fix bug in conservation of freshwater connected to
678        capping of heff, put contribution into d_HEFFbyNEG
679      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
680        by something more sensible (parameters that are what their name implies)
681      - change some defaults, so that by default exf-parameters are used for
682        things like rhoAir, cpAir,latent/sensible heat parameters, in order
683        to reproduce the old results, many data.seaice now contain funny values
684        for cpAir and latent heat of sublimation
685    o packages_readparms.F: move exf_readparms up in line so that
686        exf-parameters are visible for other packages (e.g. seaice)
687    o debugMode & debugLevel=2:
688      - differentiate between debugMode & debugLevel=2:
689        debugMode: controls printing of debug messages (sequence of S/R calls).
690        debugLevel: controls printing of algorithm intermediate results and stats.
691      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
692        => allows to print debug-stats without all sequence of call messages.
693      - switch control of debug print from debugLevel to debugMode in many S/R.
694    o pkg/obcs (obcs-sponge):
695        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
696        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
697    o pkg/generic_advdiff:
698      - record overlap minimum size for each advection scheme;
699      - refine criteria on overlap minimum size;
700      - check and stop (in gad_check) if overlap size is too small.
701    o pkg/obcs:
702      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
703        once, in ptracers_implicit.F)
704      - with seaice: remove test on empty file name in obcs_apply_seaice (always
705        apply OB values when tile has OB)
706    o model/src, coriolis setting:
707      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
708        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
709        files (selectCoriMap=3) with any grid.
710      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
711    o pkg/seaice/seaice_growth.F:
712        a few cosmetic changes that reduce the number of lines of code
713    o pkg/obcs: add boundary conditions following Stevens (1990)
714      - the code follows old MOM/NAOSIM code
715      - so far it is only implemented for the eastern and western boundaries
716        and NOT for pTracers
717    o pkg/rbcs:
718      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
719        beginning of the first rbcs forcing period.
720      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
721        offline package, i.e., one file per time, labeled by iteration number;
722        deltaTrbcs sets the timestep with which the data was generated;
723        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
724      - rbcsForcingCycle=0 makes forcing non-cyclic.
725      - make arithmetic safe for negative times and odd forcing periods.
726    
727    checkpoint62n (2010/11/09)
728    o pkg/seaice:
729        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
730    o pkg/obcs:
731       New S/R to copy tracer value from the OB location to narrow band region
732        (width = same as overlap) beyond the OB: preserve OB value (needed for
733        high-order scheme) which were overwritten by EXCH call if in overlap
734        region. Applied to theta, salt, ptracer and advected seaice variables.
735       With seaice: use maskInC in similar way as in gad_advection.F,
736        in seaice_advection.F and advect.F.
737       Update output of experiment seaice_obcs and change exp4 to test OBCS with
738        4th order Adv.Scheme. for pasive salt and ptracer.
739    o tools/genmake2:
740      - when looking for an optfile (not specified), only search for Fortran compiler
741        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
742      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
743        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
744      - set default for CPP to "cpp -traditional -P" (was the case without specifying
745        an optfile, but otherwise default was just "cpp".
746      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
747      - when "CC" is not set in the optfile, look for possible C compiler
748        (instead of just setting CC=cc)
749      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
750        => add a ".F" to ".o" rule for source files with no "#include" (such as
751           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
752      - move gfortran before g77 in list of possible Fortran compiler (consistent
753        with reference compiler switch from g77 to gfortran)
754    o pkg/seaice:
755      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
756        seaice_check that stops the model, when the CPP flag is used.
757      o seaice_growth.F: make capping of ice volume conserving by returning the
758        capped ice as freshwater to EmPmR. This does not change the verification
759        experiments but will change runs where the capping is acutally active
760    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
761      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
762         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
763         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
764    o tools/genmake2:
765      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
766      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
767      - clean previous genmake log files before anything else.
768      - change Makefile to remove testreport log files (*.tr_log) and genmake log
769        files only with "CLEAN" target (instead of "Clean");
770    o pkg/generic_advdiff:
771      Change OBCS in multiDim advection (gad_advection.F):
772       Use maskInC to prevent intermediate update of tracer-field in OB regions,
773       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
774       which were applying future time-step OB values.
775      This way, all explicit calculations use current-time-step OB values
776       (simpler and more consistent).
777      Affects results when set-up uses time-varying OBC and multi-dim advection;
778       update output of experiment seaice_obcs.
779    o pkg/seaice:
780      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
781       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
782         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
783      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
784       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
785       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
786    o pkg aim (2010/10/26):
787      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
788        formulation with obliquity, eccentricity, ... as run-time parameters,
789      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
790        upward shortwave radition at the surface (all-sky and clear-sky).
791    o pkg/obcs:
792      - writing sections with globalFiles=T does not work: switch to tiled-files
793        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
794      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
795      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
796    
797    checkpoint62m (2010/10/21)
798    o pkg/seaice: vectorize seaice_solve4temp.F
799      - move iterations loops outside of i/j-loops
800      - requires 2D arrays for TB and effConduct
801      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
802        modified in this routine
803      - a little bit of clean up, adjusting indentation, etc.
804      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
805        performance and '**TWO' by '**2' (because TWO is a float),
806        replaced ONE, ZERO
807    o eesupp/src:
808       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
809    o pkg/seaice/seaice_growth.F
810      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
811      merging process. The merged routine has two branches, and one activates the 'evolution'
812      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
813      In summary, here is what the '10/10 revision' did consist of
814        part 1: seaice_growth.F revisions 1.71 to 1.75
815          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
816            The emphasis here was on improving readability (e.g. by trying to use meaningful
817            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
818        part 1.5:
819          - revising the lab_sea experiment to make it a more useful (i.e. stable
820            and representative of an actual model run). This was done by generating a
821            (winter) pickup to start from, switching back the main experiment dynamic
822            solver from evp to lsr, having one of the experiments use the free drift solution.
823        part 2: seaice_growth.F revisions 1.76 to 1.85
824          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
825          - Sorting out the various fields units and sign (set early on and reset at the end)
826            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
827            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
828          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
829            and simplifying logical expressions to further improve readibility.
830        part 3: seaice_growth.F revisions 1.86 to 1.89
831          - Re-organize the blocks of code more logically.
832          - Merging the '_if.F' pieces that add something new.
833    o pkg/thsice:
834      - vectorize thsice_solve4temp and thsice_get_exf.
835        Problem: thsice_solve4temp has an unvectorizable statement that
836        might also be problematic for TAF
837      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
838        does not change the verifcation experiment, but will change all
839        experiments that have this flag undefined (not tested in verification);
840        a little reorganization to save a few 2D fields and recomputations
841      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
842      - 2nd step:  fix some store dirs
843        o seems to work somewhat, i.e. using ifort but not g77
844        o likely cause are incomplete init. or recomputation
845        o start verification/global_ocean.cs32x15/input_ad.thsice
846    o pkg/obcs: add support for exch2
847      - the position of the boundary and prescribed values are specified using
848        a global domain with exch2 facets stacked
849        - in x for N,S boundaries (like W2_mapIO=-1)
850        - in y for E,W boundaries (so E,W boundaries do not overlap)
851    o pkg/mdsio: add support for writing global sections with exch2
852        file layout is as for obcs described above:
853        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
854        - for y-z sections, facets are stacked in y
855    o pkg/thsice:
856       - change a few routines for better vectorization: thsice_albedo.F,
857         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
858         not affected, but in particular the latter routine has changed
859         dramatically (not necessarily easier to read now).
860       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
861       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
862    o verification/lab_sea:
863      - overhaul of the forward model experiments. The main motivation
864        for this revision is that lab_sea has proven quite fragile (when
865        changing the sea-ice code, and switching platforms) to a point
866        when failures were very hard to attribute to specific code problems.
867      - the suspected reason for this fragility is noise amplification by evp so,
868        to start with, we decided to replace evp with lsr in the main experiment.
869      - the input.lsr experiment thus became obsolete and was removed.
870      - it was replaced with the input.fd experiment that uses an
871        analytical "free drift" solution as the ice velocity field.
872      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
873        will hopefully allow us to discriminate problems due to dynamic solvers
874        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
875        us to test additional options, along with the salt plume package.
876      - Finally a pickup was generated (at the end of a one year run) to
877        make the tests more representative of an actual model run. Previously
878        the tests starting point was a 1m thickness of ice everywhere.
879    o pkg/seaice:
880      - introducing S\R seaice_freedrift.F that compute the
881        analytical solution to an approximate ice momentum
882        equation (i.e. the simple stress/coriolis balance).
883      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
884        of the free drift velocity field, and enable its use.
885        To actually use the free drift solution as the model ice
886        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
887    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
888    
889    checkpoint62l (2010/10/04)
890    o pkg/seaice:
891      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
892      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
893       version (with USE_ORIGINAL_SBI undef);
894    o add hooks for new packages OASIS, the package will follow
895      (hooks exclude the seaice pkg for now)
896    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
897      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
898      rather than mdsio_readvector.F/mdsio_writevector.F, within
899      adread_adwrite.F to read/write adjoint-related tapes to disk.
900    o eesupp and pkg/mdsio: ALLOW_WHIO
901      Option to write/read 2D fields to files including tiles halos.
902      The main purpose is for adjoint related "tape I/O".
903      The secondary purpose is for debugging phases.
904      A word on those rather specifically intended purposes.
905      The code was meant to be stripped down to the bare minimum.
906      Typically, there is a unique and basic mapping to the global
907      buffer (tile by tile, then proc by proc, then level by level), and
908      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
909      meant to generate user friendly outputs of various shapes and forms.
910      Rather it is intended, for the knowledgeabale developers,
911      to be largely independent of the many mdsio options, to allow
912      outputs of tiles+halos in debugging phases and in adjoint runs,
913      and to allow some flexibility in tuning (adoint) I/O depending on each
914      file system behavior. With regard to tuning, most of the potential knobs
915      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
916      to specify directories, to specify the typical size of I/O calls, etc.)
917      are not yet included, and will be added if they prove useful.
918    o pkg/seaice:
919       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
920    o pkg/seaice:
921       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
922       code (seaice_budget_ice_if.F) which enable to recover old standard
923       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
924       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
925    o model/src (rStar):
926       use simple average (not area weighted) of rStarFac at U,V point when using
927       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
928       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
929    
930    checkpoint62k (2010/09/17)
931    o adjoint
932       * changed verification/global_ocean.cs32x15 ; adjoint now tests
933         Adams-Bashforth 3 + NLFS + RSTAR
934       * some more modifs required for ECCO-GODAE v4
935    o pkg/seaice
936       add SEAICE_AGE_VOL option to use volume instead of area for
937       integrating SEAICE_AGE
938  o model/src:  o model/src:
939     first check-in of sigma & hybrid-sigma coordinate code ; also includes     first check-in of sigma & hybrid-sigma coordinate code ; also includes
940     non-linear free-surface parts ; but pressure-gradient not yet coded.     non-linear free-surface parts ; but pressure-gradient not yet coded.
# Line 273  o tools/build_options: Line 1204  o tools/build_options:
1204      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1205  o pkg/ecco  o pkg/ecco
1206    - allow user defined cost function contributions    - allow user defined cost function contributions
1207          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1208          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1209    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1210        the two options are complementary.        the two options are complementary.
1211  o pkg/smooth  o pkg/smooth
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