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revision 1.1271 by mlosch, Mon May 17 14:23:42 2010 UTC revision 1.1464 by ifenty, Fri Jun 24 15:51:59 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/exf/exf_bulk_largeyeager04.F: rewrite for better vectorization, changes  o verification 1D_ocean_ice_column:
8       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
9       update results
10    o pkg/diagnostics:
11     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
12       which are not filled-up but computed from other diags ; In this case, the mate
13       diag points to the primary (filled-up) diag to used for post processing.
14     - Update Velocity-potential computation using post-processed diag framework.
15     ==> Change the ordering of fields and time-periods in MDS output file
16       when using periodic averaging: now writes one time record with the full set
17       of fields for this time period, then the next time reccord (it used to be
18       one field with the full set of time records then the next field).
19         Note: this is now similar to NetCDF (MNC) output file. <==
20     - Extend the use of "missing_value" setting from data.diagnostics for the case
21       of counter-diagnostics (where fraction-weight is zero). This applies both to
22       MNC and MDS output files.
23    
24    checkpoint62z (2011/06/21)
25    o adjoint monitor:
26     - Add adjoint monitor output for packages exf, seaice
27       and update relevant testreport output
28    o pkg/seaice:
29     - re-order diags inits so that they appear in order in available_diagnostics.log
30     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
31       area/heff/hsnow preceeding thermodynamic growth/melt.
32     - modified diag: SIdA; output actual effect, as the description states.
33     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
34     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
35       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
36        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
37     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
38     - added diagnostics for seaice generic tracers (SItr*).
39     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
40     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
41     I. Fenty: 18-Jun-2011:
42     Minor changes to seaice package:
43     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
44        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
45       - Differentiated "regularization variables" from "floor variables"
46        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
47        * hiceMin became SEAICE_hice_reg (old hiceMin)
48          (with _reg meaning regularization variable)
49       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
50        so as to ensure energy conservation when going between phases
51      - A22 was not used anywhere
52     2) Changed regularization procedure for heffActual and hsnowActual to ensure
53        well-boundedness and smooth adjoint in seaice_growth.F
54     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
55        because the old regularization always set heffActual >= 0.05 cm
56     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
57        on AREA when HEFF > 0.
58      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
59        requiring that DISABLE_AREA_FLOOR *not* be defined
60     Affected verifications:
61      - 1D_ocean_ice_column (output.txt output_adm.txt)
62      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
63    o pkg/diagnostics:
64      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
65      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
66        (was _RL, now integer) with option = 0 to retrieve all levels.
67      - add pieces of code to compute velocity potential at each level (new diagnostics
68        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
69        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
70      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
71        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
72        and in diagnostics_fract_fill.F (do not need a valid pointer for the
73        diagnostics counter-mate); check that definition of counter-diagnostic
74        includes a valid counter-mate (in diagnostics_set_levels.F).
75    o model/src (rStar):
76      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
77        affect solution only if z* with full pressure in EOS;
78        update output of test-exp global_ocean.90x40x15.
79    o pkg/seaice:
80      - introduce siEps=1e-5 parameter
81      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
82      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
83      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
84        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
85        as well as ice cover age and ridging index (attached to AREA).
86        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
87        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
88        Up to SItrMaxNum=3 tracers can be used simultaneously.
89    o pkg/salt_plume:
90      -introduce SPsalFRAC run time parameter that sets the fraction of the
91       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
92       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
93    o model debug options:
94      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
95        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
96      - Refine debug-msg printing selection (3 new levels):
97        debugMode  : controls printing of debug messages (sequence of S/R calls).
98        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
99         debLevZero =  0 ; /* level of disabled aux. msg printing */
100         debLevA =  1 ; /* level of minimum  aux. msg printing */
101         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
102         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
103         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
104         debLevE =  5 ; /* level of extensive debug printing */
105        New debugLevel default: with default debugMode value (=F),
106          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
107          and if debugMode=T, default debugLevel = 4 (debLevD).
108        Relation with previous settings:
109         debLevB (=2) corresponds to former debLevA (=1)
110         debLevD (=4) corresponds to former debLevB (=2)
111        Note:
112         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
113         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
114            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
115      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
116        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
117    o pkg/obcs:
118      - change OBCSfixTopo default from True to False (should not change the results);
119        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
120    o pkg/thsice:
121      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
122        2nd layer seaice sublimation (unlikely to happen)
123      - use Interior mask for OBCS in thsice_advection.F (similar to what is
124        done in gad_advection & seaice_advection).
125    o adjoint:
126      bug fix spotted by Gael Forget:
127      seaice_advection and thsice_advection still had
128      legacy CPP options to avoid CS corner updates for adjoint
129    o pkg/seaice:
130      => Change some of the defaults (2011/05/29):
131         - change SEAICEuseFluxForm default (from False to True)
132         - change DIFF1 default (from 0.004 m/s to 0. m/s)
133         And print warnings if DIFF1 is not set in data.seaice and centered
134          avection scheme is used without any diffusion.
135      also:
136      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
137      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
138      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
139        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
140        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
141      update results of test exp.:
142         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
143             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
144             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
145         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
146         seaice_obcs: output (SEAICEuseFluxForm=T)
147      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
148          for standard fwd & AD lab_sea tests (to keep the same output).
149    o pkg/seaice/seaice_growth.F:
150      - use Ian Fenty's capping formulas for actual ice
151      thickness thoughout EVOLUTION branch.
152      - put treatment pathological case #2) in CPP brackets
153      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
154      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
155    o pkg/seaice:
156      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
157      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
158      also pass fac as a param, which can be 1. (to update the tendency
159      field) or the time step (to update the field itself).
160      - seaice_advdiff.F: for multidim, call seaice_diffusion with
161      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
162      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
163      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
164      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
165    o pkg/seaice:
166      diffusion with centered advection scheme (diffus.F & advect.F):
167      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
168        to just compute the laplacian of input-field.
169      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
170      - fix flux-form version in diffus.F to conserve tracer.
171      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
172       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
173    
174    checkpoint62y (2011/05/26)
175    o pkg/seaice:
176     - seaice_growth.F : in EVOLUTION branch, always include
177       a_QSWbyATM_cover in qnet (as it should be).
178     - verification/global_ocean.cs32x15 : update results accordingly
179       (output.seaice.txt output_adm.seaice.txt).
180    o pkg/seaice + obcs:
181     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
182       equivalent of assuming no tracer gradient outside the OB region.
183       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
184     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
185       after changes above);
186     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
187       only at OB location (instead of over a band of OLx width).
188    o pkg/seaice:
189     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
190       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
191    o pkg/obcs:
192      - split header file "OBCS.h" into 4 separated files:
193        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
194       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
195         (contain no conditional statement which depends on OBCS options).
196      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
197        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
198    o ctrl, cost, grdchk & autodiff pkgs:
199      - make options file more standard (like other {PKG}_OPTIONS.h file but
200        with AD_CONFIG.h); clean-up some of the included header files.
201    o pkg/obcs:
202      - do not mask tracer when applying OB (tracer == 0 could generate problems)
203      - apply tracer OB values to tracer field only at OB location (instead of
204        over a band of OLx width)
205      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
206      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
207        obcs_apply_tloc.F & obcs_apply_sloc.F
208    o obcs in model/src:
209      - call OBCS_APPLY_W only if NonHydrostatic.
210      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
211      - reset dEtaHdt and wVel to zero outside OB interior region ;
212      - leave tracer unchanged outside OB interior region: This has no effect
213        on the solution but just to prevent unrealistic tracer value outside OB.
214      - zero out velocity outside OB interior region: This has no effect on
215        the solution but just to prevent unrealistic velocity outside OB.
216    o obcs and non-lin free-surf:
217       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
218       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
219       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
220       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
221       update results of test-exp. exp4(nlfs).
222    o exp4 (nlfs) test-exp:
223       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
224       with NonLin-FreeSurf); update output.nlfs.txt
225    o obcs and 2d/3d solver norm:
226       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
227       and outside OB interior region (will allow to place OB further inside the
228       domain). Depending on the domain, can affects cg2d-Norm (previous
229       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
230       and cg3d-Norm (previous Norm was computed before canceling OB terms),
231       e.g. in tutorial_plume_on_slope.
232      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
233    o pkg rbcs:
234      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
235      - add capability to apply relaxation to horizontal velocity uVel & vVel.
236    o pkg/grdchk: add gradient check for control variable xx_shifwflx
237    o pkg/shelfice/shelfice_init_fixed.F
238      fix CPP-flag combinations
239    o pkg/seaice: Merge iceage code of Pierre Rampal
240      * update/change/correct ice age calculations
241      * add age updates for pathological cases
242      Probably needs more testing...
243    
244    checkpoint62x (2011/05/13)
245    o pkg/mom_vecinv:
246       high-order vorticity scheme: use interior masks (maskInW & S)
247       to zero-out (outside OB) gradient of vorticity.
248    o verification exp.:
249       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
250       hs94.128x64x5 and seaice_obcs ; update results.
251    o pkg/obcs:
252      fix bug in OBeta for YZ sections in obcs_exf_load.F
253    o pkg/ctrl, pkg/shelfice, and optim:
254      - add new control variable xx_shifwflx (fresh water flux underneath ice
255        shelves). This is almost as tedious as obcs-ctrl, because the
256        variables needs its own mask.
257      - add a cost function term that penalizes the deviation of xx_shifwflx
258        from the first guess (zero) in analogy to other control variables
259    o pkg/shelfice:
260      - start basic adjoint
261    o pkg/ctrl:
262      - remove extra 2D field "for good measure" when initializing in
263        ctrl_set_globfld_[xy/xz/yz].F
264      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
265      - improve error messages in ctrl_set_unpack_*
266    o OBC implementation in momentum:
267       use interior masks (maskInC,W & S) in momentum S/R:
268       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
269       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
270       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
271       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
272       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
273        (and also with Leith/Smagorinsky harmonic-viscosity).
274       Update output of experiment dome and exp4 (+nlfs).
275    o exp4 test-exp:
276      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
277        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
278        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
279        time-varying OB at Western-side for wVel (NonHyd); update output.
280      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
281        and biharmonic-viscosity ; also use prescribed time varying OB.
282    o pkg/obcs:
283      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
284    o model/src:
285      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
286      - initialise startTime & nIter0 with unlikely values: allows to set one
287        from the other without ambiguity.
288    o seaice_obcs test-exp.:
289      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
290    o pkg/obcs:
291      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
292        no longer needed with maskInC,W,S in pkg/generic_advdiff.
293    o pkg/seaice:
294      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
295        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
296      - fixed bug in the initialization of sea ice salinity variable HSALT
297        in seaice_init_varia.F  (removed dependence on ICE2WATR)
298    o fizhi-cs test exp.:
299       switch reference output convention for these 2 non-standard test-exp,
300        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
301          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
302       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
303    o model/inc:
304      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
305        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
306    o pkg/seaice:
307      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
308    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
309      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
310        and initial HSALT
311    
312    checkpoint62w (2011/04/26)
313    o pkg/mom_fluxform:
314      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
315      - use parameter "sideDragFactor" in no-slip BC side-drag part.
316      - update output of exp. global_ocean.90x40x15
317    o pkg/mom_vecinv:
318      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
319    o update seaice exp.:
320      use more consistent parameter values (remove "backward compatability only":
321       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
322      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
323       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
324    o update test-exp global_ocean.90x40x15:
325      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
326      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
327      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
328      o turn on zStar & viscA4 in standard set-up (dir input/)
329        and update output files: output.txt & output.dwnslp.txt
330    o new AD-test experiment: obcs_ctrl
331      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
332    o pkg/dic:
333      fix two bugs in handling water vapour pressure in carbonate chemistry
334      and air-sea fluxes. Found by Val Bennington and Galen McKinley
335      (add DIC Option = WATERVAP_BUG to recover old results)
336      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
337    o adding allowInteriorFreezing option to check for water below freezing point
338      at depth and bring the negative heat anomaly to the surface level
339    o pkgs _fields_load:
340      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
341      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
342        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
343        rbcs to get interpolation weights and time reccord number.
344      - fix multi-threading in aim_fields_load.F
345      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
346    o external_fields_load:
347      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
348       interpolation weights) to use in a periodic time-series ; do not divide by
349       time-step to convert to integer:
350       - this fixes case where externForcingPeriod is not multiple of time-step
351          (Thanks to Christopher L. Wolfe)
352       - this fixes case where externForcingPeriod is an odd multiple of time-step
353         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
354      store index of time-record which is currently loaded:
355       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
356       - needed for the adjoint but not yet used because of extensive recomputations;
357         (to be fixed soon)
358    
359    checkpoint62v (2011/04/02)
360    o verification/1D_ocean_ice_column added to test Ian Fenty's
361      pkg/seaice_growth.F modifications for improving sea ice code differentiability
362    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
363      (new velocity statistics after changing maskInW & maskInS definition)
364    o pkg/generic_advdiff with OBCS:
365      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
366      equivalent to assumption of no tracer gradient outside the OB region.
367      This will affect the results if using obcs+biharmonic diffusion.
368      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
369    o pkg/obcs:
370      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
371      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
372      in Interior region. No impact on solution but affects Velocity monitor stats.
373    o pkg/ptracers (adjoint)
374      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
375      tape file for each tracer
376    o model/inc/src and pkg/autodiff: add parameters that allow to turn
377      of parts of the adjoint code at run time. For now, there are only
378      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
379      parameters are set in data.pkg.
380      This is the lazy coward's version of doing this, but still useful for
381      debugging. In order to do it right, everything needs to be moved to
382      pkg/autodiff.
383    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
384      the end; this fixes the adjoint balancing code for open boundaries.
385    o pkg/ctrl:
386      - change behavior of xx_${varname}period to be analogous to exf-conventions:
387        xx_${varname}period =   0.,  means time-independent control part
388        xx_${varname}period = -12., means one-year-periodic monthly control part
389      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
390        clean up ctrl_init a little, remove unused variables
391      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
392      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
393    
394    checkpoint62u (2011/03/15)
395    o model/src:
396      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
397        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
398      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
399        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
400    o pkg/ctrl/obcs/ecco:
401      - remove obsolete, unused, and partially broken code:
402        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
403        ALLOW_CTRL_OBCS_BALANCE
404      - put a stop statement into ecco/cost_obcsvol.F, but also add
405        cost_obcsvol to ecco_ad_diff.list
406    o pkg/ecco: fix counting cost function contributions for obcs (code
407      by Matt M.) and diffkr for diagnostics
408    o pkg/ecco, pkg/ctrl, pkg/grdchk:
409      add cost penalty terms for initial uvel, vvel, eta controls
410      and I/O for prior error files
411    o pkg/mdsio:
412       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
413       (new argument) to check for tiled file in mdsioLocalDir : this fix the
414       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
415    o pkg/ctrl:
416     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
417       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
418       unused and superfluous variables
419     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
420    o pkg/ecco
421     - enable adjoint of Stevens OB
422    o pkg/ctrl/ecco/grdchk:
423      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
424        Fortunately, we do not have any tests for the numerous cpp-flagged
425        option of "obcs as control parameters" so we will never know
426        if this is an improvement (but at least now things compile).
427      - remove an obsolete initialization from ecco_cost_init_barfiles.F
428      - fix some problems within never used ifdefs to make the code compile
429    o pkg/obcs:
430     - Refine Interior mask definition to work with more complex OB (e.g.
431       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
432       read in Interior mask from file. Check if Interior mask is consistent
433       with OB list of indices.
434    o pkg/seaice
435     - beginning code for a seaice tracer package,
436       but currently only used for seaice age: SEAICE_AGE
437       SEAICE_num = 4
438       iTracer = 1: area-weighted ice age
439               = 2: volume-weighted ice age
440               = 3, 4: template for one-year vs. multi-year ice
441       data.seaice has new namelist SEAICE_PARM03 for arrays related to
442       SEAICE_num
443    
444    checkpoint62t (2011/03/05)
445    o pkg/obcs:
446     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
447       then normal component. This ensures that the normal component is set
448       correctly even when it conficts with tangential setting from an other OB.
449       Affects results of test-experiment seaice_obcs: update the output.txt
450    o pkg/obcs:
451     - add code to monitor statistics of dynamical fields at OB.
452     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
453       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
454       - change default: balance the Net inflow through all OB (instead of balancing
455         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
456     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
457       to match Nortern OB inflow (OBCS_balanceFacN=0).
458    o pkg/seaice:
459     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
460    o pkg/seaice (seaice_growth v 1.113):
461     - reverting seaice_growth to v 1.111 in order to have code with exact bit
462       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
463       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
464       runtime flag SEAICEareaFormula is kept but is inactive
465    o model/src:
466     - add new param to scale curvilinear grid distance and area when using
467       a different sphere radius from the grid-files.
468     - test/check multi-threads EXCH applied to local variable (cg2d_x)
469    o adjoint:
470     - enable adjoint of Stevens OB
471     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
472       (a bit delicate because of potentially modified adj. common block structure;
473       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
474    
475    checkpoint62s (2011/02/15)
476    o pkg/seaice (seaice_growth v 1.112):
477     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
478       computing the ice cover tendency from effective thickness tendencies. Include
479       Ian Fenty's formula.
480     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
481       SEAICEareaFormula.
482     - simplify notations for the various d_HEFF/d_AREA terms.
483    o pkg/gmredi:
484     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
485       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
486       add a verification test-run (front_relax.bvp) to test GM_useBVP.
487    o pkg/seaice (seaice_growth v 1.111):
488     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
489     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
490       also melt ice.
491    o pkg/seaice:
492     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
493     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
494    o pkg/cheapaml:
495     - from Nico Wienders: New version of this package.
496    o pkg/flt:
497     - add CPP options to prevent floats to re-enter the opposite side of
498       a periodic domain (default: keep periodicity)
499    o pkg/gmredi:
500     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
501       (needed for multi-dim advection).
502     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
503    o model/src:
504     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
505    o tutorial_tracer_adjsens
506     - extend to NLFS and replace maskC by hFacC
507       (change reference output accordingly)
508    
509    checkpoint62r (2011/01/24)
510    o testreport:
511     - add option -deloutp (-do) to remove output file after successful run
512     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
513       extract exact list of procs from this file ; adjust COMMAND by
514       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
515    o pkg/ecco: replace old ineffective way of penalizing deviations from
516      first guess (of obcs) with code by Matt Mazloff
517    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
518      exf/cal
519      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
520        and handle case of obcs?period == 0
521        Not affected by these changes: There is still an inconsistency in
522        the computation of start/endrec for the obcs variables for ALLOW_CAL
523        defined (see comment by Menemenlis, 7-Mar-2003)
524      - make S/R ctrl_get_gen_rec return something meaningful even if
525        ALLOW_CAL is not defined
526      - ctrl_getobcs?: simplify code so that it does not need to use
527                       S/R exf_swapfields
528    o testreport:
529       allow to test MPI with different number of processors for each experiment:
530       create file "SIZE.h.mpi" in each build dir.
531       Note: update of "-command" argument not yet implemented.
532    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
533      alleviate the need for additional 3D tapes when using
534      the non-inear free surface in the adjoint. This is done
535      by adding an 'update' of hfacc etc. to their current
536      value at the beginning of forward_step.F.
537    o pkg/seaice
538      seaice_lsr: move stress-divergence computations out of outer pseudo-
539      timestepping loop
540    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
541      up, so that the calls of the ctrl_* subroutines are really at the end
542      of the routine.
543    o pkg/gmredi:
544      allow to specify a 2-D horizontal map and a 1-D vertical profil
545      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
546    o pkg/seaice:
547      move lsr iterations from seaice_dynsolver to seaice_lsr.
548    o pkg/seaice:
549      reduce memory footprint of seaice mutldim advection tapes,
550      by using a 2D tape independent of the generic_advdiff ones,
551      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
552    
553    checkpoint62q (2010/12/29)
554    o model/src:
555      - check horizontal grid-spacing for unset or zero/negative values.
556      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
557    o pkg/flt:
558      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
559      - precision of input and output files set according to readBinaryPrec
560        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
561      - initial float position from tiled file was not converted to index space
562        (looks like a bug): fixed to make it similar to initial pos. global file.
563    o global_ocean.cs32x15:
564       change SIZE.h of AD set-up to get same tiling as with MPI.
565       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
566    o model/src:
567       add flag to control printing of domain fields (bathymetry, hFac ...) in
568       ini_mask_etc (call to plot_fieds_xy*).
569    o pkg/thsice:
570       if useEXF, some forcing fields are not valid in overlap: fixed by computing
571       over the interior only + apply EXCH at the end (like with SEAICE advection).
572    o pkg/mdsio:
573      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
574        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
575      - change barrier call for safe multi-threads access to 3-D shared buffer.
576      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
577      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
578        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
579    o pkg/flt:
580      - add fourth-order Runge-Kutta integration
581      - add basic exch2 support (only 1 facet supported so far!)
582    o pkg/mdsio+rw:
583      new S/R to read local (or tile independent) vector (read counterpart of
584       mds_writevec_loc, and front-end write_glvec_rl/rs).
585    o global_ocean.cs32x15: additional input_ad.seaice experiment
586        that uses pkg/seaice rather than pkg/thsice.
587        (using multidim advection for seaice)
588    o towards more F95 syntax for array specification in namelist:
589      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
590        of all verification experiments.
591           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
592          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
593      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
594    o global_ocean.cs32x15: additional input.seaice experiment
595        that uses pkg/seaice rather than pkg/thsice.
596    
597    checkpoint62p (2010/12/17)
598    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
599        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
600    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
601        allow for use of multim. advection in seaice adjoint.
602    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
603      - first attempt to close budgets by taking into account the freshwater
604        flux implied by the sublimation of snow and ice. So far only the
605        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
606        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
607    o eesupp/src:
608      new S/R with new option (NML_EXTENDED_F77) to change array specification
609      from F95 standard to commonly accepted extended F77 form.
610      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
611      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
612      for less tolerant f77 compiler (e.g., pgf77, g77).
613    o globalFiles:
614      commented out in parameter file "data" since it's not safe with MPI
615      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
616      in this case); no longer commented out in restart test (tst_2+2).
617    o add adTapeDir to specify a special directory where adjoint tapes are
618      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
619      and cannot be used together with mdsioLocalDir.
620    o nesting pkgs:
621      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
622      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
623      - add parameter files + utils dir + output from short run on beagle.
624    o pkg/seaice:
625        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
626    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
627      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
628    
629    checkpoint62o (2010/11/25)
630    o pkg/exf:
631      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
632    o pkg/seaice:
633      - seaice_ocean_stress: split a loop for better vectorization of the
634        adjoint code
635      - seaice_growth.F: fix bug in conservation of freshwater connected to
636        capping of heff, put contribution into d_HEFFbyNEG
637      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
638        by something more sensible (parameters that are what their name implies)
639      - change some defaults, so that by default exf-parameters are used for
640        things like rhoAir, cpAir,latent/sensible heat parameters, in order
641        to reproduce the old results, many data.seaice now contain funny values
642        for cpAir and latent heat of sublimation
643    o packages_readparms.F: move exf_readparms up in line so that
644        exf-parameters are visible for other packages (e.g. seaice)
645    o debugMode & debugLevel=2:
646      - differentiate between debugMode & debugLevel=2:
647        debugMode: controls printing of debug messages (sequence of S/R calls).
648        debugLevel: controls printing of algorithm intermediate results and stats.
649      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
650        => allows to print debug-stats without all sequence of call messages.
651      - switch control of debug print from debugLevel to debugMode in many S/R.
652    o pkg/obcs (obcs-sponge):
653        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
654        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
655    o pkg/generic_advdiff:
656      - record overlap minimum size for each advection scheme;
657      - refine criteria on overlap minimum size;
658      - check and stop (in gad_check) if overlap size is too small.
659    o pkg/obcs:
660      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
661        once, in ptracers_implicit.F)
662      - with seaice: remove test on empty file name in obcs_apply_seaice (always
663        apply OB values when tile has OB)
664    o model/src, coriolis setting:
665      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
666        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
667        files (selectCoriMap=3) with any grid.
668      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
669    o pkg/seaice/seaice_growth.F:
670        a few cosmetic changes that reduce the number of lines of code
671    o pkg/obcs: add boundary conditions following Stevens (1990)
672      - the code follows old MOM/NAOSIM code
673      - so far it is only implemented for the eastern and western boundaries
674        and NOT for pTracers
675    o pkg/rbcs:
676      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
677        beginning of the first rbcs forcing period.
678      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
679        offline package, i.e., one file per time, labeled by iteration number;
680        deltaTrbcs sets the timestep with which the data was generated;
681        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
682      - rbcsForcingCycle=0 makes forcing non-cyclic.
683      - make arithmetic safe for negative times and odd forcing periods.
684    
685    checkpoint62n (2010/11/09)
686    o pkg/seaice:
687        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
688    o pkg/obcs:
689       New S/R to copy tracer value from the OB location to narrow band region
690        (width = same as overlap) beyond the OB: preserve OB value (needed for
691        high-order scheme) which were overwritten by EXCH call if in overlap
692        region. Applied to theta, salt, ptracer and advected seaice variables.
693       With seaice: use maskInC in similar way as in gad_advection.F,
694        in seaice_advection.F and advect.F.
695       Update output of experiment seaice_obcs and change exp4 to test OBCS with
696        4th order Adv.Scheme. for pasive salt and ptracer.
697    o tools/genmake2:
698      - when looking for an optfile (not specified), only search for Fortran compiler
699        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
700      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
701        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
702      - set default for CPP to "cpp -traditional -P" (was the case without specifying
703        an optfile, but otherwise default was just "cpp".
704      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
705      - when "CC" is not set in the optfile, look for possible C compiler
706        (instead of just setting CC=cc)
707      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
708        => add a ".F" to ".o" rule for source files with no "#include" (such as
709           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
710      - move gfortran before g77 in list of possible Fortran compiler (consistent
711        with reference compiler switch from g77 to gfortran)
712    o pkg/seaice:
713      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
714        seaice_check that stops the model, when the CPP flag is used.
715      o seaice_growth.F: make capping of ice volume conserving by returning the
716        capped ice as freshwater to EmPmR. This does not change the verification
717        experiments but will change runs where the capping is acutally active
718    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
719      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
720         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
721         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
722    o tools/genmake2:
723      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
724      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
725      - clean previous genmake log files before anything else.
726      - change Makefile to remove testreport log files (*.tr_log) and genmake log
727        files only with "CLEAN" target (instead of "Clean");
728    o pkg/generic_advdiff:
729      Change OBCS in multiDim advection (gad_advection.F):
730       Use maskInC to prevent intermediate update of tracer-field in OB regions,
731       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
732       which were applying future time-step OB values.
733      This way, all explicit calculations use current-time-step OB values
734       (simpler and more consistent).
735      Affects results when set-up uses time-varying OBC and multi-dim advection;
736       update output of experiment seaice_obcs.
737    o pkg/seaice:
738      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
739       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
740         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
741      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
742       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
743       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
744    o pkg aim (2010/10/26):
745      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
746        formulation with obliquity, eccentricity, ... as run-time parameters,
747      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
748        upward shortwave radition at the surface (all-sky and clear-sky).
749    o pkg/obcs:
750      - writing sections with globalFiles=T does not work: switch to tiled-files
751        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
752      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
753      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
754    
755    checkpoint62m (2010/10/21)
756    o pkg/seaice: vectorize seaice_solve4temp.F
757      - move iterations loops outside of i/j-loops
758      - requires 2D arrays for TB and effConduct
759      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
760        modified in this routine
761      - a little bit of clean up, adjusting indentation, etc.
762      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
763        performance and '**TWO' by '**2' (because TWO is a float),
764        replaced ONE, ZERO
765    o eesupp/src:
766       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
767    o pkg/seaice/seaice_growth.F
768      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
769      merging process. The merged routine has two branches, and one activates the 'evolution'
770      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
771      In summary, here is what the '10/10 revision' did consist of
772        part 1: seaice_growth.F revisions 1.71 to 1.75
773          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
774            The emphasis here was on improving readability (e.g. by trying to use meaningful
775            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
776        part 1.5:
777          - revising the lab_sea experiment to make it a more useful (i.e. stable
778            and representative of an actual model run). This was done by generating a
779            (winter) pickup to start from, switching back the main experiment dynamic
780            solver from evp to lsr, having one of the experiments use the free drift solution.
781        part 2: seaice_growth.F revisions 1.76 to 1.85
782          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
783          - Sorting out the various fields units and sign (set early on and reset at the end)
784            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
785            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
786          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
787            and simplifying logical expressions to further improve readibility.
788        part 3: seaice_growth.F revisions 1.86 to 1.89
789          - Re-organize the blocks of code more logically.
790          - Merging the '_if.F' pieces that add something new.
791    o pkg/thsice:
792      - vectorize thsice_solve4temp and thsice_get_exf.
793        Problem: thsice_solve4temp has an unvectorizable statement that
794        might also be problematic for TAF
795      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
796        does not change the verifcation experiment, but will change all
797        experiments that have this flag undefined (not tested in verification);
798        a little reorganization to save a few 2D fields and recomputations
799      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
800      - 2nd step:  fix some store dirs
801        o seems to work somewhat, i.e. using ifort but not g77
802        o likely cause are incomplete init. or recomputation
803        o start verification/global_ocean.cs32x15/input_ad.thsice
804    o pkg/obcs: add support for exch2
805      - the position of the boundary and prescribed values are specified using
806        a global domain with exch2 facets stacked
807        - in x for N,S boundaries (like W2_mapIO=-1)
808        - in y for E,W boundaries (so E,W boundaries do not overlap)
809    o pkg/mdsio: add support for writing global sections with exch2
810        file layout is as for obcs described above:
811        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
812        - for y-z sections, facets are stacked in y
813    o pkg/thsice:
814       - change a few routines for better vectorization: thsice_albedo.F,
815         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
816         not affected, but in particular the latter routine has changed
817         dramatically (not necessarily easier to read now).
818       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
819       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
820    o verification/lab_sea:
821      - overhaul of the forward model experiments. The main motivation
822        for this revision is that lab_sea has proven quite fragile (when
823        changing the sea-ice code, and switching platforms) to a point
824        when failures were very hard to attribute to specific code problems.
825      - the suspected reason for this fragility is noise amplification by evp so,
826        to start with, we decided to replace evp with lsr in the main experiment.
827      - the input.lsr experiment thus became obsolete and was removed.
828      - it was replaced with the input.fd experiment that uses an
829        analytical "free drift" solution as the ice velocity field.
830      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
831        will hopefully allow us to discriminate problems due to dynamic solvers
832        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
833        us to test additional options, along with the salt plume package.
834      - Finally a pickup was generated (at the end of a one year run) to
835        make the tests more representative of an actual model run. Previously
836        the tests starting point was a 1m thickness of ice everywhere.
837    o pkg/seaice:
838      - introducing S\R seaice_freedrift.F that compute the
839        analytical solution to an approximate ice momentum
840        equation (i.e. the simple stress/coriolis balance).
841      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
842        of the free drift velocity field, and enable its use.
843        To actually use the free drift solution as the model ice
844        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
845    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
846    
847    checkpoint62l (2010/10/04)
848    o pkg/seaice:
849      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
850      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
851       version (with USE_ORIGINAL_SBI undef);
852    o add hooks for new packages OASIS, the package will follow
853      (hooks exclude the seaice pkg for now)
854    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
855      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
856      rather than mdsio_readvector.F/mdsio_writevector.F, within
857      adread_adwrite.F to read/write adjoint-related tapes to disk.
858    o eesupp and pkg/mdsio: ALLOW_WHIO
859      Option to write/read 2D fields to files including tiles halos.
860      The main purpose is for adjoint related "tape I/O".
861      The secondary purpose is for debugging phases.
862      A word on those rather specifically intended purposes.
863      The code was meant to be stripped down to the bare minimum.
864      Typically, there is a unique and basic mapping to the global
865      buffer (tile by tile, then proc by proc, then level by level), and
866      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
867      meant to generate user friendly outputs of various shapes and forms.
868      Rather it is intended, for the knowledgeabale developers,
869      to be largely independent of the many mdsio options, to allow
870      outputs of tiles+halos in debugging phases and in adjoint runs,
871      and to allow some flexibility in tuning (adoint) I/O depending on each
872      file system behavior. With regard to tuning, most of the potential knobs
873      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
874      to specify directories, to specify the typical size of I/O calls, etc.)
875      are not yet included, and will be added if they prove useful.
876    o pkg/seaice:
877       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
878    o pkg/seaice:
879       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
880       code (seaice_budget_ice_if.F) which enable to recover old standard
881       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
882       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
883    o model/src (rStar):
884       use simple average (not area weighted) of rStarFac at U,V point when using
885       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
886       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
887    
888    checkpoint62k (2010/09/17)
889    o adjoint
890       * changed verification/global_ocean.cs32x15 ; adjoint now tests
891         Adams-Bashforth 3 + NLFS + RSTAR
892       * some more modifs required for ECCO-GODAE v4
893    o pkg/seaice
894       add SEAICE_AGE_VOL option to use volume instead of area for
895       integrating SEAICE_AGE
896    o model/src:
897       first check-in of sigma & hybrid-sigma coordinate code ; also includes
898       non-linear free-surface parts ; but pressure-gradient not yet coded.
899    o pkg/ptracers:
900       option for ptracer to convert Salt Relax into additional EmP.
901        tested in exp. global_ocean.90x40x15.dwnslp (update output)
902    
903    checkpoint62j (2010/08/25)
904    o pkg/ggl90:
905       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
906    o pkg/dic: car_flux.F, phos_flux.F
907      - reduce number of exp-calls in order to improve performance
908      - clean up a little (replace fields by their macros, etc., fix
909        typo in CPP-flag)
910    o pkg/ggl90: minor changes
911      - GGL90diffKrS was removed --> always use GGL90diffKr
912      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
913      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
914        (commented out for now)
915      - change in max/min operations to ensure that smoothing is ok
916      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
917      - always use diffKrNrT as background profile (i.e. never use diffKr field)
918    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
919    o pkg/dic:
920      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
921        vectorization
922      - small bug fix in insol for the unlikely case of a cartesian grid
923      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
924        + now vectorize, which also removes adjoint recomputations;
925        + replace integer maksp1 by _RL maskp1
926        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
927    
928    checkpoint62i (2010/07/21)
929    o pkg/flt:
930      - with OBCS: stop floats which enter the OB region
931    o model/src:
932      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
933        for implicit vertical advection.
934    o pkg/seaice:
935     - account for melting in seaice age evolution.
936     - remove double counting of seaice ridging effect on seaice age.
937    
938    checkpoint62h (2010/06/18)
939    o pkg/exch2:
940     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
941    o tools/genmake2
942      - remove "-pdefault" option: redundant with the use of "packages.conf";
943      - remove file pkg/pkg_default : set the default as a pkg group
944        ("default_pkg_list") defined in pkg/pkg_groups;
945      - fix for case pkg/pkg_depend is missing (was hanging before);
946      - add option "-pgroups" to specify a different pkg_groups than the default.
947    o verification/adjustment.cs-32x32x1:
948       add a "minimal" set-up test (code_min & input_min) which only compiles
949       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
950    o tools/genmake2
951      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
952      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
953    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
954      files are nearly the same anyway.
955      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
956       - redefinition of tau(i,i) (by a factor of ustar)
957       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
958       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
959       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
960       - replace
961         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
962         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
963         by
964         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
965         (changes results)
966       -> exf_bulkformulae v1.22,
967          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
968          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
969                    output.txt 1.63
970           offline_exf_seaice: output.seaicetd.txt 1.7
971           seaice_obcs: output.txt 1.10)
972      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
973       -> exf_bulkformulae v1.23,
974          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
975          and global_ocean.cs32x15.icedyn (only 11 matching digits)
976      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
977    o adjoint of exch-1:
978     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
979       (note: was already like this when using EXCH-2) and remove flow dir
980       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
981     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
982     - update pkg/exch2 diff list.
983    
984    checkpoint62g (2010/05/19)
985    o eesupp/src (exch-1):
986     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
987       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
988       (renamed to exch1_*rx_cube.F).
989     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
990       to call new exch1 S/R ; update Makefile and .cvsignore.
991     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
992       exch2_xy_rx later)
993      Note: after updating your code, need to run "make clean" in eesupp/src
994    o test experiment bottom_ctrl_5x5:
995       new output_adm.txt with fewer grdchk & less monitor output.
996    o model/src:
997      remove the call to ini_cori in initialise_varia.F (just keep the usual one
998       in initialise_fixed.F). More consistent with coriolis & horizontal grid
999       beeing treated in the same way (ini_grid is not called a 2nd time).
1000    o pkg/exf:
1001      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1002    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1003      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1004      - cosmetic changes to exf_bulkformulae.F to make it look more like
1005        exf_bulk_largeyeager04.F
1006  o eesupp/src (exch-1):  o eesupp/src (exch-1):
1007    - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).    - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1008    - Separate buffer filling and MPI sending: allow EXCH-1 to work for local    - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
# Line 14  o eesupp/src (exch-1): Line 1011  o eesupp/src (exch-1):
1011    - Message mode: move RecvAck setting (indicator of buffer being ready)    - Message mode: move RecvAck setting (indicator of buffer being ready)
1012      from send_put to recv_get S/R (was useless before, but not sure if      from send_put to recv_get S/R (was useless before, but not sure if
1013      it's much more useful now);      it's much more useful now);
1014    - switch the order of sync: MPI-proc 1rst and then threads;    - Switch the order of sync: MPI-proc 1rst and then threads;
1015    - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.    - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1016      - fix AD code for communication mode ='get' (but not used).
1017  o model/src:  o model/src:
1018    initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does    initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1019    not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).    not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
# Line 164  o tools/build_options: Line 1162  o tools/build_options:
1162      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1163  o pkg/ecco  o pkg/ecco
1164    - allow user defined cost function contributions    - allow user defined cost function contributions
1165          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1166          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1167    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1168        the two options are complementary.        the two options are complementary.
1169  o pkg/smooth  o pkg/smooth
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