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revision 1.1214 by jmc, Tue Jan 12 00:23:23 2010 UTC revision 1.1466 by jmc, Mon Jun 27 22:45:33 2011 UTC
# Line 5  $Name$ Line 5  $Name$
5      ==============================      ==============================
6    
7  o pkg/diagnostics:  o pkg/diagnostics:
8     - add run-time parameter "useMissingValue" (def=False) to fill land-point
9        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
10       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
11     - Extend the use of "missing_value" setting from data.diagnostics for the case
12       of counter-diagnostics (where fraction-weight is zero). This applies both to
13       MNC and MDS output files.
14    o pkg/seaice/seaice_growth.F:
15      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
16       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
17      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
18       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
19      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
20      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
21    o verification 1D_ocean_ice_column:
22       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
23       update results
24    o pkg/diagnostics:
25     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
26       which are not filled-up but computed from other diags ; In this case, the mate
27       diag points to the primary (filled-up) diag to used for post processing.
28     - Update Velocity-potential computation using post-processed diag framework.
29     ==> Change the ordering of fields and time-periods in MDS output file
30       when using periodic averaging: now writes one time record with the full set
31       of fields for this time period, then the next time reccord (it used to be
32       one field with the full set of time records then the next field).
33         Note: this is now similar to NetCDF (MNC) output file. <==
34    
35    checkpoint62z (2011/06/21)
36    o adjoint monitor:
37     - Add adjoint monitor output for packages exf, seaice
38       and update relevant testreport output
39    o pkg/seaice:
40     - re-order diags inits so that they appear in order in available_diagnostics.log
41     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
42       area/heff/hsnow preceeding thermodynamic growth/melt.
43     - modified diag: SIdA; output actual effect, as the description states.
44     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
45     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
46       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
47        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
48     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
49     - added diagnostics for seaice generic tracers (SItr*).
50     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
51     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
52     I. Fenty: 18-Jun-2011:
53     Minor changes to seaice package:
54     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
55        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
56       - Differentiated "regularization variables" from "floor variables"
57        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
58        * hiceMin became SEAICE_hice_reg (old hiceMin)
59          (with _reg meaning regularization variable)
60       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
61        so as to ensure energy conservation when going between phases
62      - A22 was not used anywhere
63     2) Changed regularization procedure for heffActual and hsnowActual to ensure
64        well-boundedness and smooth adjoint in seaice_growth.F
65     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
66        because the old regularization always set heffActual >= 0.05 cm
67     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
68        on AREA when HEFF > 0.
69      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
70        requiring that DISABLE_AREA_FLOOR *not* be defined
71     Affected verifications:
72      - 1D_ocean_ice_column (output.txt output_adm.txt)
73      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
74    o pkg/diagnostics:
75      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
76      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
77        (was _RL, now integer) with option = 0 to retrieve all levels.
78      - add pieces of code to compute velocity potential at each level (new diagnostics
79        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
80        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
81      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
82        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
83        and in diagnostics_fract_fill.F (do not need a valid pointer for the
84        diagnostics counter-mate); check that definition of counter-diagnostic
85        includes a valid counter-mate (in diagnostics_set_levels.F).
86    o model/src (rStar):
87      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
88        affect solution only if z* with full pressure in EOS;
89        update output of test-exp global_ocean.90x40x15.
90    o pkg/seaice:
91      - introduce siEps=1e-5 parameter
92      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
93      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
94      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
95        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
96        as well as ice cover age and ridging index (attached to AREA).
97        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
98        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
99        Up to SItrMaxNum=3 tracers can be used simultaneously.
100    o pkg/salt_plume:
101      -introduce SPsalFRAC run time parameter that sets the fraction of the
102       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
103       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
104    o model debug options:
105      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
106        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
107      - Refine debug-msg printing selection (3 new levels):
108        debugMode  : controls printing of debug messages (sequence of S/R calls).
109        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
110         debLevZero =  0 ; /* level of disabled aux. msg printing */
111         debLevA =  1 ; /* level of minimum  aux. msg printing */
112         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
113         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
114         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
115         debLevE =  5 ; /* level of extensive debug printing */
116        New debugLevel default: with default debugMode value (=F),
117          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
118          and if debugMode=T, default debugLevel = 4 (debLevD).
119        Relation with previous settings:
120         debLevB (=2) corresponds to former debLevA (=1)
121         debLevD (=4) corresponds to former debLevB (=2)
122        Note:
123         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
124         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
125            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
126      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
127        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
128    o pkg/obcs:
129      - change OBCSfixTopo default from True to False (should not change the results);
130        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
131    o pkg/thsice:
132      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
133        2nd layer seaice sublimation (unlikely to happen)
134      - use Interior mask for OBCS in thsice_advection.F (similar to what is
135        done in gad_advection & seaice_advection).
136    o adjoint:
137      bug fix spotted by Gael Forget:
138      seaice_advection and thsice_advection still had
139      legacy CPP options to avoid CS corner updates for adjoint
140    o pkg/seaice:
141      => Change some of the defaults (2011/05/29):
142         - change SEAICEuseFluxForm default (from False to True)
143         - change DIFF1 default (from 0.004 m/s to 0. m/s)
144         And print warnings if DIFF1 is not set in data.seaice and centered
145          avection scheme is used without any diffusion.
146      also:
147      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
148      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
149      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
150        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
151        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
152      update results of test exp.:
153         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
154             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
155             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
156         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
157         seaice_obcs: output (SEAICEuseFluxForm=T)
158      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
159          for standard fwd & AD lab_sea tests (to keep the same output).
160    o pkg/seaice/seaice_growth.F:
161      - use Ian Fenty's capping formulas for actual ice
162      thickness thoughout EVOLUTION branch.
163      - put treatment pathological case #2) in CPP brackets
164      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
165      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
166    o pkg/seaice:
167      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
168      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
169      also pass fac as a param, which can be 1. (to update the tendency
170      field) or the time step (to update the field itself).
171      - seaice_advdiff.F: for multidim, call seaice_diffusion with
172      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
173      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
174      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
175      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
176    o pkg/seaice:
177      diffusion with centered advection scheme (diffus.F & advect.F):
178      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
179        to just compute the laplacian of input-field.
180      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
181      - fix flux-form version in diffus.F to conserve tracer.
182      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
183       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
184    
185    checkpoint62y (2011/05/26)
186    o pkg/seaice:
187     - seaice_growth.F : in EVOLUTION branch, always include
188       a_QSWbyATM_cover in qnet (as it should be).
189     - verification/global_ocean.cs32x15 : update results accordingly
190       (output.seaice.txt output_adm.seaice.txt).
191    o pkg/seaice + obcs:
192     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
193       equivalent of assuming no tracer gradient outside the OB region.
194       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
195     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
196       after changes above);
197     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
198       only at OB location (instead of over a band of OLx width).
199    o pkg/seaice:
200     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
201       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
202    o pkg/obcs:
203      - split header file "OBCS.h" into 4 separated files:
204        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
205       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
206         (contain no conditional statement which depends on OBCS options).
207      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
208        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
209    o ctrl, cost, grdchk & autodiff pkgs:
210      - make options file more standard (like other {PKG}_OPTIONS.h file but
211        with AD_CONFIG.h); clean-up some of the included header files.
212    o pkg/obcs:
213      - do not mask tracer when applying OB (tracer == 0 could generate problems)
214      - apply tracer OB values to tracer field only at OB location (instead of
215        over a band of OLx width)
216      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
217      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
218        obcs_apply_tloc.F & obcs_apply_sloc.F
219    o obcs in model/src:
220      - call OBCS_APPLY_W only if NonHydrostatic.
221      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
222      - reset dEtaHdt and wVel to zero outside OB interior region ;
223      - leave tracer unchanged outside OB interior region: This has no effect
224        on the solution but just to prevent unrealistic tracer value outside OB.
225      - zero out velocity outside OB interior region: This has no effect on
226        the solution but just to prevent unrealistic velocity outside OB.
227    o obcs and non-lin free-surf:
228       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
229       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
230       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
231       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
232       update results of test-exp. exp4(nlfs).
233    o exp4 (nlfs) test-exp:
234       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
235       with NonLin-FreeSurf); update output.nlfs.txt
236    o obcs and 2d/3d solver norm:
237       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
238       and outside OB interior region (will allow to place OB further inside the
239       domain). Depending on the domain, can affects cg2d-Norm (previous
240       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
241       and cg3d-Norm (previous Norm was computed before canceling OB terms),
242       e.g. in tutorial_plume_on_slope.
243      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
244    o pkg rbcs:
245      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
246      - add capability to apply relaxation to horizontal velocity uVel & vVel.
247    o pkg/grdchk: add gradient check for control variable xx_shifwflx
248    o pkg/shelfice/shelfice_init_fixed.F
249      fix CPP-flag combinations
250    o pkg/seaice: Merge iceage code of Pierre Rampal
251      * update/change/correct ice age calculations
252      * add age updates for pathological cases
253      Probably needs more testing...
254    
255    checkpoint62x (2011/05/13)
256    o pkg/mom_vecinv:
257       high-order vorticity scheme: use interior masks (maskInW & S)
258       to zero-out (outside OB) gradient of vorticity.
259    o verification exp.:
260       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
261       hs94.128x64x5 and seaice_obcs ; update results.
262    o pkg/obcs:
263      fix bug in OBeta for YZ sections in obcs_exf_load.F
264    o pkg/ctrl, pkg/shelfice, and optim:
265      - add new control variable xx_shifwflx (fresh water flux underneath ice
266        shelves). This is almost as tedious as obcs-ctrl, because the
267        variables needs its own mask.
268      - add a cost function term that penalizes the deviation of xx_shifwflx
269        from the first guess (zero) in analogy to other control variables
270    o pkg/shelfice:
271      - start basic adjoint
272    o pkg/ctrl:
273      - remove extra 2D field "for good measure" when initializing in
274        ctrl_set_globfld_[xy/xz/yz].F
275      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
276      - improve error messages in ctrl_set_unpack_*
277    o OBC implementation in momentum:
278       use interior masks (maskInC,W & S) in momentum S/R:
279       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
280       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
281       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
282       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
283       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
284        (and also with Leith/Smagorinsky harmonic-viscosity).
285       Update output of experiment dome and exp4 (+nlfs).
286    o exp4 test-exp:
287      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
288        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
289        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
290        time-varying OB at Western-side for wVel (NonHyd); update output.
291      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
292        and biharmonic-viscosity ; also use prescribed time varying OB.
293    o pkg/obcs:
294      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
295    o model/src:
296      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
297      - initialise startTime & nIter0 with unlikely values: allows to set one
298        from the other without ambiguity.
299    o seaice_obcs test-exp.:
300      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
301    o pkg/obcs:
302      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
303        no longer needed with maskInC,W,S in pkg/generic_advdiff.
304    o pkg/seaice:
305      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
306        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
307      - fixed bug in the initialization of sea ice salinity variable HSALT
308        in seaice_init_varia.F  (removed dependence on ICE2WATR)
309    o fizhi-cs test exp.:
310       switch reference output convention for these 2 non-standard test-exp,
311        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
312          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
313       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
314    o model/inc:
315      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
316        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
317    o pkg/seaice:
318      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
319    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
320      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
321        and initial HSALT
322    
323    checkpoint62w (2011/04/26)
324    o pkg/mom_fluxform:
325      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
326      - use parameter "sideDragFactor" in no-slip BC side-drag part.
327      - update output of exp. global_ocean.90x40x15
328    o pkg/mom_vecinv:
329      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
330    o update seaice exp.:
331      use more consistent parameter values (remove "backward compatability only":
332       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
333      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
334       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
335    o update test-exp global_ocean.90x40x15:
336      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
337      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
338      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
339      o turn on zStar & viscA4 in standard set-up (dir input/)
340        and update output files: output.txt & output.dwnslp.txt
341    o new AD-test experiment: obcs_ctrl
342      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
343    o pkg/dic:
344      fix two bugs in handling water vapour pressure in carbonate chemistry
345      and air-sea fluxes. Found by Val Bennington and Galen McKinley
346      (add DIC Option = WATERVAP_BUG to recover old results)
347      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
348    o adding allowInteriorFreezing option to check for water below freezing point
349      at depth and bring the negative heat anomaly to the surface level
350    o pkgs _fields_load:
351      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
352      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
353        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
354        rbcs to get interpolation weights and time reccord number.
355      - fix multi-threading in aim_fields_load.F
356      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
357    o external_fields_load:
358      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
359       interpolation weights) to use in a periodic time-series ; do not divide by
360       time-step to convert to integer:
361       - this fixes case where externForcingPeriod is not multiple of time-step
362          (Thanks to Christopher L. Wolfe)
363       - this fixes case where externForcingPeriod is an odd multiple of time-step
364         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
365      store index of time-record which is currently loaded:
366       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
367       - needed for the adjoint but not yet used because of extensive recomputations;
368         (to be fixed soon)
369    
370    checkpoint62v (2011/04/02)
371    o verification/1D_ocean_ice_column added to test Ian Fenty's
372      pkg/seaice_growth.F modifications for improving sea ice code differentiability
373    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
374      (new velocity statistics after changing maskInW & maskInS definition)
375    o pkg/generic_advdiff with OBCS:
376      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
377      equivalent to assumption of no tracer gradient outside the OB region.
378      This will affect the results if using obcs+biharmonic diffusion.
379      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
380    o pkg/obcs:
381      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
382      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
383      in Interior region. No impact on solution but affects Velocity monitor stats.
384    o pkg/ptracers (adjoint)
385      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
386      tape file for each tracer
387    o model/inc/src and pkg/autodiff: add parameters that allow to turn
388      of parts of the adjoint code at run time. For now, there are only
389      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
390      parameters are set in data.pkg.
391      This is the lazy coward's version of doing this, but still useful for
392      debugging. In order to do it right, everything needs to be moved to
393      pkg/autodiff.
394    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
395      the end; this fixes the adjoint balancing code for open boundaries.
396    o pkg/ctrl:
397      - change behavior of xx_${varname}period to be analogous to exf-conventions:
398        xx_${varname}period =   0.,  means time-independent control part
399        xx_${varname}period = -12., means one-year-periodic monthly control part
400      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
401        clean up ctrl_init a little, remove unused variables
402      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
403      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
404    
405    checkpoint62u (2011/03/15)
406    o model/src:
407      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
408        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
409      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
410        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
411    o pkg/ctrl/obcs/ecco:
412      - remove obsolete, unused, and partially broken code:
413        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
414        ALLOW_CTRL_OBCS_BALANCE
415      - put a stop statement into ecco/cost_obcsvol.F, but also add
416        cost_obcsvol to ecco_ad_diff.list
417    o pkg/ecco: fix counting cost function contributions for obcs (code
418      by Matt M.) and diffkr for diagnostics
419    o pkg/ecco, pkg/ctrl, pkg/grdchk:
420      add cost penalty terms for initial uvel, vvel, eta controls
421      and I/O for prior error files
422    o pkg/mdsio:
423       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
424       (new argument) to check for tiled file in mdsioLocalDir : this fix the
425       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
426    o pkg/ctrl:
427     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
428       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
429       unused and superfluous variables
430     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
431    o pkg/ecco
432     - enable adjoint of Stevens OB
433    o pkg/ctrl/ecco/grdchk:
434      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
435        Fortunately, we do not have any tests for the numerous cpp-flagged
436        option of "obcs as control parameters" so we will never know
437        if this is an improvement (but at least now things compile).
438      - remove an obsolete initialization from ecco_cost_init_barfiles.F
439      - fix some problems within never used ifdefs to make the code compile
440    o pkg/obcs:
441     - Refine Interior mask definition to work with more complex OB (e.g.
442       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
443       read in Interior mask from file. Check if Interior mask is consistent
444       with OB list of indices.
445    o pkg/seaice
446     - beginning code for a seaice tracer package,
447       but currently only used for seaice age: SEAICE_AGE
448       SEAICE_num = 4
449       iTracer = 1: area-weighted ice age
450               = 2: volume-weighted ice age
451               = 3, 4: template for one-year vs. multi-year ice
452       data.seaice has new namelist SEAICE_PARM03 for arrays related to
453       SEAICE_num
454    
455    checkpoint62t (2011/03/05)
456    o pkg/obcs:
457     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
458       then normal component. This ensures that the normal component is set
459       correctly even when it conficts with tangential setting from an other OB.
460       Affects results of test-experiment seaice_obcs: update the output.txt
461    o pkg/obcs:
462     - add code to monitor statistics of dynamical fields at OB.
463     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
464       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
465       - change default: balance the Net inflow through all OB (instead of balancing
466         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
467     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
468       to match Nortern OB inflow (OBCS_balanceFacN=0).
469    o pkg/seaice:
470     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
471    o pkg/seaice (seaice_growth v 1.113):
472     - reverting seaice_growth to v 1.111 in order to have code with exact bit
473       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
474       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
475       runtime flag SEAICEareaFormula is kept but is inactive
476    o model/src:
477     - add new param to scale curvilinear grid distance and area when using
478       a different sphere radius from the grid-files.
479     - test/check multi-threads EXCH applied to local variable (cg2d_x)
480    o adjoint:
481     - enable adjoint of Stevens OB
482     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
483       (a bit delicate because of potentially modified adj. common block structure;
484       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
485    
486    checkpoint62s (2011/02/15)
487    o pkg/seaice (seaice_growth v 1.112):
488     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
489       computing the ice cover tendency from effective thickness tendencies. Include
490       Ian Fenty's formula.
491     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
492       SEAICEareaFormula.
493     - simplify notations for the various d_HEFF/d_AREA terms.
494    o pkg/gmredi:
495     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
496       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
497       add a verification test-run (front_relax.bvp) to test GM_useBVP.
498    o pkg/seaice (seaice_growth v 1.111):
499     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
500     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
501       also melt ice.
502    o pkg/seaice:
503     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
504     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
505    o pkg/cheapaml:
506     - from Nico Wienders: New version of this package.
507    o pkg/flt:
508     - add CPP options to prevent floats to re-enter the opposite side of
509       a periodic domain (default: keep periodicity)
510    o pkg/gmredi:
511     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
512       (needed for multi-dim advection).
513     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
514    o model/src:
515     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
516    o tutorial_tracer_adjsens
517     - extend to NLFS and replace maskC by hFacC
518       (change reference output accordingly)
519    
520    checkpoint62r (2011/01/24)
521    o testreport:
522     - add option -deloutp (-do) to remove output file after successful run
523     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
524       extract exact list of procs from this file ; adjust COMMAND by
525       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
526    o pkg/ecco: replace old ineffective way of penalizing deviations from
527      first guess (of obcs) with code by Matt Mazloff
528    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
529      exf/cal
530      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
531        and handle case of obcs?period == 0
532        Not affected by these changes: There is still an inconsistency in
533        the computation of start/endrec for the obcs variables for ALLOW_CAL
534        defined (see comment by Menemenlis, 7-Mar-2003)
535      - make S/R ctrl_get_gen_rec return something meaningful even if
536        ALLOW_CAL is not defined
537      - ctrl_getobcs?: simplify code so that it does not need to use
538                       S/R exf_swapfields
539    o testreport:
540       allow to test MPI with different number of processors for each experiment:
541       create file "SIZE.h.mpi" in each build dir.
542       Note: update of "-command" argument not yet implemented.
543    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
544      alleviate the need for additional 3D tapes when using
545      the non-inear free surface in the adjoint. This is done
546      by adding an 'update' of hfacc etc. to their current
547      value at the beginning of forward_step.F.
548    o pkg/seaice
549      seaice_lsr: move stress-divergence computations out of outer pseudo-
550      timestepping loop
551    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
552      up, so that the calls of the ctrl_* subroutines are really at the end
553      of the routine.
554    o pkg/gmredi:
555      allow to specify a 2-D horizontal map and a 1-D vertical profil
556      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
557    o pkg/seaice:
558      move lsr iterations from seaice_dynsolver to seaice_lsr.
559    o pkg/seaice:
560      reduce memory footprint of seaice mutldim advection tapes,
561      by using a 2D tape independent of the generic_advdiff ones,
562      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
563    
564    checkpoint62q (2010/12/29)
565    o model/src:
566      - check horizontal grid-spacing for unset or zero/negative values.
567      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
568    o pkg/flt:
569      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
570      - precision of input and output files set according to readBinaryPrec
571        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
572      - initial float position from tiled file was not converted to index space
573        (looks like a bug): fixed to make it similar to initial pos. global file.
574    o global_ocean.cs32x15:
575       change SIZE.h of AD set-up to get same tiling as with MPI.
576       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
577    o model/src:
578       add flag to control printing of domain fields (bathymetry, hFac ...) in
579       ini_mask_etc (call to plot_fieds_xy*).
580    o pkg/thsice:
581       if useEXF, some forcing fields are not valid in overlap: fixed by computing
582       over the interior only + apply EXCH at the end (like with SEAICE advection).
583    o pkg/mdsio:
584      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
585        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
586      - change barrier call for safe multi-threads access to 3-D shared buffer.
587      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
588      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
589        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
590    o pkg/flt:
591      - add fourth-order Runge-Kutta integration
592      - add basic exch2 support (only 1 facet supported so far!)
593    o pkg/mdsio+rw:
594      new S/R to read local (or tile independent) vector (read counterpart of
595       mds_writevec_loc, and front-end write_glvec_rl/rs).
596    o global_ocean.cs32x15: additional input_ad.seaice experiment
597        that uses pkg/seaice rather than pkg/thsice.
598        (using multidim advection for seaice)
599    o towards more F95 syntax for array specification in namelist:
600      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
601        of all verification experiments.
602           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
603          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
604      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
605    o global_ocean.cs32x15: additional input.seaice experiment
606        that uses pkg/seaice rather than pkg/thsice.
607    
608    checkpoint62p (2010/12/17)
609    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
610        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
611    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
612        allow for use of multim. advection in seaice adjoint.
613    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
614      - first attempt to close budgets by taking into account the freshwater
615        flux implied by the sublimation of snow and ice. So far only the
616        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
617        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
618    o eesupp/src:
619      new S/R with new option (NML_EXTENDED_F77) to change array specification
620      from F95 standard to commonly accepted extended F77 form.
621      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
622      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
623      for less tolerant f77 compiler (e.g., pgf77, g77).
624    o globalFiles:
625      commented out in parameter file "data" since it's not safe with MPI
626      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
627      in this case); no longer commented out in restart test (tst_2+2).
628    o add adTapeDir to specify a special directory where adjoint tapes are
629      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
630      and cannot be used together with mdsioLocalDir.
631    o nesting pkgs:
632      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
633      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
634      - add parameter files + utils dir + output from short run on beagle.
635    o pkg/seaice:
636        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
637    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
638      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
639    
640    checkpoint62o (2010/11/25)
641    o pkg/exf:
642      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
643    o pkg/seaice:
644      - seaice_ocean_stress: split a loop for better vectorization of the
645        adjoint code
646      - seaice_growth.F: fix bug in conservation of freshwater connected to
647        capping of heff, put contribution into d_HEFFbyNEG
648      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
649        by something more sensible (parameters that are what their name implies)
650      - change some defaults, so that by default exf-parameters are used for
651        things like rhoAir, cpAir,latent/sensible heat parameters, in order
652        to reproduce the old results, many data.seaice now contain funny values
653        for cpAir and latent heat of sublimation
654    o packages_readparms.F: move exf_readparms up in line so that
655        exf-parameters are visible for other packages (e.g. seaice)
656    o debugMode & debugLevel=2:
657      - differentiate between debugMode & debugLevel=2:
658        debugMode: controls printing of debug messages (sequence of S/R calls).
659        debugLevel: controls printing of algorithm intermediate results and stats.
660      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
661        => allows to print debug-stats without all sequence of call messages.
662      - switch control of debug print from debugLevel to debugMode in many S/R.
663    o pkg/obcs (obcs-sponge):
664        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
665        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
666    o pkg/generic_advdiff:
667      - record overlap minimum size for each advection scheme;
668      - refine criteria on overlap minimum size;
669      - check and stop (in gad_check) if overlap size is too small.
670    o pkg/obcs:
671      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
672        once, in ptracers_implicit.F)
673      - with seaice: remove test on empty file name in obcs_apply_seaice (always
674        apply OB values when tile has OB)
675    o model/src, coriolis setting:
676      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
677        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
678        files (selectCoriMap=3) with any grid.
679      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
680    o pkg/seaice/seaice_growth.F:
681        a few cosmetic changes that reduce the number of lines of code
682    o pkg/obcs: add boundary conditions following Stevens (1990)
683      - the code follows old MOM/NAOSIM code
684      - so far it is only implemented for the eastern and western boundaries
685        and NOT for pTracers
686    o pkg/rbcs:
687      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
688        beginning of the first rbcs forcing period.
689      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
690        offline package, i.e., one file per time, labeled by iteration number;
691        deltaTrbcs sets the timestep with which the data was generated;
692        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
693      - rbcsForcingCycle=0 makes forcing non-cyclic.
694      - make arithmetic safe for negative times and odd forcing periods.
695    
696    checkpoint62n (2010/11/09)
697    o pkg/seaice:
698        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
699    o pkg/obcs:
700       New S/R to copy tracer value from the OB location to narrow band region
701        (width = same as overlap) beyond the OB: preserve OB value (needed for
702        high-order scheme) which were overwritten by EXCH call if in overlap
703        region. Applied to theta, salt, ptracer and advected seaice variables.
704       With seaice: use maskInC in similar way as in gad_advection.F,
705        in seaice_advection.F and advect.F.
706       Update output of experiment seaice_obcs and change exp4 to test OBCS with
707        4th order Adv.Scheme. for pasive salt and ptracer.
708    o tools/genmake2:
709      - when looking for an optfile (not specified), only search for Fortran compiler
710        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
711      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
712        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
713      - set default for CPP to "cpp -traditional -P" (was the case without specifying
714        an optfile, but otherwise default was just "cpp".
715      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
716      - when "CC" is not set in the optfile, look for possible C compiler
717        (instead of just setting CC=cc)
718      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
719        => add a ".F" to ".o" rule for source files with no "#include" (such as
720           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
721      - move gfortran before g77 in list of possible Fortran compiler (consistent
722        with reference compiler switch from g77 to gfortran)
723    o pkg/seaice:
724      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
725        seaice_check that stops the model, when the CPP flag is used.
726      o seaice_growth.F: make capping of ice volume conserving by returning the
727        capped ice as freshwater to EmPmR. This does not change the verification
728        experiments but will change runs where the capping is acutally active
729    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
730      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
731         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
732         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
733    o tools/genmake2:
734      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
735      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
736      - clean previous genmake log files before anything else.
737      - change Makefile to remove testreport log files (*.tr_log) and genmake log
738        files only with "CLEAN" target (instead of "Clean");
739    o pkg/generic_advdiff:
740      Change OBCS in multiDim advection (gad_advection.F):
741       Use maskInC to prevent intermediate update of tracer-field in OB regions,
742       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
743       which were applying future time-step OB values.
744      This way, all explicit calculations use current-time-step OB values
745       (simpler and more consistent).
746      Affects results when set-up uses time-varying OBC and multi-dim advection;
747       update output of experiment seaice_obcs.
748    o pkg/seaice:
749      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
750       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
751         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
752      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
753       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
754       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
755    o pkg aim (2010/10/26):
756      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
757        formulation with obliquity, eccentricity, ... as run-time parameters,
758      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
759        upward shortwave radition at the surface (all-sky and clear-sky).
760    o pkg/obcs:
761      - writing sections with globalFiles=T does not work: switch to tiled-files
762        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
763      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
764      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
765    
766    checkpoint62m (2010/10/21)
767    o pkg/seaice: vectorize seaice_solve4temp.F
768      - move iterations loops outside of i/j-loops
769      - requires 2D arrays for TB and effConduct
770      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
771        modified in this routine
772      - a little bit of clean up, adjusting indentation, etc.
773      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
774        performance and '**TWO' by '**2' (because TWO is a float),
775        replaced ONE, ZERO
776    o eesupp/src:
777       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
778    o pkg/seaice/seaice_growth.F
779      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
780      merging process. The merged routine has two branches, and one activates the 'evolution'
781      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
782      In summary, here is what the '10/10 revision' did consist of
783        part 1: seaice_growth.F revisions 1.71 to 1.75
784          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
785            The emphasis here was on improving readability (e.g. by trying to use meaningful
786            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
787        part 1.5:
788          - revising the lab_sea experiment to make it a more useful (i.e. stable
789            and representative of an actual model run). This was done by generating a
790            (winter) pickup to start from, switching back the main experiment dynamic
791            solver from evp to lsr, having one of the experiments use the free drift solution.
792        part 2: seaice_growth.F revisions 1.76 to 1.85
793          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
794          - Sorting out the various fields units and sign (set early on and reset at the end)
795            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
796            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
797          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
798            and simplifying logical expressions to further improve readibility.
799        part 3: seaice_growth.F revisions 1.86 to 1.89
800          - Re-organize the blocks of code more logically.
801          - Merging the '_if.F' pieces that add something new.
802    o pkg/thsice:
803      - vectorize thsice_solve4temp and thsice_get_exf.
804        Problem: thsice_solve4temp has an unvectorizable statement that
805        might also be problematic for TAF
806      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
807        does not change the verifcation experiment, but will change all
808        experiments that have this flag undefined (not tested in verification);
809        a little reorganization to save a few 2D fields and recomputations
810      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
811      - 2nd step:  fix some store dirs
812        o seems to work somewhat, i.e. using ifort but not g77
813        o likely cause are incomplete init. or recomputation
814        o start verification/global_ocean.cs32x15/input_ad.thsice
815    o pkg/obcs: add support for exch2
816      - the position of the boundary and prescribed values are specified using
817        a global domain with exch2 facets stacked
818        - in x for N,S boundaries (like W2_mapIO=-1)
819        - in y for E,W boundaries (so E,W boundaries do not overlap)
820    o pkg/mdsio: add support for writing global sections with exch2
821        file layout is as for obcs described above:
822        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
823        - for y-z sections, facets are stacked in y
824    o pkg/thsice:
825       - change a few routines for better vectorization: thsice_albedo.F,
826         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
827         not affected, but in particular the latter routine has changed
828         dramatically (not necessarily easier to read now).
829       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
830       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
831    o verification/lab_sea:
832      - overhaul of the forward model experiments. The main motivation
833        for this revision is that lab_sea has proven quite fragile (when
834        changing the sea-ice code, and switching platforms) to a point
835        when failures were very hard to attribute to specific code problems.
836      - the suspected reason for this fragility is noise amplification by evp so,
837        to start with, we decided to replace evp with lsr in the main experiment.
838      - the input.lsr experiment thus became obsolete and was removed.
839      - it was replaced with the input.fd experiment that uses an
840        analytical "free drift" solution as the ice velocity field.
841      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
842        will hopefully allow us to discriminate problems due to dynamic solvers
843        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
844        us to test additional options, along with the salt plume package.
845      - Finally a pickup was generated (at the end of a one year run) to
846        make the tests more representative of an actual model run. Previously
847        the tests starting point was a 1m thickness of ice everywhere.
848    o pkg/seaice:
849      - introducing S\R seaice_freedrift.F that compute the
850        analytical solution to an approximate ice momentum
851        equation (i.e. the simple stress/coriolis balance).
852      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
853        of the free drift velocity field, and enable its use.
854        To actually use the free drift solution as the model ice
855        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
856    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
857    
858    checkpoint62l (2010/10/04)
859    o pkg/seaice:
860      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
861      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
862       version (with USE_ORIGINAL_SBI undef);
863    o add hooks for new packages OASIS, the package will follow
864      (hooks exclude the seaice pkg for now)
865    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
866      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
867      rather than mdsio_readvector.F/mdsio_writevector.F, within
868      adread_adwrite.F to read/write adjoint-related tapes to disk.
869    o eesupp and pkg/mdsio: ALLOW_WHIO
870      Option to write/read 2D fields to files including tiles halos.
871      The main purpose is for adjoint related "tape I/O".
872      The secondary purpose is for debugging phases.
873      A word on those rather specifically intended purposes.
874      The code was meant to be stripped down to the bare minimum.
875      Typically, there is a unique and basic mapping to the global
876      buffer (tile by tile, then proc by proc, then level by level), and
877      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
878      meant to generate user friendly outputs of various shapes and forms.
879      Rather it is intended, for the knowledgeabale developers,
880      to be largely independent of the many mdsio options, to allow
881      outputs of tiles+halos in debugging phases and in adjoint runs,
882      and to allow some flexibility in tuning (adoint) I/O depending on each
883      file system behavior. With regard to tuning, most of the potential knobs
884      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
885      to specify directories, to specify the typical size of I/O calls, etc.)
886      are not yet included, and will be added if they prove useful.
887    o pkg/seaice:
888       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
889    o pkg/seaice:
890       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
891       code (seaice_budget_ice_if.F) which enable to recover old standard
892       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
893       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
894    o model/src (rStar):
895       use simple average (not area weighted) of rStarFac at U,V point when using
896       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
897       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
898    
899    checkpoint62k (2010/09/17)
900    o adjoint
901       * changed verification/global_ocean.cs32x15 ; adjoint now tests
902         Adams-Bashforth 3 + NLFS + RSTAR
903       * some more modifs required for ECCO-GODAE v4
904    o pkg/seaice
905       add SEAICE_AGE_VOL option to use volume instead of area for
906       integrating SEAICE_AGE
907    o model/src:
908       first check-in of sigma & hybrid-sigma coordinate code ; also includes
909       non-linear free-surface parts ; but pressure-gradient not yet coded.
910    o pkg/ptracers:
911       option for ptracer to convert Salt Relax into additional EmP.
912        tested in exp. global_ocean.90x40x15.dwnslp (update output)
913    
914    checkpoint62j (2010/08/25)
915    o pkg/ggl90:
916       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
917    o pkg/dic: car_flux.F, phos_flux.F
918      - reduce number of exp-calls in order to improve performance
919      - clean up a little (replace fields by their macros, etc., fix
920        typo in CPP-flag)
921    o pkg/ggl90: minor changes
922      - GGL90diffKrS was removed --> always use GGL90diffKr
923      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
924      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
925        (commented out for now)
926      - change in max/min operations to ensure that smoothing is ok
927      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
928      - always use diffKrNrT as background profile (i.e. never use diffKr field)
929    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
930    o pkg/dic:
931      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
932        vectorization
933      - small bug fix in insol for the unlikely case of a cartesian grid
934      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
935        + now vectorize, which also removes adjoint recomputations;
936        + replace integer maksp1 by _RL maskp1
937        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
938    
939    checkpoint62i (2010/07/21)
940    o pkg/flt:
941      - with OBCS: stop floats which enter the OB region
942    o model/src:
943      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
944        for implicit vertical advection.
945    o pkg/seaice:
946     - account for melting in seaice age evolution.
947     - remove double counting of seaice ridging effect on seaice age.
948    
949    checkpoint62h (2010/06/18)
950    o pkg/exch2:
951     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
952    o tools/genmake2
953      - remove "-pdefault" option: redundant with the use of "packages.conf";
954      - remove file pkg/pkg_default : set the default as a pkg group
955        ("default_pkg_list") defined in pkg/pkg_groups;
956      - fix for case pkg/pkg_depend is missing (was hanging before);
957      - add option "-pgroups" to specify a different pkg_groups than the default.
958    o verification/adjustment.cs-32x32x1:
959       add a "minimal" set-up test (code_min & input_min) which only compiles
960       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
961    o tools/genmake2
962      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
963      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
964    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
965      files are nearly the same anyway.
966      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
967       - redefinition of tau(i,i) (by a factor of ustar)
968       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
969       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
970       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
971       - replace
972         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
973         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
974         by
975         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
976         (changes results)
977       -> exf_bulkformulae v1.22,
978          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
979          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
980                    output.txt 1.63
981           offline_exf_seaice: output.seaicetd.txt 1.7
982           seaice_obcs: output.txt 1.10)
983      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
984       -> exf_bulkformulae v1.23,
985          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
986          and global_ocean.cs32x15.icedyn (only 11 matching digits)
987      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
988    o adjoint of exch-1:
989     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
990       (note: was already like this when using EXCH-2) and remove flow dir
991       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
992     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
993     - update pkg/exch2 diff list.
994    
995    checkpoint62g (2010/05/19)
996    o eesupp/src (exch-1):
997     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
998       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
999       (renamed to exch1_*rx_cube.F).
1000     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1001       to call new exch1 S/R ; update Makefile and .cvsignore.
1002     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1003       exch2_xy_rx later)
1004      Note: after updating your code, need to run "make clean" in eesupp/src
1005    o test experiment bottom_ctrl_5x5:
1006       new output_adm.txt with fewer grdchk & less monitor output.
1007    o model/src:
1008      remove the call to ini_cori in initialise_varia.F (just keep the usual one
1009       in initialise_fixed.F). More consistent with coriolis & horizontal grid
1010       beeing treated in the same way (ini_grid is not called a 2nd time).
1011    o pkg/exf:
1012      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1013      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1014      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1015      - cosmetic changes to exf_bulkformulae.F to make it look more like
1016        exf_bulk_largeyeager04.F
1017    o eesupp/src (exch-1):
1018      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1019      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1020        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1021        (even without using MPI).
1022      - Message mode: move RecvAck setting (indicator of buffer being ready)
1023        from send_put to recv_get S/R (was useless before, but not sure if
1024        it's much more useful now);
1025      - Switch the order of sync: MPI-proc 1rst and then threads;
1026      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1027      - fix AD code for communication mode ='get' (but not used).
1028    o model/src:
1029      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1030      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1031    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1032    o pkg/ctrl: require a specific set of control variables and exf-flags for
1033      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1034    o model/src:
1035     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1036       1rst forward sweep, to avoid over-writing output files during recomputations
1037       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1038     b) 2nd version:
1039      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1040      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1041         writePickupAtEnd) + seaice & ptracers output;
1042      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1043    o model/src:
1044      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1045    o pkg/exch2:
1046      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1047      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1048    o pkg/autodiff & exch2:
1049      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1050      (for now, only if ALLOW_EXCH2 is defined).
1051    o pkg/autodiff:
1052      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1053        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1054       + clean-up comments (_RS is not always real*4)
1055      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1056      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1057        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1058    o testreport (AD-tests):
1059      no longer link files from dir "../input" (1rst link files from
1060      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1061    
1062    checkpoint62f (2010/04/29)
1063    o model/src/the_main_loop.F:
1064      adjust store directives for seaice evp and multicategory according to
1065      pkg/ecco/the_main_loop.F
1066    o adjoint:
1067      global_sum_ad was incomplete (noted many times by many people ;)
1068      nice description by Jean U. as follows:
1069      * allreduce(var) in global_sum.F can be interpreted as
1070        reduce(sum) followed by broadcast of sum.
1071      * The adjoint of that is
1072        sum(adjoint) followed by broadcast(summed adjoint value)
1073        or in other words, allreduce(sum, adjoint vars)
1074      We were missing the sum(adjoint)!
1075      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1076      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1077      The fix should produce 16-digit accuracy between
1078      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1079      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1080      We'll probably change this yet again shortly
1081    o eesupp/src:
1082      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1083    o pkg/icefront
1084      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1085        specification of addmass array based on a 2D field, which is added
1086        at bottommost wet level at each horizontal location.
1087    o model/src:
1088     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1089     layout; (not always compatible with delX,delY setting; commented out for now).
1090    o pkg/exch2:
1091     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1092     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1093    
1094    checkpoint62e (2010/04/15)
1095    o pkg/obcs:
1096      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1097    o pkg/dic:
1098      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1099        (note: not presently tested in any forward verification exp.)
1100       update tutorial_global_oce_biogeo AD output file.
1101    o pkg/exf:
1102      - account for the variation of albedo as a function of zenith angle
1103        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1104    o build_options:
1105     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1106    o pkg/dic:
1107      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1108      - use binary pickup file for restart;
1109      - initialise atmos-CO2 box from dic_pCO2 parameter;
1110      - fix multi-threaded.
1111    o pkg/rbcs:
1112     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1113       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1114     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1115       and update output.txt
1116    o pkg/kpp:
1117     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1118     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1119       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1120       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1121     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1122       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1123    o pkg/offline:
1124      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1125      (bug was added in version 1.10 on 2007-08-23).
1126    o pkg/offline:
1127      - no need to specify periodicExternalForcing, etc ... to use offline pack
1128      - offline input files no longer just single prec --> parameter offlineLoadPrec
1129    o verification/lab_sea:
1130      change AD test to multi-tile setup and update all 4 AD output.
1131      NOTE: while cost function values remain very similar,
1132      gradients are very different, although gradient checks are self-consistent
1133      Should try to get to the bottom of this (cost function summation order?)
1134    o pkg/dic:
1135      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1136      a weakness of TAF that drops part of double precision in log10 derivative.
1137      <= changes removed since problem has been fixed in current TAF version 1.9.71
1138      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1139    o pkg/ecco:
1140      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1141      update all 4 lab_sea AD output.
1142    
1143    checkpoint62d (2010/03/22)
1144    o build_options:
1145      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1146    o remove unbalanced quote (single or double) in commented line of source code
1147      (may cause some warning with some preprocessor/makedepend versions).
1148    o pkg/seaice:
1149      fix seaice_model.F for adjoint (gael) and update AD results of experiments
1150       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1151    o testreport:
1152      add option '-runonly' (short: '-ro') to just do the run part (without make).
1153    o eesupp: remove JAM communication code (obsolete).
1154    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1155      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1156      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1157      (update also the output).
1158    
1159    checkpoint62c (2010/03/02)
1160    o tools/build_options :
1161       move (some) old optfiles from build_options/ to build_options/unsupported/
1162    o model/src and pkg/exf
1163       surface relaxation -- separating data and data.exf options
1164       The point is to ensure that we specify the surface relaxation
1165       either in data or in data.exf (but not half and half) and to
1166       avoid an accidental relaxation to 0 (which happened if a time
1167       scale was specified but the file name was left empty)
1168    o model/src model/inc and pkg/mom_common
1169       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1170       => addition to the viscosity field as computed by others schemes
1171    o tools/build_options:
1172      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1173        but keep the former optfile for few weeks for smooth transition
1174    o pkg/ecco
1175      - allow user defined cost function contributions
1176         CPP: ALLOW_USERCOST_CONTRIBUTION
1177         USAGE: compute contributions in cost_usercost_all.F
1178      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1179          the two options are complementary.
1180    o pkg/smooth
1181      - migration from contrib to the main repository
1182    
1183    checkpoint62b (2010/01/26)
1184    o pkg/monitor:
1185      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1186        (in case someone forgot to update customized pieces of code)
1187    o nonHydrostatic:
1188      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1189      - add a simple 2-D experiment (short_surf_wave) to test it.
1190    o pkg/icefront:
1191       adding the shell of, and the hooks to, a new package that
1192       will model melting and freezing of vertical glacier ice fronts
1193    o momentum:
1194      add diagnostics of momentum tendency from Hydrostatic pressure gradient
1195       (without surf.pressure term: would need a 2nd filling since implicit term).
1196    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1197      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1198      cannot deal with the former
1199    o cleaning:
1200      - remove all (except OpenAD) old TLM output from results_ad dirs.
1201      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1202      - comment out maskH definition (replaced by maskInC)
1203    o pkg/monitor:
1204      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1205        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1206    
1207    checkpoint62a (2010/01/15)
1208    o model/src:
1209      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1210    o pkg/diagnostics:
1211      - add optional level number diagnostics (i.e., level number to be define
1212        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
1213      - strictly check for valid parser-code(10) ;
1214      - check if adding diag to the list from the right place.
1215    o pkg/longstep:
1216      - change parameters and fix tracer conservation with rstar/nonlinear free surface
1217    o diagnostics:
1218     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
1219       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
1220    o pkg/diagnostics:
1221   - Add option for writing vertical integral (sum of selected levels) of an output   - Add option for writing vertical integral (sum of selected levels) of an output
1222      field instead of writing output field levels. Activate this option on a per      field instead of writing output field levels. Activate this option on a per
1223      output-file basis, by setting the 2nd character of fileflag to 'I'.      output-file basis, by setting the 2nd character of fileflag to 'I'.
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