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revision 1.1295 by jmc, Sat Sep 11 21:39:13 2010 UTC revision 1.1463 by jmc, Thu Jun 23 15:43:39 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/diagnostics:
8     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
9       which are not filled-up but computed from other diags ; In this case, the mate
10       diag points to the primary (filled-up) diag to used for post processing.
11     - Update Velocity-potential computation using post-processed diag framework.
12     ==> Change the ordering of fields and time-periods in MDS output file
13       when using periodic averaging: now writes one time record with the full set
14       of fields for this time period, then the next time reccord (it used to be
15       one field with the full set of time records then the next field).
16         Note: this is now similar to NetCDF (MNC) output file. <==
17     - Extend the use of "missing_value" setting from data.diagnostics for the case
18       of counter-diagnostics (where fraction-weight is zero). This applies both to
19       MNC and MDS output files.
20    
21    checkpoint62z (2011/06/21)
22    o adjoint monitor:
23     - Add adjoint monitor output for packages exf, seaice
24       and update relevant testreport output
25    o pkg/seaice:
26     - re-order diags inits so that they appear in order in available_diagnostics.log
27     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
28       area/heff/hsnow preceeding thermodynamic growth/melt.
29     - modified diag: SIdA; output actual effect, as the description states.
30     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
31     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
32       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
33        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
34     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
35     - added diagnostics for seaice generic tracers (SItr*).
36     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
37     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
38     I. Fenty: 18-Jun-2011:
39     Minor changes to seaice package:
40     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
41        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
42       - Differentiated "regularization variables" from "floor variables"
43        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
44        * hiceMin became SEAICE_hice_reg (old hiceMin)
45          (with _reg meaning regularization variable)
46       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
47        so as to ensure energy conservation when going between phases
48      - A22 was not used anywhere
49     2) Changed regularization procedure for heffActual and hsnowActual to ensure
50        well-boundedness and smooth adjoint in seaice_growth.F
51     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
52        because the old regularization always set heffActual >= 0.05 cm
53     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
54        on AREA when HEFF > 0.
55      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
56        requiring that DISABLE_AREA_FLOOR *not* be defined
57     Affected verifications:
58      - 1D_ocean_ice_column (output.txt output_adm.txt)
59      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
60    o pkg/diagnostics:
61      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
62      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
63        (was _RL, now integer) with option = 0 to retrieve all levels.
64      - add pieces of code to compute velocity potential at each level (new diagnostics
65        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
66        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
67      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
68        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
69        and in diagnostics_fract_fill.F (do not need a valid pointer for the
70        diagnostics counter-mate); check that definition of counter-diagnostic
71        includes a valid counter-mate (in diagnostics_set_levels.F).
72    o model/src (rStar):
73      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
74        affect solution only if z* with full pressure in EOS;
75        update output of test-exp global_ocean.90x40x15.
76    o pkg/seaice:
77      - introduce siEps=1e-5 parameter
78      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
79      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
80      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
81        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
82        as well as ice cover age and ridging index (attached to AREA).
83        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
84        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
85        Up to SItrMaxNum=3 tracers can be used simultaneously.
86    o pkg/salt_plume:
87      -introduce SPsalFRAC run time parameter that sets the fraction of the
88       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
89       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
90    o model debug options:
91      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
92        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
93      - Refine debug-msg printing selection (3 new levels):
94        debugMode  : controls printing of debug messages (sequence of S/R calls).
95        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
96         debLevZero =  0 ; /* level of disabled aux. msg printing */
97         debLevA =  1 ; /* level of minimum  aux. msg printing */
98         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
99         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
100         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
101         debLevE =  5 ; /* level of extensive debug printing */
102        New debugLevel default: with default debugMode value (=F),
103          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
104          and if debugMode=T, default debugLevel = 4 (debLevD).
105        Relation with previous settings:
106         debLevB (=2) corresponds to former debLevA (=1)
107         debLevD (=4) corresponds to former debLevB (=2)
108        Note:
109         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
110         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
111            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
112      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
113        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
114    o pkg/obcs:
115      - change OBCSfixTopo default from True to False (should not change the results);
116        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
117    o pkg/thsice:
118      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
119        2nd layer seaice sublimation (unlikely to happen)
120      - use Interior mask for OBCS in thsice_advection.F (similar to what is
121        done in gad_advection & seaice_advection).
122    o adjoint:
123      bug fix spotted by Gael Forget:
124      seaice_advection and thsice_advection still had
125      legacy CPP options to avoid CS corner updates for adjoint
126    o pkg/seaice:
127      => Change some of the defaults (2011/05/29):
128         - change SEAICEuseFluxForm default (from False to True)
129         - change DIFF1 default (from 0.004 m/s to 0. m/s)
130         And print warnings if DIFF1 is not set in data.seaice and centered
131          avection scheme is used without any diffusion.
132      also:
133      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
134      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
135      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
136        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
137        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
138      update results of test exp.:
139         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
140             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
141             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
142         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
143         seaice_obcs: output (SEAICEuseFluxForm=T)
144      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
145          for standard fwd & AD lab_sea tests (to keep the same output).
146    o pkg/seaice/seaice_growth.F:
147      - use Ian Fenty's capping formulas for actual ice
148      thickness thoughout EVOLUTION branch.
149      - put treatment pathological case #2) in CPP brackets
150      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
151      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
152    o pkg/seaice:
153      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
154      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
155      also pass fac as a param, which can be 1. (to update the tendency
156      field) or the time step (to update the field itself).
157      - seaice_advdiff.F: for multidim, call seaice_diffusion with
158      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
159      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
160      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
161      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
162    o pkg/seaice:
163      diffusion with centered advection scheme (diffus.F & advect.F):
164      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
165        to just compute the laplacian of input-field.
166      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
167      - fix flux-form version in diffus.F to conserve tracer.
168      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
169       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
170    
171    checkpoint62y (2011/05/26)
172    o pkg/seaice:
173     - seaice_growth.F : in EVOLUTION branch, always include
174       a_QSWbyATM_cover in qnet (as it should be).
175     - verification/global_ocean.cs32x15 : update results accordingly
176       (output.seaice.txt output_adm.seaice.txt).
177    o pkg/seaice + obcs:
178     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
179       equivalent of assuming no tracer gradient outside the OB region.
180       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
181     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
182       after changes above);
183     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
184       only at OB location (instead of over a band of OLx width).
185    o pkg/seaice:
186     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
187       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
188    o pkg/obcs:
189      - split header file "OBCS.h" into 4 separated files:
190        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
191       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
192         (contain no conditional statement which depends on OBCS options).
193      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
194        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
195    o ctrl, cost, grdchk & autodiff pkgs:
196      - make options file more standard (like other {PKG}_OPTIONS.h file but
197        with AD_CONFIG.h); clean-up some of the included header files.
198    o pkg/obcs:
199      - do not mask tracer when applying OB (tracer == 0 could generate problems)
200      - apply tracer OB values to tracer field only at OB location (instead of
201        over a band of OLx width)
202      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
203      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
204        obcs_apply_tloc.F & obcs_apply_sloc.F
205    o obcs in model/src:
206      - call OBCS_APPLY_W only if NonHydrostatic.
207      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
208      - reset dEtaHdt and wVel to zero outside OB interior region ;
209      - leave tracer unchanged outside OB interior region: This has no effect
210        on the solution but just to prevent unrealistic tracer value outside OB.
211      - zero out velocity outside OB interior region: This has no effect on
212        the solution but just to prevent unrealistic velocity outside OB.
213    o obcs and non-lin free-surf:
214       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
215       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
216       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
217       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
218       update results of test-exp. exp4(nlfs).
219    o exp4 (nlfs) test-exp:
220       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
221       with NonLin-FreeSurf); update output.nlfs.txt
222    o obcs and 2d/3d solver norm:
223       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
224       and outside OB interior region (will allow to place OB further inside the
225       domain). Depending on the domain, can affects cg2d-Norm (previous
226       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
227       and cg3d-Norm (previous Norm was computed before canceling OB terms),
228       e.g. in tutorial_plume_on_slope.
229      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
230    o pkg rbcs:
231      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
232      - add capability to apply relaxation to horizontal velocity uVel & vVel.
233    o pkg/grdchk: add gradient check for control variable xx_shifwflx
234    o pkg/shelfice/shelfice_init_fixed.F
235      fix CPP-flag combinations
236    o pkg/seaice: Merge iceage code of Pierre Rampal
237      * update/change/correct ice age calculations
238      * add age updates for pathological cases
239      Probably needs more testing...
240    
241    checkpoint62x (2011/05/13)
242    o pkg/mom_vecinv:
243       high-order vorticity scheme: use interior masks (maskInW & S)
244       to zero-out (outside OB) gradient of vorticity.
245    o verification exp.:
246       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
247       hs94.128x64x5 and seaice_obcs ; update results.
248    o pkg/obcs:
249      fix bug in OBeta for YZ sections in obcs_exf_load.F
250    o pkg/ctrl, pkg/shelfice, and optim:
251      - add new control variable xx_shifwflx (fresh water flux underneath ice
252        shelves). This is almost as tedious as obcs-ctrl, because the
253        variables needs its own mask.
254      - add a cost function term that penalizes the deviation of xx_shifwflx
255        from the first guess (zero) in analogy to other control variables
256    o pkg/shelfice:
257      - start basic adjoint
258    o pkg/ctrl:
259      - remove extra 2D field "for good measure" when initializing in
260        ctrl_set_globfld_[xy/xz/yz].F
261      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
262      - improve error messages in ctrl_set_unpack_*
263    o OBC implementation in momentum:
264       use interior masks (maskInC,W & S) in momentum S/R:
265       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
266       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
267       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
268       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
269       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
270        (and also with Leith/Smagorinsky harmonic-viscosity).
271       Update output of experiment dome and exp4 (+nlfs).
272    o exp4 test-exp:
273      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
274        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
275        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
276        time-varying OB at Western-side for wVel (NonHyd); update output.
277      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
278        and biharmonic-viscosity ; also use prescribed time varying OB.
279    o pkg/obcs:
280      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
281    o model/src:
282      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
283      - initialise startTime & nIter0 with unlikely values: allows to set one
284        from the other without ambiguity.
285    o seaice_obcs test-exp.:
286      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
287    o pkg/obcs:
288      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
289        no longer needed with maskInC,W,S in pkg/generic_advdiff.
290    o pkg/seaice:
291      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
292        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
293      - fixed bug in the initialization of sea ice salinity variable HSALT
294        in seaice_init_varia.F  (removed dependence on ICE2WATR)
295    o fizhi-cs test exp.:
296       switch reference output convention for these 2 non-standard test-exp,
297        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
298          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
299       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
300    o model/inc:
301      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
302        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
303    o pkg/seaice:
304      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
305    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
306      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
307        and initial HSALT
308    
309    checkpoint62w (2011/04/26)
310    o pkg/mom_fluxform:
311      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
312      - use parameter "sideDragFactor" in no-slip BC side-drag part.
313      - update output of exp. global_ocean.90x40x15
314    o pkg/mom_vecinv:
315      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
316    o update seaice exp.:
317      use more consistent parameter values (remove "backward compatability only":
318       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
319      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
320       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
321    o update test-exp global_ocean.90x40x15:
322      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
323      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
324      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
325      o turn on zStar & viscA4 in standard set-up (dir input/)
326        and update output files: output.txt & output.dwnslp.txt
327    o new AD-test experiment: obcs_ctrl
328      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
329    o pkg/dic:
330      fix two bugs in handling water vapour pressure in carbonate chemistry
331      and air-sea fluxes. Found by Val Bennington and Galen McKinley
332      (add DIC Option = WATERVAP_BUG to recover old results)
333      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
334    o adding allowInteriorFreezing option to check for water below freezing point
335      at depth and bring the negative heat anomaly to the surface level
336    o pkgs _fields_load:
337      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
338      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
339        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
340        rbcs to get interpolation weights and time reccord number.
341      - fix multi-threading in aim_fields_load.F
342      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
343    o external_fields_load:
344      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
345       interpolation weights) to use in a periodic time-series ; do not divide by
346       time-step to convert to integer:
347       - this fixes case where externForcingPeriod is not multiple of time-step
348          (Thanks to Christopher L. Wolfe)
349       - this fixes case where externForcingPeriod is an odd multiple of time-step
350         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
351      store index of time-record which is currently loaded:
352       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
353       - needed for the adjoint but not yet used because of extensive recomputations;
354         (to be fixed soon)
355    
356    checkpoint62v (2011/04/02)
357    o verification/1D_ocean_ice_column added to test Ian Fenty's
358      pkg/seaice_growth.F modifications for improving sea ice code differentiability
359    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
360      (new velocity statistics after changing maskInW & maskInS definition)
361    o pkg/generic_advdiff with OBCS:
362      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
363      equivalent to assumption of no tracer gradient outside the OB region.
364      This will affect the results if using obcs+biharmonic diffusion.
365      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
366    o pkg/obcs:
367      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
368      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
369      in Interior region. No impact on solution but affects Velocity monitor stats.
370    o pkg/ptracers (adjoint)
371      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
372      tape file for each tracer
373    o model/inc/src and pkg/autodiff: add parameters that allow to turn
374      of parts of the adjoint code at run time. For now, there are only
375      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
376      parameters are set in data.pkg.
377      This is the lazy coward's version of doing this, but still useful for
378      debugging. In order to do it right, everything needs to be moved to
379      pkg/autodiff.
380    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
381      the end; this fixes the adjoint balancing code for open boundaries.
382    o pkg/ctrl:
383      - change behavior of xx_${varname}period to be analogous to exf-conventions:
384        xx_${varname}period =   0.,  means time-independent control part
385        xx_${varname}period = -12., means one-year-periodic monthly control part
386      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
387        clean up ctrl_init a little, remove unused variables
388      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
389      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
390    
391    checkpoint62u (2011/03/15)
392    o model/src:
393      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
394        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
395      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
396        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
397    o pkg/ctrl/obcs/ecco:
398      - remove obsolete, unused, and partially broken code:
399        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
400        ALLOW_CTRL_OBCS_BALANCE
401      - put a stop statement into ecco/cost_obcsvol.F, but also add
402        cost_obcsvol to ecco_ad_diff.list
403    o pkg/ecco: fix counting cost function contributions for obcs (code
404      by Matt M.) and diffkr for diagnostics
405    o pkg/ecco, pkg/ctrl, pkg/grdchk:
406      add cost penalty terms for initial uvel, vvel, eta controls
407      and I/O for prior error files
408    o pkg/mdsio:
409       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
410       (new argument) to check for tiled file in mdsioLocalDir : this fix the
411       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
412    o pkg/ctrl:
413     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
414       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
415       unused and superfluous variables
416     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
417    o pkg/ecco
418     - enable adjoint of Stevens OB
419    o pkg/ctrl/ecco/grdchk:
420      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
421        Fortunately, we do not have any tests for the numerous cpp-flagged
422        option of "obcs as control parameters" so we will never know
423        if this is an improvement (but at least now things compile).
424      - remove an obsolete initialization from ecco_cost_init_barfiles.F
425      - fix some problems within never used ifdefs to make the code compile
426    o pkg/obcs:
427     - Refine Interior mask definition to work with more complex OB (e.g.
428       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
429       read in Interior mask from file. Check if Interior mask is consistent
430       with OB list of indices.
431    o pkg/seaice
432     - beginning code for a seaice tracer package,
433       but currently only used for seaice age: SEAICE_AGE
434       SEAICE_num = 4
435       iTracer = 1: area-weighted ice age
436               = 2: volume-weighted ice age
437               = 3, 4: template for one-year vs. multi-year ice
438       data.seaice has new namelist SEAICE_PARM03 for arrays related to
439       SEAICE_num
440    
441    checkpoint62t (2011/03/05)
442    o pkg/obcs:
443     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
444       then normal component. This ensures that the normal component is set
445       correctly even when it conficts with tangential setting from an other OB.
446       Affects results of test-experiment seaice_obcs: update the output.txt
447    o pkg/obcs:
448     - add code to monitor statistics of dynamical fields at OB.
449     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
450       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
451       - change default: balance the Net inflow through all OB (instead of balancing
452         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
453     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
454       to match Nortern OB inflow (OBCS_balanceFacN=0).
455    o pkg/seaice:
456     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
457    o pkg/seaice (seaice_growth v 1.113):
458     - reverting seaice_growth to v 1.111 in order to have code with exact bit
459       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
460       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
461       runtime flag SEAICEareaFormula is kept but is inactive
462    o model/src:
463     - add new param to scale curvilinear grid distance and area when using
464       a different sphere radius from the grid-files.
465     - test/check multi-threads EXCH applied to local variable (cg2d_x)
466    o adjoint:
467     - enable adjoint of Stevens OB
468     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
469       (a bit delicate because of potentially modified adj. common block structure;
470       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
471    
472    checkpoint62s (2011/02/15)
473    o pkg/seaice (seaice_growth v 1.112):
474     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
475       computing the ice cover tendency from effective thickness tendencies. Include
476       Ian Fenty's formula.
477     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
478       SEAICEareaFormula.
479     - simplify notations for the various d_HEFF/d_AREA terms.
480    o pkg/gmredi:
481     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
482       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
483       add a verification test-run (front_relax.bvp) to test GM_useBVP.
484    o pkg/seaice (seaice_growth v 1.111):
485     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
486     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
487       also melt ice.
488    o pkg/seaice:
489     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
490     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
491    o pkg/cheapaml:
492     - from Nico Wienders: New version of this package.
493    o pkg/flt:
494     - add CPP options to prevent floats to re-enter the opposite side of
495       a periodic domain (default: keep periodicity)
496    o pkg/gmredi:
497     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
498       (needed for multi-dim advection).
499     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
500    o model/src:
501     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
502    o tutorial_tracer_adjsens
503     - extend to NLFS and replace maskC by hFacC
504       (change reference output accordingly)
505    
506    checkpoint62r (2011/01/24)
507    o testreport:
508     - add option -deloutp (-do) to remove output file after successful run
509     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
510       extract exact list of procs from this file ; adjust COMMAND by
511       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
512    o pkg/ecco: replace old ineffective way of penalizing deviations from
513      first guess (of obcs) with code by Matt Mazloff
514    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
515      exf/cal
516      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
517        and handle case of obcs?period == 0
518        Not affected by these changes: There is still an inconsistency in
519        the computation of start/endrec for the obcs variables for ALLOW_CAL
520        defined (see comment by Menemenlis, 7-Mar-2003)
521      - make S/R ctrl_get_gen_rec return something meaningful even if
522        ALLOW_CAL is not defined
523      - ctrl_getobcs?: simplify code so that it does not need to use
524                       S/R exf_swapfields
525    o testreport:
526       allow to test MPI with different number of processors for each experiment:
527       create file "SIZE.h.mpi" in each build dir.
528       Note: update of "-command" argument not yet implemented.
529    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
530      alleviate the need for additional 3D tapes when using
531      the non-inear free surface in the adjoint. This is done
532      by adding an 'update' of hfacc etc. to their current
533      value at the beginning of forward_step.F.
534    o pkg/seaice
535      seaice_lsr: move stress-divergence computations out of outer pseudo-
536      timestepping loop
537    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
538      up, so that the calls of the ctrl_* subroutines are really at the end
539      of the routine.
540    o pkg/gmredi:
541      allow to specify a 2-D horizontal map and a 1-D vertical profil
542      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
543    o pkg/seaice:
544      move lsr iterations from seaice_dynsolver to seaice_lsr.
545    o pkg/seaice:
546      reduce memory footprint of seaice mutldim advection tapes,
547      by using a 2D tape independent of the generic_advdiff ones,
548      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
549    
550    checkpoint62q (2010/12/29)
551    o model/src:
552      - check horizontal grid-spacing for unset or zero/negative values.
553      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
554    o pkg/flt:
555      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
556      - precision of input and output files set according to readBinaryPrec
557        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
558      - initial float position from tiled file was not converted to index space
559        (looks like a bug): fixed to make it similar to initial pos. global file.
560    o global_ocean.cs32x15:
561       change SIZE.h of AD set-up to get same tiling as with MPI.
562       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
563    o model/src:
564       add flag to control printing of domain fields (bathymetry, hFac ...) in
565       ini_mask_etc (call to plot_fieds_xy*).
566    o pkg/thsice:
567       if useEXF, some forcing fields are not valid in overlap: fixed by computing
568       over the interior only + apply EXCH at the end (like with SEAICE advection).
569    o pkg/mdsio:
570      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
571        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
572      - change barrier call for safe multi-threads access to 3-D shared buffer.
573      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
574      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
575        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
576    o pkg/flt:
577      - add fourth-order Runge-Kutta integration
578      - add basic exch2 support (only 1 facet supported so far!)
579    o pkg/mdsio+rw:
580      new S/R to read local (or tile independent) vector (read counterpart of
581       mds_writevec_loc, and front-end write_glvec_rl/rs).
582    o global_ocean.cs32x15: additional input_ad.seaice experiment
583        that uses pkg/seaice rather than pkg/thsice.
584        (using multidim advection for seaice)
585    o towards more F95 syntax for array specification in namelist:
586      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
587        of all verification experiments.
588           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
589          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
590      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
591    o global_ocean.cs32x15: additional input.seaice experiment
592        that uses pkg/seaice rather than pkg/thsice.
593    
594    checkpoint62p (2010/12/17)
595    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
596        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
597    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
598        allow for use of multim. advection in seaice adjoint.
599    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
600      - first attempt to close budgets by taking into account the freshwater
601        flux implied by the sublimation of snow and ice. So far only the
602        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
603        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
604    o eesupp/src:
605      new S/R with new option (NML_EXTENDED_F77) to change array specification
606      from F95 standard to commonly accepted extended F77 form.
607      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
608      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
609      for less tolerant f77 compiler (e.g., pgf77, g77).
610    o globalFiles:
611      commented out in parameter file "data" since it's not safe with MPI
612      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
613      in this case); no longer commented out in restart test (tst_2+2).
614    o add adTapeDir to specify a special directory where adjoint tapes are
615      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
616      and cannot be used together with mdsioLocalDir.
617    o nesting pkgs:
618      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
619      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
620      - add parameter files + utils dir + output from short run on beagle.
621    o pkg/seaice:
622        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
623    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
624      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
625    
626    checkpoint62o (2010/11/25)
627    o pkg/exf:
628      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
629    o pkg/seaice:
630      - seaice_ocean_stress: split a loop for better vectorization of the
631        adjoint code
632      - seaice_growth.F: fix bug in conservation of freshwater connected to
633        capping of heff, put contribution into d_HEFFbyNEG
634      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
635        by something more sensible (parameters that are what their name implies)
636      - change some defaults, so that by default exf-parameters are used for
637        things like rhoAir, cpAir,latent/sensible heat parameters, in order
638        to reproduce the old results, many data.seaice now contain funny values
639        for cpAir and latent heat of sublimation
640    o packages_readparms.F: move exf_readparms up in line so that
641        exf-parameters are visible for other packages (e.g. seaice)
642    o debugMode & debugLevel=2:
643      - differentiate between debugMode & debugLevel=2:
644        debugMode: controls printing of debug messages (sequence of S/R calls).
645        debugLevel: controls printing of algorithm intermediate results and stats.
646      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
647        => allows to print debug-stats without all sequence of call messages.
648      - switch control of debug print from debugLevel to debugMode in many S/R.
649    o pkg/obcs (obcs-sponge):
650        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
651        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
652    o pkg/generic_advdiff:
653      - record overlap minimum size for each advection scheme;
654      - refine criteria on overlap minimum size;
655      - check and stop (in gad_check) if overlap size is too small.
656    o pkg/obcs:
657      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
658        once, in ptracers_implicit.F)
659      - with seaice: remove test on empty file name in obcs_apply_seaice (always
660        apply OB values when tile has OB)
661    o model/src, coriolis setting:
662      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
663        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
664        files (selectCoriMap=3) with any grid.
665      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
666    o pkg/seaice/seaice_growth.F:
667        a few cosmetic changes that reduce the number of lines of code
668    o pkg/obcs: add boundary conditions following Stevens (1990)
669      - the code follows old MOM/NAOSIM code
670      - so far it is only implemented for the eastern and western boundaries
671        and NOT for pTracers
672    o pkg/rbcs:
673      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
674        beginning of the first rbcs forcing period.
675      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
676        offline package, i.e., one file per time, labeled by iteration number;
677        deltaTrbcs sets the timestep with which the data was generated;
678        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
679      - rbcsForcingCycle=0 makes forcing non-cyclic.
680      - make arithmetic safe for negative times and odd forcing periods.
681    
682    checkpoint62n (2010/11/09)
683    o pkg/seaice:
684        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
685    o pkg/obcs:
686       New S/R to copy tracer value from the OB location to narrow band region
687        (width = same as overlap) beyond the OB: preserve OB value (needed for
688        high-order scheme) which were overwritten by EXCH call if in overlap
689        region. Applied to theta, salt, ptracer and advected seaice variables.
690       With seaice: use maskInC in similar way as in gad_advection.F,
691        in seaice_advection.F and advect.F.
692       Update output of experiment seaice_obcs and change exp4 to test OBCS with
693        4th order Adv.Scheme. for pasive salt and ptracer.
694    o tools/genmake2:
695      - when looking for an optfile (not specified), only search for Fortran compiler
696        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
697      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
698        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
699      - set default for CPP to "cpp -traditional -P" (was the case without specifying
700        an optfile, but otherwise default was just "cpp".
701      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
702      - when "CC" is not set in the optfile, look for possible C compiler
703        (instead of just setting CC=cc)
704      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
705        => add a ".F" to ".o" rule for source files with no "#include" (such as
706           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
707      - move gfortran before g77 in list of possible Fortran compiler (consistent
708        with reference compiler switch from g77 to gfortran)
709    o pkg/seaice:
710      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
711        seaice_check that stops the model, when the CPP flag is used.
712      o seaice_growth.F: make capping of ice volume conserving by returning the
713        capped ice as freshwater to EmPmR. This does not change the verification
714        experiments but will change runs where the capping is acutally active
715    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
716      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
717         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
718         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
719    o tools/genmake2:
720      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
721      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
722      - clean previous genmake log files before anything else.
723      - change Makefile to remove testreport log files (*.tr_log) and genmake log
724        files only with "CLEAN" target (instead of "Clean");
725    o pkg/generic_advdiff:
726      Change OBCS in multiDim advection (gad_advection.F):
727       Use maskInC to prevent intermediate update of tracer-field in OB regions,
728       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
729       which were applying future time-step OB values.
730      This way, all explicit calculations use current-time-step OB values
731       (simpler and more consistent).
732      Affects results when set-up uses time-varying OBC and multi-dim advection;
733       update output of experiment seaice_obcs.
734    o pkg/seaice:
735      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
736       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
737         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
738      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
739       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
740       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
741    o pkg aim (2010/10/26):
742      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
743        formulation with obliquity, eccentricity, ... as run-time parameters,
744      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
745        upward shortwave radition at the surface (all-sky and clear-sky).
746    o pkg/obcs:
747      - writing sections with globalFiles=T does not work: switch to tiled-files
748        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
749      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
750      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
751    
752    checkpoint62m (2010/10/21)
753    o pkg/seaice: vectorize seaice_solve4temp.F
754      - move iterations loops outside of i/j-loops
755      - requires 2D arrays for TB and effConduct
756      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
757        modified in this routine
758      - a little bit of clean up, adjusting indentation, etc.
759      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
760        performance and '**TWO' by '**2' (because TWO is a float),
761        replaced ONE, ZERO
762    o eesupp/src:
763       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
764    o pkg/seaice/seaice_growth.F
765      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
766      merging process. The merged routine has two branches, and one activates the 'evolution'
767      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
768      In summary, here is what the '10/10 revision' did consist of
769        part 1: seaice_growth.F revisions 1.71 to 1.75
770          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
771            The emphasis here was on improving readability (e.g. by trying to use meaningful
772            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
773        part 1.5:
774          - revising the lab_sea experiment to make it a more useful (i.e. stable
775            and representative of an actual model run). This was done by generating a
776            (winter) pickup to start from, switching back the main experiment dynamic
777            solver from evp to lsr, having one of the experiments use the free drift solution.
778        part 2: seaice_growth.F revisions 1.76 to 1.85
779          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
780          - Sorting out the various fields units and sign (set early on and reset at the end)
781            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
782            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
783          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
784            and simplifying logical expressions to further improve readibility.
785        part 3: seaice_growth.F revisions 1.86 to 1.89
786          - Re-organize the blocks of code more logically.
787          - Merging the '_if.F' pieces that add something new.
788    o pkg/thsice:
789      - vectorize thsice_solve4temp and thsice_get_exf.
790        Problem: thsice_solve4temp has an unvectorizable statement that
791        might also be problematic for TAF
792      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
793        does not change the verifcation experiment, but will change all
794        experiments that have this flag undefined (not tested in verification);
795        a little reorganization to save a few 2D fields and recomputations
796      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
797      - 2nd step:  fix some store dirs
798        o seems to work somewhat, i.e. using ifort but not g77
799        o likely cause are incomplete init. or recomputation
800        o start verification/global_ocean.cs32x15/input_ad.thsice
801    o pkg/obcs: add support for exch2
802      - the position of the boundary and prescribed values are specified using
803        a global domain with exch2 facets stacked
804        - in x for N,S boundaries (like W2_mapIO=-1)
805        - in y for E,W boundaries (so E,W boundaries do not overlap)
806    o pkg/mdsio: add support for writing global sections with exch2
807        file layout is as for obcs described above:
808        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
809        - for y-z sections, facets are stacked in y
810    o pkg/thsice:
811       - change a few routines for better vectorization: thsice_albedo.F,
812         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
813         not affected, but in particular the latter routine has changed
814         dramatically (not necessarily easier to read now).
815       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
816       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
817    o verification/lab_sea:
818      - overhaul of the forward model experiments. The main motivation
819        for this revision is that lab_sea has proven quite fragile (when
820        changing the sea-ice code, and switching platforms) to a point
821        when failures were very hard to attribute to specific code problems.
822      - the suspected reason for this fragility is noise amplification by evp so,
823        to start with, we decided to replace evp with lsr in the main experiment.
824      - the input.lsr experiment thus became obsolete and was removed.
825      - it was replaced with the input.fd experiment that uses an
826        analytical "free drift" solution as the ice velocity field.
827      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
828        will hopefully allow us to discriminate problems due to dynamic solvers
829        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
830        us to test additional options, along with the salt plume package.
831      - Finally a pickup was generated (at the end of a one year run) to
832        make the tests more representative of an actual model run. Previously
833        the tests starting point was a 1m thickness of ice everywhere.
834    o pkg/seaice:
835      - introducing S\R seaice_freedrift.F that compute the
836        analytical solution to an approximate ice momentum
837        equation (i.e. the simple stress/coriolis balance).
838      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
839        of the free drift velocity field, and enable its use.
840        To actually use the free drift solution as the model ice
841        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
842    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
843    
844    checkpoint62l (2010/10/04)
845    o pkg/seaice:
846      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
847      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
848       version (with USE_ORIGINAL_SBI undef);
849    o add hooks for new packages OASIS, the package will follow
850      (hooks exclude the seaice pkg for now)
851    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
852      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
853      rather than mdsio_readvector.F/mdsio_writevector.F, within
854      adread_adwrite.F to read/write adjoint-related tapes to disk.
855    o eesupp and pkg/mdsio: ALLOW_WHIO
856      Option to write/read 2D fields to files including tiles halos.
857      The main purpose is for adjoint related "tape I/O".
858      The secondary purpose is for debugging phases.
859      A word on those rather specifically intended purposes.
860      The code was meant to be stripped down to the bare minimum.
861      Typically, there is a unique and basic mapping to the global
862      buffer (tile by tile, then proc by proc, then level by level), and
863      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
864      meant to generate user friendly outputs of various shapes and forms.
865      Rather it is intended, for the knowledgeabale developers,
866      to be largely independent of the many mdsio options, to allow
867      outputs of tiles+halos in debugging phases and in adjoint runs,
868      and to allow some flexibility in tuning (adoint) I/O depending on each
869      file system behavior. With regard to tuning, most of the potential knobs
870      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
871      to specify directories, to specify the typical size of I/O calls, etc.)
872      are not yet included, and will be added if they prove useful.
873    o pkg/seaice:
874       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
875    o pkg/seaice:
876       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
877       code (seaice_budget_ice_if.F) which enable to recover old standard
878       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
879       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
880    o model/src (rStar):
881       use simple average (not area weighted) of rStarFac at U,V point when using
882       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
883       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
884    
885    checkpoint62k (2010/09/17)
886    o adjoint
887       * changed verification/global_ocean.cs32x15 ; adjoint now tests
888         Adams-Bashforth 3 + NLFS + RSTAR
889       * some more modifs required for ECCO-GODAE v4
890    o pkg/seaice
891       add SEAICE_AGE_VOL option to use volume instead of area for
892       integrating SEAICE_AGE
893  o model/src:  o model/src:
894     first check-in of sigma & hybrid-sigma coordinate code ; also includes     first check-in of sigma & hybrid-sigma coordinate code ; also includes
895     non-linear free-surface parts ; but pressure-gradient not yet coded.     non-linear free-surface parts ; but pressure-gradient not yet coded.
# Line 273  o tools/build_options: Line 1159  o tools/build_options:
1159      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1160  o pkg/ecco  o pkg/ecco
1161    - allow user defined cost function contributions    - allow user defined cost function contributions
1162          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1163          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1164    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1165        the two options are complementary.        the two options are complementary.
1166  o pkg/smooth  o pkg/smooth
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