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revision 1.1273 by jmc, Tue May 18 22:53:25 2010 UTC revision 1.1468 by heimbach, Wed Jun 29 16:28:46 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/shelfice
8     - Implement friction velocity-dependent transfer coefficients following
9       Holland and Jenkins, JPO, 1999
10       Original code by M. Losch with small modifs.
11       Enable with CPP option SHI_ALLOW_GAMMAFRICT
12       and runtime flag SHELFICEuseGammaFrict
13    o verification lab_sea & global_ocean.cs32x15:
14     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
15       does not miss some dependencies (but is slower) and also works with many files
16       (default makedepend limitation for AD built).
17     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
18    o pkg/diagnostics:
19     - add run-time parameter "useMissingValue" (def=False) to fill land-point
20        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
21       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
22     - Extend the use of "missing_value" setting from data.diagnostics for the case
23       of counter-diagnostics (where fraction-weight is zero). This applies both to
24       MNC and MDS output files.
25    o pkg/seaice/seaice_growth.F:
26      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
27       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
28      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
29       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
30      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
31      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
32    o verification 1D_ocean_ice_column:
33       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
34       update results
35    o pkg/diagnostics:
36     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
37       which are not filled-up but computed from other diags ; In this case, the mate
38       diag points to the primary (filled-up) diag to used for post processing.
39     - Update Velocity-potential computation using post-processed diag framework.
40     ==> Change the ordering of fields and time-periods in MDS output file
41       when using periodic averaging: now writes one time record with the full set
42       of fields for this time period, then the next time reccord (it used to be
43       one field with the full set of time records then the next field).
44         Note: this is now similar to NetCDF (MNC) output file. <==
45    
46    checkpoint62z (2011/06/21)
47    o adjoint monitor:
48     - Add adjoint monitor output for packages exf, seaice
49       and update relevant testreport output
50    o pkg/seaice:
51     - re-order diags inits so that they appear in order in available_diagnostics.log
52     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
53       area/heff/hsnow preceeding thermodynamic growth/melt.
54     - modified diag: SIdA; output actual effect, as the description states.
55     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
56     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
57       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
58        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
59     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
60     - added diagnostics for seaice generic tracers (SItr*).
61     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
62     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
63     I. Fenty: 18-Jun-2011:
64     Minor changes to seaice package:
65     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
66        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
67       - Differentiated "regularization variables" from "floor variables"
68        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
69        * hiceMin became SEAICE_hice_reg (old hiceMin)
70          (with _reg meaning regularization variable)
71       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
72        so as to ensure energy conservation when going between phases
73      - A22 was not used anywhere
74     2) Changed regularization procedure for heffActual and hsnowActual to ensure
75        well-boundedness and smooth adjoint in seaice_growth.F
76     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
77        because the old regularization always set heffActual >= 0.05 cm
78     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
79        on AREA when HEFF > 0.
80      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
81        requiring that DISABLE_AREA_FLOOR *not* be defined
82     Affected verifications:
83      - 1D_ocean_ice_column (output.txt output_adm.txt)
84      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
85    o pkg/diagnostics:
86      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
87      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
88        (was _RL, now integer) with option = 0 to retrieve all levels.
89      - add pieces of code to compute velocity potential at each level (new diagnostics
90        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
91        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
92      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
93        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
94        and in diagnostics_fract_fill.F (do not need a valid pointer for the
95        diagnostics counter-mate); check that definition of counter-diagnostic
96        includes a valid counter-mate (in diagnostics_set_levels.F).
97    o model/src (rStar):
98      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
99        affect solution only if z* with full pressure in EOS;
100        update output of test-exp global_ocean.90x40x15.
101    o pkg/seaice:
102      - introduce siEps=1e-5 parameter
103      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
104      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
105      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
106        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
107        as well as ice cover age and ridging index (attached to AREA).
108        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
109        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
110        Up to SItrMaxNum=3 tracers can be used simultaneously.
111    o pkg/salt_plume:
112      -introduce SPsalFRAC run time parameter that sets the fraction of the
113       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
114       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
115    o model debug options:
116      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
117        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
118      - Refine debug-msg printing selection (3 new levels):
119        debugMode  : controls printing of debug messages (sequence of S/R calls).
120        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
121         debLevZero =  0 ; /* level of disabled aux. msg printing */
122         debLevA =  1 ; /* level of minimum  aux. msg printing */
123         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
124         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
125         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
126         debLevE =  5 ; /* level of extensive debug printing */
127        New debugLevel default: with default debugMode value (=F),
128          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
129          and if debugMode=T, default debugLevel = 4 (debLevD).
130        Relation with previous settings:
131         debLevB (=2) corresponds to former debLevA (=1)
132         debLevD (=4) corresponds to former debLevB (=2)
133        Note:
134         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
135         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
136            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
137      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
138        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
139    o pkg/obcs:
140      - change OBCSfixTopo default from True to False (should not change the results);
141        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
142    o pkg/thsice:
143      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
144        2nd layer seaice sublimation (unlikely to happen)
145      - use Interior mask for OBCS in thsice_advection.F (similar to what is
146        done in gad_advection & seaice_advection).
147    o adjoint:
148      bug fix spotted by Gael Forget:
149      seaice_advection and thsice_advection still had
150      legacy CPP options to avoid CS corner updates for adjoint
151    o pkg/seaice:
152      => Change some of the defaults (2011/05/29):
153         - change SEAICEuseFluxForm default (from False to True)
154         - change DIFF1 default (from 0.004 m/s to 0. m/s)
155         And print warnings if DIFF1 is not set in data.seaice and centered
156          avection scheme is used without any diffusion.
157      also:
158      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
159      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
160      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
161        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
162        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
163      update results of test exp.:
164         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
165             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
166             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
167         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
168         seaice_obcs: output (SEAICEuseFluxForm=T)
169      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
170          for standard fwd & AD lab_sea tests (to keep the same output).
171    o pkg/seaice/seaice_growth.F:
172      - use Ian Fenty's capping formulas for actual ice
173      thickness thoughout EVOLUTION branch.
174      - put treatment pathological case #2) in CPP brackets
175      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
176      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
177    o pkg/seaice:
178      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
179      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
180      also pass fac as a param, which can be 1. (to update the tendency
181      field) or the time step (to update the field itself).
182      - seaice_advdiff.F: for multidim, call seaice_diffusion with
183      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
184      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
185      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
186      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
187    o pkg/seaice:
188      diffusion with centered advection scheme (diffus.F & advect.F):
189      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
190        to just compute the laplacian of input-field.
191      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
192      - fix flux-form version in diffus.F to conserve tracer.
193      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
194       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
195    
196    checkpoint62y (2011/05/26)
197    o pkg/seaice:
198     - seaice_growth.F : in EVOLUTION branch, always include
199       a_QSWbyATM_cover in qnet (as it should be).
200     - verification/global_ocean.cs32x15 : update results accordingly
201       (output.seaice.txt output_adm.seaice.txt).
202    o pkg/seaice + obcs:
203     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
204       equivalent of assuming no tracer gradient outside the OB region.
205       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
206     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
207       after changes above);
208     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
209       only at OB location (instead of over a band of OLx width).
210    o pkg/seaice:
211     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
212       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
213    o pkg/obcs:
214      - split header file "OBCS.h" into 4 separated files:
215        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
216       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
217         (contain no conditional statement which depends on OBCS options).
218      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
219        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
220    o ctrl, cost, grdchk & autodiff pkgs:
221      - make options file more standard (like other {PKG}_OPTIONS.h file but
222        with AD_CONFIG.h); clean-up some of the included header files.
223    o pkg/obcs:
224      - do not mask tracer when applying OB (tracer == 0 could generate problems)
225      - apply tracer OB values to tracer field only at OB location (instead of
226        over a band of OLx width)
227      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
228      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
229        obcs_apply_tloc.F & obcs_apply_sloc.F
230    o obcs in model/src:
231      - call OBCS_APPLY_W only if NonHydrostatic.
232      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
233      - reset dEtaHdt and wVel to zero outside OB interior region ;
234      - leave tracer unchanged outside OB interior region: This has no effect
235        on the solution but just to prevent unrealistic tracer value outside OB.
236      - zero out velocity outside OB interior region: This has no effect on
237        the solution but just to prevent unrealistic velocity outside OB.
238    o obcs and non-lin free-surf:
239       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
240       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
241       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
242       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
243       update results of test-exp. exp4(nlfs).
244    o exp4 (nlfs) test-exp:
245       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
246       with NonLin-FreeSurf); update output.nlfs.txt
247    o obcs and 2d/3d solver norm:
248       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
249       and outside OB interior region (will allow to place OB further inside the
250       domain). Depending on the domain, can affects cg2d-Norm (previous
251       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
252       and cg3d-Norm (previous Norm was computed before canceling OB terms),
253       e.g. in tutorial_plume_on_slope.
254      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
255    o pkg rbcs:
256      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
257      - add capability to apply relaxation to horizontal velocity uVel & vVel.
258    o pkg/grdchk: add gradient check for control variable xx_shifwflx
259    o pkg/shelfice/shelfice_init_fixed.F
260      fix CPP-flag combinations
261    o pkg/seaice: Merge iceage code of Pierre Rampal
262      * update/change/correct ice age calculations
263      * add age updates for pathological cases
264      Probably needs more testing...
265    
266    checkpoint62x (2011/05/13)
267    o pkg/mom_vecinv:
268       high-order vorticity scheme: use interior masks (maskInW & S)
269       to zero-out (outside OB) gradient of vorticity.
270    o verification exp.:
271       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
272       hs94.128x64x5 and seaice_obcs ; update results.
273    o pkg/obcs:
274      fix bug in OBeta for YZ sections in obcs_exf_load.F
275    o pkg/ctrl, pkg/shelfice, and optim:
276      - add new control variable xx_shifwflx (fresh water flux underneath ice
277        shelves). This is almost as tedious as obcs-ctrl, because the
278        variables needs its own mask.
279      - add a cost function term that penalizes the deviation of xx_shifwflx
280        from the first guess (zero) in analogy to other control variables
281    o pkg/shelfice:
282      - start basic adjoint
283    o pkg/ctrl:
284      - remove extra 2D field "for good measure" when initializing in
285        ctrl_set_globfld_[xy/xz/yz].F
286      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
287      - improve error messages in ctrl_set_unpack_*
288    o OBC implementation in momentum:
289       use interior masks (maskInC,W & S) in momentum S/R:
290       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
291       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
292       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
293       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
294       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
295        (and also with Leith/Smagorinsky harmonic-viscosity).
296       Update output of experiment dome and exp4 (+nlfs).
297    o exp4 test-exp:
298      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
299        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
300        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
301        time-varying OB at Western-side for wVel (NonHyd); update output.
302      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
303        and biharmonic-viscosity ; also use prescribed time varying OB.
304    o pkg/obcs:
305      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
306    o model/src:
307      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
308      - initialise startTime & nIter0 with unlikely values: allows to set one
309        from the other without ambiguity.
310    o seaice_obcs test-exp.:
311      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
312    o pkg/obcs:
313      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
314        no longer needed with maskInC,W,S in pkg/generic_advdiff.
315    o pkg/seaice:
316      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
317        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
318      - fixed bug in the initialization of sea ice salinity variable HSALT
319        in seaice_init_varia.F  (removed dependence on ICE2WATR)
320    o fizhi-cs test exp.:
321       switch reference output convention for these 2 non-standard test-exp,
322        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
323          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
324       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
325    o model/inc:
326      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
327        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
328    o pkg/seaice:
329      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
330    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
331      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
332        and initial HSALT
333    
334    checkpoint62w (2011/04/26)
335    o pkg/mom_fluxform:
336      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
337      - use parameter "sideDragFactor" in no-slip BC side-drag part.
338      - update output of exp. global_ocean.90x40x15
339    o pkg/mom_vecinv:
340      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
341    o update seaice exp.:
342      use more consistent parameter values (remove "backward compatability only":
343       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
344      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
345       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
346    o update test-exp global_ocean.90x40x15:
347      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
348      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
349      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
350      o turn on zStar & viscA4 in standard set-up (dir input/)
351        and update output files: output.txt & output.dwnslp.txt
352    o new AD-test experiment: obcs_ctrl
353      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
354    o pkg/dic:
355      fix two bugs in handling water vapour pressure in carbonate chemistry
356      and air-sea fluxes. Found by Val Bennington and Galen McKinley
357      (add DIC Option = WATERVAP_BUG to recover old results)
358      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
359    o adding allowInteriorFreezing option to check for water below freezing point
360      at depth and bring the negative heat anomaly to the surface level
361    o pkgs _fields_load:
362      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
363      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
364        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
365        rbcs to get interpolation weights and time reccord number.
366      - fix multi-threading in aim_fields_load.F
367      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
368    o external_fields_load:
369      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
370       interpolation weights) to use in a periodic time-series ; do not divide by
371       time-step to convert to integer:
372       - this fixes case where externForcingPeriod is not multiple of time-step
373          (Thanks to Christopher L. Wolfe)
374       - this fixes case where externForcingPeriod is an odd multiple of time-step
375         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
376      store index of time-record which is currently loaded:
377       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
378       - needed for the adjoint but not yet used because of extensive recomputations;
379         (to be fixed soon)
380    
381    checkpoint62v (2011/04/02)
382    o verification/1D_ocean_ice_column added to test Ian Fenty's
383      pkg/seaice_growth.F modifications for improving sea ice code differentiability
384    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
385      (new velocity statistics after changing maskInW & maskInS definition)
386    o pkg/generic_advdiff with OBCS:
387      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
388      equivalent to assumption of no tracer gradient outside the OB region.
389      This will affect the results if using obcs+biharmonic diffusion.
390      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
391    o pkg/obcs:
392      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
393      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
394      in Interior region. No impact on solution but affects Velocity monitor stats.
395    o pkg/ptracers (adjoint)
396      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
397      tape file for each tracer
398    o model/inc/src and pkg/autodiff: add parameters that allow to turn
399      of parts of the adjoint code at run time. For now, there are only
400      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
401      parameters are set in data.pkg.
402      This is the lazy coward's version of doing this, but still useful for
403      debugging. In order to do it right, everything needs to be moved to
404      pkg/autodiff.
405    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
406      the end; this fixes the adjoint balancing code for open boundaries.
407    o pkg/ctrl:
408      - change behavior of xx_${varname}period to be analogous to exf-conventions:
409        xx_${varname}period =   0.,  means time-independent control part
410        xx_${varname}period = -12., means one-year-periodic monthly control part
411      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
412        clean up ctrl_init a little, remove unused variables
413      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
414      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
415    
416    checkpoint62u (2011/03/15)
417    o model/src:
418      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
419        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
420      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
421        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
422    o pkg/ctrl/obcs/ecco:
423      - remove obsolete, unused, and partially broken code:
424        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
425        ALLOW_CTRL_OBCS_BALANCE
426      - put a stop statement into ecco/cost_obcsvol.F, but also add
427        cost_obcsvol to ecco_ad_diff.list
428    o pkg/ecco: fix counting cost function contributions for obcs (code
429      by Matt M.) and diffkr for diagnostics
430    o pkg/ecco, pkg/ctrl, pkg/grdchk:
431      add cost penalty terms for initial uvel, vvel, eta controls
432      and I/O for prior error files
433    o pkg/mdsio:
434       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
435       (new argument) to check for tiled file in mdsioLocalDir : this fix the
436       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
437    o pkg/ctrl:
438     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
439       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
440       unused and superfluous variables
441     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
442    o pkg/ecco
443     - enable adjoint of Stevens OB
444    o pkg/ctrl/ecco/grdchk:
445      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
446        Fortunately, we do not have any tests for the numerous cpp-flagged
447        option of "obcs as control parameters" so we will never know
448        if this is an improvement (but at least now things compile).
449      - remove an obsolete initialization from ecco_cost_init_barfiles.F
450      - fix some problems within never used ifdefs to make the code compile
451    o pkg/obcs:
452     - Refine Interior mask definition to work with more complex OB (e.g.
453       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
454       read in Interior mask from file. Check if Interior mask is consistent
455       with OB list of indices.
456    o pkg/seaice
457     - beginning code for a seaice tracer package,
458       but currently only used for seaice age: SEAICE_AGE
459       SEAICE_num = 4
460       iTracer = 1: area-weighted ice age
461               = 2: volume-weighted ice age
462               = 3, 4: template for one-year vs. multi-year ice
463       data.seaice has new namelist SEAICE_PARM03 for arrays related to
464       SEAICE_num
465    
466    checkpoint62t (2011/03/05)
467    o pkg/obcs:
468     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
469       then normal component. This ensures that the normal component is set
470       correctly even when it conficts with tangential setting from an other OB.
471       Affects results of test-experiment seaice_obcs: update the output.txt
472    o pkg/obcs:
473     - add code to monitor statistics of dynamical fields at OB.
474     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
475       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
476       - change default: balance the Net inflow through all OB (instead of balancing
477         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
478     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
479       to match Nortern OB inflow (OBCS_balanceFacN=0).
480    o pkg/seaice:
481     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
482    o pkg/seaice (seaice_growth v 1.113):
483     - reverting seaice_growth to v 1.111 in order to have code with exact bit
484       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
485       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
486       runtime flag SEAICEareaFormula is kept but is inactive
487    o model/src:
488     - add new param to scale curvilinear grid distance and area when using
489       a different sphere radius from the grid-files.
490     - test/check multi-threads EXCH applied to local variable (cg2d_x)
491    o adjoint:
492     - enable adjoint of Stevens OB
493     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
494       (a bit delicate because of potentially modified adj. common block structure;
495       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
496    
497    checkpoint62s (2011/02/15)
498    o pkg/seaice (seaice_growth v 1.112):
499     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
500       computing the ice cover tendency from effective thickness tendencies. Include
501       Ian Fenty's formula.
502     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
503       SEAICEareaFormula.
504     - simplify notations for the various d_HEFF/d_AREA terms.
505    o pkg/gmredi:
506     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
507       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
508       add a verification test-run (front_relax.bvp) to test GM_useBVP.
509    o pkg/seaice (seaice_growth v 1.111):
510     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
511     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
512       also melt ice.
513    o pkg/seaice:
514     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
515     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
516    o pkg/cheapaml:
517     - from Nico Wienders: New version of this package.
518    o pkg/flt:
519     - add CPP options to prevent floats to re-enter the opposite side of
520       a periodic domain (default: keep periodicity)
521    o pkg/gmredi:
522     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
523       (needed for multi-dim advection).
524     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
525    o model/src:
526     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
527    o tutorial_tracer_adjsens
528     - extend to NLFS and replace maskC by hFacC
529       (change reference output accordingly)
530    
531    checkpoint62r (2011/01/24)
532    o testreport:
533     - add option -deloutp (-do) to remove output file after successful run
534     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
535       extract exact list of procs from this file ; adjust COMMAND by
536       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
537    o pkg/ecco: replace old ineffective way of penalizing deviations from
538      first guess (of obcs) with code by Matt Mazloff
539    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
540      exf/cal
541      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
542        and handle case of obcs?period == 0
543        Not affected by these changes: There is still an inconsistency in
544        the computation of start/endrec for the obcs variables for ALLOW_CAL
545        defined (see comment by Menemenlis, 7-Mar-2003)
546      - make S/R ctrl_get_gen_rec return something meaningful even if
547        ALLOW_CAL is not defined
548      - ctrl_getobcs?: simplify code so that it does not need to use
549                       S/R exf_swapfields
550    o testreport:
551       allow to test MPI with different number of processors for each experiment:
552       create file "SIZE.h.mpi" in each build dir.
553       Note: update of "-command" argument not yet implemented.
554    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
555      alleviate the need for additional 3D tapes when using
556      the non-inear free surface in the adjoint. This is done
557      by adding an 'update' of hfacc etc. to their current
558      value at the beginning of forward_step.F.
559    o pkg/seaice
560      seaice_lsr: move stress-divergence computations out of outer pseudo-
561      timestepping loop
562    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
563      up, so that the calls of the ctrl_* subroutines are really at the end
564      of the routine.
565    o pkg/gmredi:
566      allow to specify a 2-D horizontal map and a 1-D vertical profil
567      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
568    o pkg/seaice:
569      move lsr iterations from seaice_dynsolver to seaice_lsr.
570    o pkg/seaice:
571      reduce memory footprint of seaice mutldim advection tapes,
572      by using a 2D tape independent of the generic_advdiff ones,
573      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
574    
575    checkpoint62q (2010/12/29)
576    o model/src:
577      - check horizontal grid-spacing for unset or zero/negative values.
578      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
579    o pkg/flt:
580      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
581      - precision of input and output files set according to readBinaryPrec
582        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
583      - initial float position from tiled file was not converted to index space
584        (looks like a bug): fixed to make it similar to initial pos. global file.
585    o global_ocean.cs32x15:
586       change SIZE.h of AD set-up to get same tiling as with MPI.
587       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
588    o model/src:
589       add flag to control printing of domain fields (bathymetry, hFac ...) in
590       ini_mask_etc (call to plot_fieds_xy*).
591    o pkg/thsice:
592       if useEXF, some forcing fields are not valid in overlap: fixed by computing
593       over the interior only + apply EXCH at the end (like with SEAICE advection).
594    o pkg/mdsio:
595      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
596        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
597      - change barrier call for safe multi-threads access to 3-D shared buffer.
598      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
599      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
600        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
601    o pkg/flt:
602      - add fourth-order Runge-Kutta integration
603      - add basic exch2 support (only 1 facet supported so far!)
604    o pkg/mdsio+rw:
605      new S/R to read local (or tile independent) vector (read counterpart of
606       mds_writevec_loc, and front-end write_glvec_rl/rs).
607    o global_ocean.cs32x15: additional input_ad.seaice experiment
608        that uses pkg/seaice rather than pkg/thsice.
609        (using multidim advection for seaice)
610    o towards more F95 syntax for array specification in namelist:
611      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
612        of all verification experiments.
613           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
614          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
615      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
616    o global_ocean.cs32x15: additional input.seaice experiment
617        that uses pkg/seaice rather than pkg/thsice.
618    
619    checkpoint62p (2010/12/17)
620    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
621        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
622    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
623        allow for use of multim. advection in seaice adjoint.
624    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
625      - first attempt to close budgets by taking into account the freshwater
626        flux implied by the sublimation of snow and ice. So far only the
627        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
628        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
629    o eesupp/src:
630      new S/R with new option (NML_EXTENDED_F77) to change array specification
631      from F95 standard to commonly accepted extended F77 form.
632      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
633      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
634      for less tolerant f77 compiler (e.g., pgf77, g77).
635    o globalFiles:
636      commented out in parameter file "data" since it's not safe with MPI
637      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
638      in this case); no longer commented out in restart test (tst_2+2).
639    o add adTapeDir to specify a special directory where adjoint tapes are
640      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
641      and cannot be used together with mdsioLocalDir.
642    o nesting pkgs:
643      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
644      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
645      - add parameter files + utils dir + output from short run on beagle.
646    o pkg/seaice:
647        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
648    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
649      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
650    
651    checkpoint62o (2010/11/25)
652    o pkg/exf:
653      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
654    o pkg/seaice:
655      - seaice_ocean_stress: split a loop for better vectorization of the
656        adjoint code
657      - seaice_growth.F: fix bug in conservation of freshwater connected to
658        capping of heff, put contribution into d_HEFFbyNEG
659      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
660        by something more sensible (parameters that are what their name implies)
661      - change some defaults, so that by default exf-parameters are used for
662        things like rhoAir, cpAir,latent/sensible heat parameters, in order
663        to reproduce the old results, many data.seaice now contain funny values
664        for cpAir and latent heat of sublimation
665    o packages_readparms.F: move exf_readparms up in line so that
666        exf-parameters are visible for other packages (e.g. seaice)
667    o debugMode & debugLevel=2:
668      - differentiate between debugMode & debugLevel=2:
669        debugMode: controls printing of debug messages (sequence of S/R calls).
670        debugLevel: controls printing of algorithm intermediate results and stats.
671      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
672        => allows to print debug-stats without all sequence of call messages.
673      - switch control of debug print from debugLevel to debugMode in many S/R.
674    o pkg/obcs (obcs-sponge):
675        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
676        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
677    o pkg/generic_advdiff:
678      - record overlap minimum size for each advection scheme;
679      - refine criteria on overlap minimum size;
680      - check and stop (in gad_check) if overlap size is too small.
681    o pkg/obcs:
682      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
683        once, in ptracers_implicit.F)
684      - with seaice: remove test on empty file name in obcs_apply_seaice (always
685        apply OB values when tile has OB)
686    o model/src, coriolis setting:
687      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
688        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
689        files (selectCoriMap=3) with any grid.
690      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
691    o pkg/seaice/seaice_growth.F:
692        a few cosmetic changes that reduce the number of lines of code
693    o pkg/obcs: add boundary conditions following Stevens (1990)
694      - the code follows old MOM/NAOSIM code
695      - so far it is only implemented for the eastern and western boundaries
696        and NOT for pTracers
697    o pkg/rbcs:
698      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
699        beginning of the first rbcs forcing period.
700      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
701        offline package, i.e., one file per time, labeled by iteration number;
702        deltaTrbcs sets the timestep with which the data was generated;
703        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
704      - rbcsForcingCycle=0 makes forcing non-cyclic.
705      - make arithmetic safe for negative times and odd forcing periods.
706    
707    checkpoint62n (2010/11/09)
708    o pkg/seaice:
709        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
710    o pkg/obcs:
711       New S/R to copy tracer value from the OB location to narrow band region
712        (width = same as overlap) beyond the OB: preserve OB value (needed for
713        high-order scheme) which were overwritten by EXCH call if in overlap
714        region. Applied to theta, salt, ptracer and advected seaice variables.
715       With seaice: use maskInC in similar way as in gad_advection.F,
716        in seaice_advection.F and advect.F.
717       Update output of experiment seaice_obcs and change exp4 to test OBCS with
718        4th order Adv.Scheme. for pasive salt and ptracer.
719    o tools/genmake2:
720      - when looking for an optfile (not specified), only search for Fortran compiler
721        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
722      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
723        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
724      - set default for CPP to "cpp -traditional -P" (was the case without specifying
725        an optfile, but otherwise default was just "cpp".
726      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
727      - when "CC" is not set in the optfile, look for possible C compiler
728        (instead of just setting CC=cc)
729      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
730        => add a ".F" to ".o" rule for source files with no "#include" (such as
731           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
732      - move gfortran before g77 in list of possible Fortran compiler (consistent
733        with reference compiler switch from g77 to gfortran)
734    o pkg/seaice:
735      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
736        seaice_check that stops the model, when the CPP flag is used.
737      o seaice_growth.F: make capping of ice volume conserving by returning the
738        capped ice as freshwater to EmPmR. This does not change the verification
739        experiments but will change runs where the capping is acutally active
740    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
741      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
742         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
743         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
744    o tools/genmake2:
745      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
746      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
747      - clean previous genmake log files before anything else.
748      - change Makefile to remove testreport log files (*.tr_log) and genmake log
749        files only with "CLEAN" target (instead of "Clean");
750    o pkg/generic_advdiff:
751      Change OBCS in multiDim advection (gad_advection.F):
752       Use maskInC to prevent intermediate update of tracer-field in OB regions,
753       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
754       which were applying future time-step OB values.
755      This way, all explicit calculations use current-time-step OB values
756       (simpler and more consistent).
757      Affects results when set-up uses time-varying OBC and multi-dim advection;
758       update output of experiment seaice_obcs.
759    o pkg/seaice:
760      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
761       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
762         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
763      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
764       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
765       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
766    o pkg aim (2010/10/26):
767      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
768        formulation with obliquity, eccentricity, ... as run-time parameters,
769      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
770        upward shortwave radition at the surface (all-sky and clear-sky).
771    o pkg/obcs:
772      - writing sections with globalFiles=T does not work: switch to tiled-files
773        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
774      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
775      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
776    
777    checkpoint62m (2010/10/21)
778    o pkg/seaice: vectorize seaice_solve4temp.F
779      - move iterations loops outside of i/j-loops
780      - requires 2D arrays for TB and effConduct
781      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
782        modified in this routine
783      - a little bit of clean up, adjusting indentation, etc.
784      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
785        performance and '**TWO' by '**2' (because TWO is a float),
786        replaced ONE, ZERO
787    o eesupp/src:
788       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
789    o pkg/seaice/seaice_growth.F
790      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
791      merging process. The merged routine has two branches, and one activates the 'evolution'
792      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
793      In summary, here is what the '10/10 revision' did consist of
794        part 1: seaice_growth.F revisions 1.71 to 1.75
795          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
796            The emphasis here was on improving readability (e.g. by trying to use meaningful
797            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
798        part 1.5:
799          - revising the lab_sea experiment to make it a more useful (i.e. stable
800            and representative of an actual model run). This was done by generating a
801            (winter) pickup to start from, switching back the main experiment dynamic
802            solver from evp to lsr, having one of the experiments use the free drift solution.
803        part 2: seaice_growth.F revisions 1.76 to 1.85
804          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
805          - Sorting out the various fields units and sign (set early on and reset at the end)
806            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
807            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
808          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
809            and simplifying logical expressions to further improve readibility.
810        part 3: seaice_growth.F revisions 1.86 to 1.89
811          - Re-organize the blocks of code more logically.
812          - Merging the '_if.F' pieces that add something new.
813    o pkg/thsice:
814      - vectorize thsice_solve4temp and thsice_get_exf.
815        Problem: thsice_solve4temp has an unvectorizable statement that
816        might also be problematic for TAF
817      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
818        does not change the verifcation experiment, but will change all
819        experiments that have this flag undefined (not tested in verification);
820        a little reorganization to save a few 2D fields and recomputations
821      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
822      - 2nd step:  fix some store dirs
823        o seems to work somewhat, i.e. using ifort but not g77
824        o likely cause are incomplete init. or recomputation
825        o start verification/global_ocean.cs32x15/input_ad.thsice
826    o pkg/obcs: add support for exch2
827      - the position of the boundary and prescribed values are specified using
828        a global domain with exch2 facets stacked
829        - in x for N,S boundaries (like W2_mapIO=-1)
830        - in y for E,W boundaries (so E,W boundaries do not overlap)
831    o pkg/mdsio: add support for writing global sections with exch2
832        file layout is as for obcs described above:
833        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
834        - for y-z sections, facets are stacked in y
835    o pkg/thsice:
836       - change a few routines for better vectorization: thsice_albedo.F,
837         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
838         not affected, but in particular the latter routine has changed
839         dramatically (not necessarily easier to read now).
840       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
841       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
842    o verification/lab_sea:
843      - overhaul of the forward model experiments. The main motivation
844        for this revision is that lab_sea has proven quite fragile (when
845        changing the sea-ice code, and switching platforms) to a point
846        when failures were very hard to attribute to specific code problems.
847      - the suspected reason for this fragility is noise amplification by evp so,
848        to start with, we decided to replace evp with lsr in the main experiment.
849      - the input.lsr experiment thus became obsolete and was removed.
850      - it was replaced with the input.fd experiment that uses an
851        analytical "free drift" solution as the ice velocity field.
852      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
853        will hopefully allow us to discriminate problems due to dynamic solvers
854        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
855        us to test additional options, along with the salt plume package.
856      - Finally a pickup was generated (at the end of a one year run) to
857        make the tests more representative of an actual model run. Previously
858        the tests starting point was a 1m thickness of ice everywhere.
859    o pkg/seaice:
860      - introducing S\R seaice_freedrift.F that compute the
861        analytical solution to an approximate ice momentum
862        equation (i.e. the simple stress/coriolis balance).
863      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
864        of the free drift velocity field, and enable its use.
865        To actually use the free drift solution as the model ice
866        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
867    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
868    
869    checkpoint62l (2010/10/04)
870    o pkg/seaice:
871      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
872      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
873       version (with USE_ORIGINAL_SBI undef);
874    o add hooks for new packages OASIS, the package will follow
875      (hooks exclude the seaice pkg for now)
876    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
877      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
878      rather than mdsio_readvector.F/mdsio_writevector.F, within
879      adread_adwrite.F to read/write adjoint-related tapes to disk.
880    o eesupp and pkg/mdsio: ALLOW_WHIO
881      Option to write/read 2D fields to files including tiles halos.
882      The main purpose is for adjoint related "tape I/O".
883      The secondary purpose is for debugging phases.
884      A word on those rather specifically intended purposes.
885      The code was meant to be stripped down to the bare minimum.
886      Typically, there is a unique and basic mapping to the global
887      buffer (tile by tile, then proc by proc, then level by level), and
888      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
889      meant to generate user friendly outputs of various shapes and forms.
890      Rather it is intended, for the knowledgeabale developers,
891      to be largely independent of the many mdsio options, to allow
892      outputs of tiles+halos in debugging phases and in adjoint runs,
893      and to allow some flexibility in tuning (adoint) I/O depending on each
894      file system behavior. With regard to tuning, most of the potential knobs
895      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
896      to specify directories, to specify the typical size of I/O calls, etc.)
897      are not yet included, and will be added if they prove useful.
898    o pkg/seaice:
899       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
900    o pkg/seaice:
901       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
902       code (seaice_budget_ice_if.F) which enable to recover old standard
903       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
904       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
905    o model/src (rStar):
906       use simple average (not area weighted) of rStarFac at U,V point when using
907       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
908       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
909    
910    checkpoint62k (2010/09/17)
911    o adjoint
912       * changed verification/global_ocean.cs32x15 ; adjoint now tests
913         Adams-Bashforth 3 + NLFS + RSTAR
914       * some more modifs required for ECCO-GODAE v4
915    o pkg/seaice
916       add SEAICE_AGE_VOL option to use volume instead of area for
917       integrating SEAICE_AGE
918    o model/src:
919       first check-in of sigma & hybrid-sigma coordinate code ; also includes
920       non-linear free-surface parts ; but pressure-gradient not yet coded.
921    o pkg/ptracers:
922       option for ptracer to convert Salt Relax into additional EmP.
923        tested in exp. global_ocean.90x40x15.dwnslp (update output)
924    
925    checkpoint62j (2010/08/25)
926    o pkg/ggl90:
927       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
928    o pkg/dic: car_flux.F, phos_flux.F
929      - reduce number of exp-calls in order to improve performance
930      - clean up a little (replace fields by their macros, etc., fix
931        typo in CPP-flag)
932    o pkg/ggl90: minor changes
933      - GGL90diffKrS was removed --> always use GGL90diffKr
934      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
935      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
936        (commented out for now)
937      - change in max/min operations to ensure that smoothing is ok
938      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
939      - always use diffKrNrT as background profile (i.e. never use diffKr field)
940    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
941    o pkg/dic:
942      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
943        vectorization
944      - small bug fix in insol for the unlikely case of a cartesian grid
945      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
946        + now vectorize, which also removes adjoint recomputations;
947        + replace integer maksp1 by _RL maskp1
948        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
949    
950    checkpoint62i (2010/07/21)
951    o pkg/flt:
952      - with OBCS: stop floats which enter the OB region
953    o model/src:
954      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
955        for implicit vertical advection.
956    o pkg/seaice:
957     - account for melting in seaice age evolution.
958     - remove double counting of seaice ridging effect on seaice age.
959    
960    checkpoint62h (2010/06/18)
961    o pkg/exch2:
962     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
963    o tools/genmake2
964      - remove "-pdefault" option: redundant with the use of "packages.conf";
965      - remove file pkg/pkg_default : set the default as a pkg group
966        ("default_pkg_list") defined in pkg/pkg_groups;
967      - fix for case pkg/pkg_depend is missing (was hanging before);
968      - add option "-pgroups" to specify a different pkg_groups than the default.
969    o verification/adjustment.cs-32x32x1:
970       add a "minimal" set-up test (code_min & input_min) which only compiles
971       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
972    o tools/genmake2
973      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
974      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
975    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
976      files are nearly the same anyway.
977      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
978       - redefinition of tau(i,i) (by a factor of ustar)
979       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
980       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
981       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
982       - replace
983         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
984         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
985         by
986         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
987         (changes results)
988       -> exf_bulkformulae v1.22,
989          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
990          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
991                    output.txt 1.63
992           offline_exf_seaice: output.seaicetd.txt 1.7
993           seaice_obcs: output.txt 1.10)
994      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
995       -> exf_bulkformulae v1.23,
996          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
997          and global_ocean.cs32x15.icedyn (only 11 matching digits)
998      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
999    o adjoint of exch-1:
1000     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1001       (note: was already like this when using EXCH-2) and remove flow dir
1002       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1003     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1004     - update pkg/exch2 diff list.
1005    
1006    checkpoint62g (2010/05/19)
1007    o eesupp/src (exch-1):
1008     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1009       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1010       (renamed to exch1_*rx_cube.F).
1011     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1012       to call new exch1 S/R ; update Makefile and .cvsignore.
1013     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1014       exch2_xy_rx later)
1015      Note: after updating your code, need to run "make clean" in eesupp/src
1016  o test experiment bottom_ctrl_5x5:  o test experiment bottom_ctrl_5x5:
1017     new output_adm.txt with fewer grdchk & less monitor output.     new output_adm.txt with fewer grdchk & less monitor output.
1018  o model/src:  o model/src:
1019    remove the call to ini_cori in initialise_varia.F (just keep the usual one    remove the call to ini_cori in initialise_varia.F (just keep the usual one
1020     in initialise_fixed.F). More consistent with coriolis & horizontal grid     in initialise_fixed.F). More consistent with coriolis & horizontal grid
1021     beeing treated in the same way (ini_grid is not called a 2nd time).     beeing treated in the same way (ini_grid is not called a 2nd time).
1022  o pkg/exf:  o pkg/exf:
1023    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1024    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1025    - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)    - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
# Line 175  o tools/build_options: Line 1184  o tools/build_options:
1184      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1185  o pkg/ecco  o pkg/ecco
1186    - allow user defined cost function contributions    - allow user defined cost function contributions
1187          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1188          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1189    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1190        the two options are complementary.        the two options are complementary.
1191  o pkg/smooth  o pkg/smooth

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