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revision 1.1304 by mlosch, Sat Sep 25 23:10:51 2010 UTC revision 1.1482 by mlosch, Mon Jul 25 08:59:32 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 optim/optim_readdata.F:
8      - add some output about obcs variables that might help debugging
9      - add a check about nvarlength
10    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
11    o pkg/diagnostics (velocity potential):
12      - fix mask for OBCS (still problems in stream-function with OBCS);
13      - add specific parameter (default = main code CG2D params) for solver;
14      - in case of poor convergence, use solution corresponding to lowest residual.
15    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
16      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
17      and should be avoided where possible.
18    o model/src (rStar):
19      - include r* effect on reference-state (PhiRef) in totPhiHyd
20        (so that it's really the potential anomaly at the cell center);
21        affect solution only if z* with full pressure in EOS.
22      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
23        update output (because of z* in totPhiHyd and viscA4 changes);
24      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
25        @ constant r) until interpolation at constant r is implemented.
26    o pkg/diagnostics
27      - fix RCENTER diagnostics in case cell center is not at interface middle
28    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
29      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
30      that THETA and SALT are "conservative temperature" and "absolute
31      salinity"
32    o pkg/ctrl
33      - fix computation of endrec in s/r ctrl_init_rec
34      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
35    o pkg/seaice/seaice_growth.F
36      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
37        remove then obsolete STORE directives
38      - fix STORE directives for tice and tices, so that only the
39        appropriate part of the fields are stored (and not the entire
40        field); update global_ocean.cs32x15.seaice AD output.
41      - cosmetic changes: adjust CPP flags and indentation for better
42        legibilty
43    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
44      Chris Wilson)
45    o pkg/gmredi:
46       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
47       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
48    
49    checkpoint63 (2011/07/11)
50    o pkg/exch2:
51     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
52     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
53       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
54       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
55    o pkg/diagnostics:
56     - deal with pairs of post-processed diags which are computed together; in
57       particular, re-order list of diags within 1 file to save 2nd computation.
58     - add S/R to compute velocity stream-function (called after velocity-potential
59       calculation) from divergence free transport -> new diagnostics "PsiVEL".
60     - add parameter to select grid-point location where PsiVEL == 0.
61    o eesupp/src:
62       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
63       (specific S/R needed with exch2 topology - for now, just print an error msg)
64    o pkg/shelfice
65     - Implement friction velocity-dependent transfer coefficients following
66       Holland and Jenkins, JPO, 1999
67       Original code by M. Losch with small modifs.
68       Enable with CPP option SHI_ALLOW_GAMMAFRICT
69       and runtime flag SHELFICEuseGammaFrict
70    o verification lab_sea & global_ocean.cs32x15:
71     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
72       does not miss some dependencies (but is slower) and also works with many files
73       (default makedepend limitation for AD built).
74     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
75    o pkg/diagnostics:
76     - add run-time parameter "useMissingValue" (def=False) to fill land-point
77        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
78       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
79     - Extend the use of "missing_value" setting from data.diagnostics for the case
80       of counter-diagnostics (where fraction-weight is zero). This applies both to
81       MNC and MDS output files.
82    o pkg/seaice/seaice_growth.F:
83      - add 'a priori' cap of latent heat flux based on actual mass considerations
84        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
85        non-legacy seaice_solve4temp.
86      - add diagnostic of the residual sublimation freshwater flux (the freshwater
87        flux taken from the ocean if the total actual latent heat fluxes exceed
88        the maximum)
89      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
90       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
91      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
92       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
93      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
94      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
95    o verification 1D_ocean_ice_column:
96       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
97       update results
98    o pkg/diagnostics:
99     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
100       which are not filled-up but computed from other diags ; In this case, the mate
101       diag points to the primary (filled-up) diag to used for post processing.
102     - Update Velocity-potential computation using post-processed diag framework.
103     ==> Change the ordering of fields and time-periods in MDS output file
104       when using periodic averaging: now writes one time record with the full set
105       of fields for this time period, then the next time reccord (it used to be
106       one field with the full set of time records then the next field).
107         Note: this is now similar to NetCDF (MNC) output file. <==
108    
109    checkpoint62z (2011/06/21)
110    o adjoint monitor:
111     - Add adjoint monitor output for packages exf, seaice
112       and update relevant testreport output
113    o pkg/seaice:
114     - re-order diags inits so that they appear in order in available_diagnostics.log
115     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
116       area/heff/hsnow preceeding thermodynamic growth/melt.
117     - modified diag: SIdA; output actual effect, as the description states.
118     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
119     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
120       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
121        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
122     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
123     - added diagnostics for seaice generic tracers (SItr*).
124     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
125     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
126     I. Fenty: 18-Jun-2011:
127     Minor changes to seaice package:
128     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
129        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
130       - Differentiated "regularization variables" from "floor variables"
131        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
132        * hiceMin became SEAICE_hice_reg (old hiceMin)
133          (with _reg meaning regularization variable)
134       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
135        so as to ensure energy conservation when going between phases
136      - A22 was not used anywhere
137     2) Changed regularization procedure for heffActual and hsnowActual to ensure
138        well-boundedness and smooth adjoint in seaice_growth.F
139     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
140        because the old regularization always set heffActual >= 0.05 cm
141     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
142        on AREA when HEFF > 0.
143      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
144        requiring that DISABLE_AREA_FLOOR *not* be defined
145     Affected verifications:
146      - 1D_ocean_ice_column (output.txt output_adm.txt)
147      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
148    o pkg/diagnostics:
149      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
150      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
151        (was _RL, now integer) with option = 0 to retrieve all levels.
152      - add pieces of code to compute velocity potential at each level (new diagnostics
153        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
154        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
155      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
156        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
157        and in diagnostics_fract_fill.F (do not need a valid pointer for the
158        diagnostics counter-mate); check that definition of counter-diagnostic
159        includes a valid counter-mate (in diagnostics_set_levels.F).
160    o model/src (rStar):
161      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
162        affect solution only if z* with full pressure in EOS;
163        update output of test-exp global_ocean.90x40x15.
164    o pkg/seaice:
165      - introduce siEps=1e-5 parameter
166      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
167      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
168      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
169        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
170        as well as ice cover age and ridging index (attached to AREA).
171        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
172        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
173        Up to SItrMaxNum=3 tracers can be used simultaneously.
174    o pkg/salt_plume:
175      -introduce SPsalFRAC run time parameter that sets the fraction of the
176       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
177       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
178    o model debug options:
179      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
180        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
181      - Refine debug-msg printing selection (3 new levels):
182        debugMode  : controls printing of debug messages (sequence of S/R calls).
183        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
184         debLevZero =  0 ; /* level of disabled aux. msg printing */
185         debLevA =  1 ; /* level of minimum  aux. msg printing */
186         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
187         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
188         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
189         debLevE =  5 ; /* level of extensive debug printing */
190        New debugLevel default: with default debugMode value (=F),
191          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
192          and if debugMode=T, default debugLevel = 4 (debLevD).
193        Relation with previous settings:
194         debLevB (=2) corresponds to former debLevA (=1)
195         debLevD (=4) corresponds to former debLevB (=2)
196        Note:
197         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
198         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
199            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
200      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
201        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
202    o pkg/obcs:
203      - change OBCSfixTopo default from True to False (should not change the results);
204        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
205    o pkg/thsice:
206      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
207        2nd layer seaice sublimation (unlikely to happen)
208      - use Interior mask for OBCS in thsice_advection.F (similar to what is
209        done in gad_advection & seaice_advection).
210    o adjoint:
211      bug fix spotted by Gael Forget:
212      seaice_advection and thsice_advection still had
213      legacy CPP options to avoid CS corner updates for adjoint
214    o pkg/seaice:
215      => Change some of the defaults (2011/05/29):
216         - change SEAICEuseFluxForm default (from False to True)
217         - change DIFF1 default (from 0.004 m/s to 0. m/s)
218         And print warnings if DIFF1 is not set in data.seaice and centered
219          avection scheme is used without any diffusion.
220      also:
221      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
222      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
223      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
224        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
225        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
226      update results of test exp.:
227         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
228             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
229             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
230         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
231         seaice_obcs: output (SEAICEuseFluxForm=T)
232      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
233          for standard fwd & AD lab_sea tests (to keep the same output).
234    o pkg/seaice/seaice_growth.F:
235      - use Ian Fenty's capping formulas for actual ice
236      thickness thoughout EVOLUTION branch.
237      - put treatment pathological case #2) in CPP brackets
238      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
239      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
240    o pkg/seaice:
241      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
242      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
243      also pass fac as a param, which can be 1. (to update the tendency
244      field) or the time step (to update the field itself).
245      - seaice_advdiff.F: for multidim, call seaice_diffusion with
246      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
247      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
248      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
249      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
250    o pkg/seaice:
251      diffusion with centered advection scheme (diffus.F & advect.F):
252      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
253        to just compute the laplacian of input-field.
254      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
255      - fix flux-form version in diffus.F to conserve tracer.
256      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
257       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
258    
259    checkpoint62y (2011/05/26)
260    o pkg/seaice:
261     - seaice_growth.F : in EVOLUTION branch, always include
262       a_QSWbyATM_cover in qnet (as it should be).
263     - verification/global_ocean.cs32x15 : update results accordingly
264       (output.seaice.txt output_adm.seaice.txt).
265    o pkg/seaice + obcs:
266     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
267       equivalent of assuming no tracer gradient outside the OB region.
268       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
269     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
270       after changes above);
271     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
272       only at OB location (instead of over a band of OLx width).
273    o pkg/seaice:
274     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
275       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
276    o pkg/obcs:
277      - split header file "OBCS.h" into 4 separated files:
278        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
279       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
280         (contain no conditional statement which depends on OBCS options).
281      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
282        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
283    o ctrl, cost, grdchk & autodiff pkgs:
284      - make options file more standard (like other {PKG}_OPTIONS.h file but
285        with AD_CONFIG.h); clean-up some of the included header files.
286    o pkg/obcs:
287      - do not mask tracer when applying OB (tracer == 0 could generate problems)
288      - apply tracer OB values to tracer field only at OB location (instead of
289        over a band of OLx width)
290      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
291      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
292        obcs_apply_tloc.F & obcs_apply_sloc.F
293    o obcs in model/src:
294      - call OBCS_APPLY_W only if NonHydrostatic.
295      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
296      - reset dEtaHdt and wVel to zero outside OB interior region ;
297      - leave tracer unchanged outside OB interior region: This has no effect
298        on the solution but just to prevent unrealistic tracer value outside OB.
299      - zero out velocity outside OB interior region: This has no effect on
300        the solution but just to prevent unrealistic velocity outside OB.
301    o obcs and non-lin free-surf:
302       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
303       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
304       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
305       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
306       update results of test-exp. exp4(nlfs).
307    o exp4 (nlfs) test-exp:
308       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
309       with NonLin-FreeSurf); update output.nlfs.txt
310    o obcs and 2d/3d solver norm:
311       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
312       and outside OB interior region (will allow to place OB further inside the
313       domain). Depending on the domain, can affects cg2d-Norm (previous
314       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
315       and cg3d-Norm (previous Norm was computed before canceling OB terms),
316       e.g. in tutorial_plume_on_slope.
317      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
318    o pkg rbcs:
319      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
320      - add capability to apply relaxation to horizontal velocity uVel & vVel.
321    o pkg/grdchk: add gradient check for control variable xx_shifwflx
322    o pkg/shelfice/shelfice_init_fixed.F
323      fix CPP-flag combinations
324    o pkg/seaice: Merge iceage code of Pierre Rampal
325      * update/change/correct ice age calculations
326      * add age updates for pathological cases
327      Probably needs more testing...
328    
329    checkpoint62x (2011/05/13)
330    o pkg/mom_vecinv:
331       high-order vorticity scheme: use interior masks (maskInW & S)
332       to zero-out (outside OB) gradient of vorticity.
333    o verification exp.:
334       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
335       hs94.128x64x5 and seaice_obcs ; update results.
336    o pkg/obcs:
337      fix bug in OBeta for YZ sections in obcs_exf_load.F
338    o pkg/ctrl, pkg/shelfice, and optim:
339      - add new control variable xx_shifwflx (fresh water flux underneath ice
340        shelves). This is almost as tedious as obcs-ctrl, because the
341        variables needs its own mask.
342      - add a cost function term that penalizes the deviation of xx_shifwflx
343        from the first guess (zero) in analogy to other control variables
344    o pkg/shelfice:
345      - start basic adjoint
346    o pkg/ctrl:
347      - remove extra 2D field "for good measure" when initializing in
348        ctrl_set_globfld_[xy/xz/yz].F
349      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
350      - improve error messages in ctrl_set_unpack_*
351    o OBC implementation in momentum:
352       use interior masks (maskInC,W & S) in momentum S/R:
353       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
354       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
355       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
356       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
357       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
358        (and also with Leith/Smagorinsky harmonic-viscosity).
359       Update output of experiment dome and exp4 (+nlfs).
360    o exp4 test-exp:
361      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
362        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
363        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
364        time-varying OB at Western-side for wVel (NonHyd); update output.
365      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
366        and biharmonic-viscosity ; also use prescribed time varying OB.
367    o pkg/obcs:
368      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
369    o model/src:
370      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
371      - initialise startTime & nIter0 with unlikely values: allows to set one
372        from the other without ambiguity.
373    o seaice_obcs test-exp.:
374      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
375    o pkg/obcs:
376      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
377        no longer needed with maskInC,W,S in pkg/generic_advdiff.
378    o pkg/seaice:
379      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
380        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
381      - fixed bug in the initialization of sea ice salinity variable HSALT
382        in seaice_init_varia.F  (removed dependence on ICE2WATR)
383    o fizhi-cs test exp.:
384       switch reference output convention for these 2 non-standard test-exp,
385        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
386          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
387       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
388    o model/inc:
389      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
390        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
391    o pkg/seaice:
392      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
393    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
394      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
395        and initial HSALT
396    
397    checkpoint62w (2011/04/26)
398    o pkg/mom_fluxform:
399      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
400      - use parameter "sideDragFactor" in no-slip BC side-drag part.
401      - update output of exp. global_ocean.90x40x15
402    o pkg/mom_vecinv:
403      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
404    o update seaice exp.:
405      use more consistent parameter values (remove "backward compatability only":
406       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
407      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
408       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
409    o update test-exp global_ocean.90x40x15:
410      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
411      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
412      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
413      o turn on zStar & viscA4 in standard set-up (dir input/)
414        and update output files: output.txt & output.dwnslp.txt
415    o new AD-test experiment: obcs_ctrl
416      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
417    o pkg/dic:
418      fix two bugs in handling water vapour pressure in carbonate chemistry
419      and air-sea fluxes. Found by Val Bennington and Galen McKinley
420      (add DIC Option = WATERVAP_BUG to recover old results)
421      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
422    o adding allowInteriorFreezing option to check for water below freezing point
423      at depth and bring the negative heat anomaly to the surface level
424    o pkgs _fields_load:
425      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
426      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
427        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
428        rbcs to get interpolation weights and time reccord number.
429      - fix multi-threading in aim_fields_load.F
430      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
431    o external_fields_load:
432      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
433       interpolation weights) to use in a periodic time-series ; do not divide by
434       time-step to convert to integer:
435       - this fixes case where externForcingPeriod is not multiple of time-step
436          (Thanks to Christopher L. Wolfe)
437       - this fixes case where externForcingPeriod is an odd multiple of time-step
438         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
439      store index of time-record which is currently loaded:
440       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
441       - needed for the adjoint but not yet used because of extensive recomputations;
442         (to be fixed soon)
443    
444    checkpoint62v (2011/04/02)
445    o verification/1D_ocean_ice_column added to test Ian Fenty's
446      pkg/seaice_growth.F modifications for improving sea ice code differentiability
447    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
448      (new velocity statistics after changing maskInW & maskInS definition)
449    o pkg/generic_advdiff with OBCS:
450      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
451      equivalent to assumption of no tracer gradient outside the OB region.
452      This will affect the results if using obcs+biharmonic diffusion.
453      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
454    o pkg/obcs:
455      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
456      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
457      in Interior region. No impact on solution but affects Velocity monitor stats.
458    o pkg/ptracers (adjoint)
459      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
460      tape file for each tracer
461    o model/inc/src and pkg/autodiff: add parameters that allow to turn
462      of parts of the adjoint code at run time. For now, there are only
463      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
464      parameters are set in data.pkg.
465      This is the lazy coward's version of doing this, but still useful for
466      debugging. In order to do it right, everything needs to be moved to
467      pkg/autodiff.
468    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
469      the end; this fixes the adjoint balancing code for open boundaries.
470    o pkg/ctrl:
471      - change behavior of xx_${varname}period to be analogous to exf-conventions:
472        xx_${varname}period =   0.,  means time-independent control part
473        xx_${varname}period = -12., means one-year-periodic monthly control part
474      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
475        clean up ctrl_init a little, remove unused variables
476      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
477      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
478    
479    checkpoint62u (2011/03/15)
480    o model/src:
481      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
482        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
483      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
484        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
485    o pkg/ctrl/obcs/ecco:
486      - remove obsolete, unused, and partially broken code:
487        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
488        ALLOW_CTRL_OBCS_BALANCE
489      - put a stop statement into ecco/cost_obcsvol.F, but also add
490        cost_obcsvol to ecco_ad_diff.list
491    o pkg/ecco: fix counting cost function contributions for obcs (code
492      by Matt M.) and diffkr for diagnostics
493    o pkg/ecco, pkg/ctrl, pkg/grdchk:
494      add cost penalty terms for initial uvel, vvel, eta controls
495      and I/O for prior error files
496    o pkg/mdsio:
497       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
498       (new argument) to check for tiled file in mdsioLocalDir : this fix the
499       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
500    o pkg/ctrl:
501     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
502       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
503       unused and superfluous variables
504     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
505    o pkg/ecco
506     - enable adjoint of Stevens OB
507    o pkg/ctrl/ecco/grdchk:
508      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
509        Fortunately, we do not have any tests for the numerous cpp-flagged
510        option of "obcs as control parameters" so we will never know
511        if this is an improvement (but at least now things compile).
512      - remove an obsolete initialization from ecco_cost_init_barfiles.F
513      - fix some problems within never used ifdefs to make the code compile
514    o pkg/obcs:
515     - Refine Interior mask definition to work with more complex OB (e.g.
516       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
517       read in Interior mask from file. Check if Interior mask is consistent
518       with OB list of indices.
519    o pkg/seaice
520     - beginning code for a seaice tracer package,
521       but currently only used for seaice age: SEAICE_AGE
522       SEAICE_num = 4
523       iTracer = 1: area-weighted ice age
524               = 2: volume-weighted ice age
525               = 3, 4: template for one-year vs. multi-year ice
526       data.seaice has new namelist SEAICE_PARM03 for arrays related to
527       SEAICE_num
528    
529    checkpoint62t (2011/03/05)
530    o pkg/obcs:
531     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
532       then normal component. This ensures that the normal component is set
533       correctly even when it conficts with tangential setting from an other OB.
534       Affects results of test-experiment seaice_obcs: update the output.txt
535    o pkg/obcs:
536     - add code to monitor statistics of dynamical fields at OB.
537     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
538       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
539       - change default: balance the Net inflow through all OB (instead of balancing
540         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
541     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
542       to match Nortern OB inflow (OBCS_balanceFacN=0).
543    o pkg/seaice:
544     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
545    o pkg/seaice (seaice_growth v 1.113):
546     - reverting seaice_growth to v 1.111 in order to have code with exact bit
547       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
548       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
549       runtime flag SEAICEareaFormula is kept but is inactive
550    o model/src:
551     - add new param to scale curvilinear grid distance and area when using
552       a different sphere radius from the grid-files.
553     - test/check multi-threads EXCH applied to local variable (cg2d_x)
554    o adjoint:
555     - enable adjoint of Stevens OB
556     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
557       (a bit delicate because of potentially modified adj. common block structure;
558       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
559    
560    checkpoint62s (2011/02/15)
561    o pkg/seaice (seaice_growth v 1.112):
562     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
563       computing the ice cover tendency from effective thickness tendencies. Include
564       Ian Fenty's formula.
565     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
566       SEAICEareaFormula.
567     - simplify notations for the various d_HEFF/d_AREA terms.
568    o pkg/gmredi:
569     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
570       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
571       add a verification test-run (front_relax.bvp) to test GM_useBVP.
572    o pkg/seaice (seaice_growth v 1.111):
573     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
574     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
575       also melt ice.
576    o pkg/seaice:
577     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
578     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
579    o pkg/cheapaml:
580     - from Nico Wienders: New version of this package.
581    o pkg/flt:
582     - add CPP options to prevent floats to re-enter the opposite side of
583       a periodic domain (default: keep periodicity)
584    o pkg/gmredi:
585     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
586       (needed for multi-dim advection).
587     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
588    o model/src:
589     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
590    o tutorial_tracer_adjsens
591     - extend to NLFS and replace maskC by hFacC
592       (change reference output accordingly)
593    
594    checkpoint62r (2011/01/24)
595    o testreport:
596     - add option -deloutp (-do) to remove output file after successful run
597     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
598       extract exact list of procs from this file ; adjust COMMAND by
599       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
600    o pkg/ecco: replace old ineffective way of penalizing deviations from
601      first guess (of obcs) with code by Matt Mazloff
602    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
603      exf/cal
604      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
605        and handle case of obcs?period == 0
606        Not affected by these changes: There is still an inconsistency in
607        the computation of start/endrec for the obcs variables for ALLOW_CAL
608        defined (see comment by Menemenlis, 7-Mar-2003)
609      - make S/R ctrl_get_gen_rec return something meaningful even if
610        ALLOW_CAL is not defined
611      - ctrl_getobcs?: simplify code so that it does not need to use
612                       S/R exf_swapfields
613    o testreport:
614       allow to test MPI with different number of processors for each experiment:
615       create file "SIZE.h.mpi" in each build dir.
616       Note: update of "-command" argument not yet implemented.
617    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
618      alleviate the need for additional 3D tapes when using
619      the non-inear free surface in the adjoint. This is done
620      by adding an 'update' of hfacc etc. to their current
621      value at the beginning of forward_step.F.
622    o pkg/seaice
623      seaice_lsr: move stress-divergence computations out of outer pseudo-
624      timestepping loop
625    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
626      up, so that the calls of the ctrl_* subroutines are really at the end
627      of the routine.
628    o pkg/gmredi:
629      allow to specify a 2-D horizontal map and a 1-D vertical profil
630      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
631    o pkg/seaice:
632      move lsr iterations from seaice_dynsolver to seaice_lsr.
633    o pkg/seaice:
634      reduce memory footprint of seaice mutldim advection tapes,
635      by using a 2D tape independent of the generic_advdiff ones,
636      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
637    
638    checkpoint62q (2010/12/29)
639    o model/src:
640      - check horizontal grid-spacing for unset or zero/negative values.
641      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
642    o pkg/flt:
643      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
644      - precision of input and output files set according to readBinaryPrec
645        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
646      - initial float position from tiled file was not converted to index space
647        (looks like a bug): fixed to make it similar to initial pos. global file.
648    o global_ocean.cs32x15:
649       change SIZE.h of AD set-up to get same tiling as with MPI.
650       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
651    o model/src:
652       add flag to control printing of domain fields (bathymetry, hFac ...) in
653       ini_mask_etc (call to plot_fieds_xy*).
654    o pkg/thsice:
655       if useEXF, some forcing fields are not valid in overlap: fixed by computing
656       over the interior only + apply EXCH at the end (like with SEAICE advection).
657    o pkg/mdsio:
658      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
659        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
660      - change barrier call for safe multi-threads access to 3-D shared buffer.
661      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
662      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
663        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
664    o pkg/flt:
665      - add fourth-order Runge-Kutta integration
666      - add basic exch2 support (only 1 facet supported so far!)
667    o pkg/mdsio+rw:
668      new S/R to read local (or tile independent) vector (read counterpart of
669       mds_writevec_loc, and front-end write_glvec_rl/rs).
670    o global_ocean.cs32x15: additional input_ad.seaice experiment
671        that uses pkg/seaice rather than pkg/thsice.
672        (using multidim advection for seaice)
673    o towards more F95 syntax for array specification in namelist:
674      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
675        of all verification experiments.
676           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
677          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
678      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
679    o global_ocean.cs32x15: additional input.seaice experiment
680        that uses pkg/seaice rather than pkg/thsice.
681    
682    checkpoint62p (2010/12/17)
683    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
684        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
685    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
686        allow for use of multim. advection in seaice adjoint.
687    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
688      - first attempt to close budgets by taking into account the freshwater
689        flux implied by the sublimation of snow and ice. So far only the
690        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
691        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
692    o eesupp/src:
693      new S/R with new option (NML_EXTENDED_F77) to change array specification
694      from F95 standard to commonly accepted extended F77 form.
695      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
696      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
697      for less tolerant f77 compiler (e.g., pgf77, g77).
698    o globalFiles:
699      commented out in parameter file "data" since it's not safe with MPI
700      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
701      in this case); no longer commented out in restart test (tst_2+2).
702    o add adTapeDir to specify a special directory where adjoint tapes are
703      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
704      and cannot be used together with mdsioLocalDir.
705    o nesting pkgs:
706      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
707      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
708      - add parameter files + utils dir + output from short run on beagle.
709    o pkg/seaice:
710        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
711    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
712      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
713    
714    checkpoint62o (2010/11/25)
715    o pkg/exf:
716      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
717    o pkg/seaice:
718      - seaice_ocean_stress: split a loop for better vectorization of the
719        adjoint code
720      - seaice_growth.F: fix bug in conservation of freshwater connected to
721        capping of heff, put contribution into d_HEFFbyNEG
722      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
723        by something more sensible (parameters that are what their name implies)
724      - change some defaults, so that by default exf-parameters are used for
725        things like rhoAir, cpAir,latent/sensible heat parameters, in order
726        to reproduce the old results, many data.seaice now contain funny values
727        for cpAir and latent heat of sublimation
728    o packages_readparms.F: move exf_readparms up in line so that
729        exf-parameters are visible for other packages (e.g. seaice)
730    o debugMode & debugLevel=2:
731      - differentiate between debugMode & debugLevel=2:
732        debugMode: controls printing of debug messages (sequence of S/R calls).
733        debugLevel: controls printing of algorithm intermediate results and stats.
734      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
735        => allows to print debug-stats without all sequence of call messages.
736      - switch control of debug print from debugLevel to debugMode in many S/R.
737    o pkg/obcs (obcs-sponge):
738        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
739        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
740    o pkg/generic_advdiff:
741      - record overlap minimum size for each advection scheme;
742      - refine criteria on overlap minimum size;
743      - check and stop (in gad_check) if overlap size is too small.
744    o pkg/obcs:
745      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
746        once, in ptracers_implicit.F)
747      - with seaice: remove test on empty file name in obcs_apply_seaice (always
748        apply OB values when tile has OB)
749    o model/src, coriolis setting:
750      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
751        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
752        files (selectCoriMap=3) with any grid.
753      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
754    o pkg/seaice/seaice_growth.F:
755        a few cosmetic changes that reduce the number of lines of code
756    o pkg/obcs: add boundary conditions following Stevens (1990)
757      - the code follows old MOM/NAOSIM code
758      - so far it is only implemented for the eastern and western boundaries
759        and NOT for pTracers
760    o pkg/rbcs:
761      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
762        beginning of the first rbcs forcing period.
763      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
764        offline package, i.e., one file per time, labeled by iteration number;
765        deltaTrbcs sets the timestep with which the data was generated;
766        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
767      - rbcsForcingCycle=0 makes forcing non-cyclic.
768      - make arithmetic safe for negative times and odd forcing periods.
769    
770    checkpoint62n (2010/11/09)
771    o pkg/seaice:
772        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
773    o pkg/obcs:
774       New S/R to copy tracer value from the OB location to narrow band region
775        (width = same as overlap) beyond the OB: preserve OB value (needed for
776        high-order scheme) which were overwritten by EXCH call if in overlap
777        region. Applied to theta, salt, ptracer and advected seaice variables.
778       With seaice: use maskInC in similar way as in gad_advection.F,
779        in seaice_advection.F and advect.F.
780       Update output of experiment seaice_obcs and change exp4 to test OBCS with
781        4th order Adv.Scheme. for pasive salt and ptracer.
782    o tools/genmake2:
783      - when looking for an optfile (not specified), only search for Fortran compiler
784        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
785      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
786        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
787      - set default for CPP to "cpp -traditional -P" (was the case without specifying
788        an optfile, but otherwise default was just "cpp".
789      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
790      - when "CC" is not set in the optfile, look for possible C compiler
791        (instead of just setting CC=cc)
792      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
793        => add a ".F" to ".o" rule for source files with no "#include" (such as
794           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
795      - move gfortran before g77 in list of possible Fortran compiler (consistent
796        with reference compiler switch from g77 to gfortran)
797    o pkg/seaice:
798      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
799        seaice_check that stops the model, when the CPP flag is used.
800      o seaice_growth.F: make capping of ice volume conserving by returning the
801        capped ice as freshwater to EmPmR. This does not change the verification
802        experiments but will change runs where the capping is acutally active
803    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
804      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
805         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
806         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
807    o tools/genmake2:
808      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
809      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
810      - clean previous genmake log files before anything else.
811      - change Makefile to remove testreport log files (*.tr_log) and genmake log
812        files only with "CLEAN" target (instead of "Clean");
813    o pkg/generic_advdiff:
814      Change OBCS in multiDim advection (gad_advection.F):
815       Use maskInC to prevent intermediate update of tracer-field in OB regions,
816       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
817       which were applying future time-step OB values.
818      This way, all explicit calculations use current-time-step OB values
819       (simpler and more consistent).
820      Affects results when set-up uses time-varying OBC and multi-dim advection;
821       update output of experiment seaice_obcs.
822    o pkg/seaice:
823      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
824       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
825         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
826      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
827       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
828       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
829    o pkg aim (2010/10/26):
830      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
831        formulation with obliquity, eccentricity, ... as run-time parameters,
832      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
833        upward shortwave radition at the surface (all-sky and clear-sky).
834    o pkg/obcs:
835      - writing sections with globalFiles=T does not work: switch to tiled-files
836        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
837      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
838      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
839    
840    checkpoint62m (2010/10/21)
841    o pkg/seaice: vectorize seaice_solve4temp.F
842      - move iterations loops outside of i/j-loops
843      - requires 2D arrays for TB and effConduct
844      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
845        modified in this routine
846      - a little bit of clean up, adjusting indentation, etc.
847      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
848        performance and '**TWO' by '**2' (because TWO is a float),
849        replaced ONE, ZERO
850    o eesupp/src:
851       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
852    o pkg/seaice/seaice_growth.F
853      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
854      merging process. The merged routine has two branches, and one activates the 'evolution'
855      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
856      In summary, here is what the '10/10 revision' did consist of
857        part 1: seaice_growth.F revisions 1.71 to 1.75
858          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
859            The emphasis here was on improving readability (e.g. by trying to use meaningful
860            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
861        part 1.5:
862          - revising the lab_sea experiment to make it a more useful (i.e. stable
863            and representative of an actual model run). This was done by generating a
864            (winter) pickup to start from, switching back the main experiment dynamic
865            solver from evp to lsr, having one of the experiments use the free drift solution.
866        part 2: seaice_growth.F revisions 1.76 to 1.85
867          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
868          - Sorting out the various fields units and sign (set early on and reset at the end)
869            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
870            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
871          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
872            and simplifying logical expressions to further improve readibility.
873        part 3: seaice_growth.F revisions 1.86 to 1.89
874          - Re-organize the blocks of code more logically.
875          - Merging the '_if.F' pieces that add something new.
876    o pkg/thsice:
877      - vectorize thsice_solve4temp and thsice_get_exf.
878        Problem: thsice_solve4temp has an unvectorizable statement that
879        might also be problematic for TAF
880      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
881        does not change the verifcation experiment, but will change all
882        experiments that have this flag undefined (not tested in verification);
883        a little reorganization to save a few 2D fields and recomputations
884      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
885      - 2nd step:  fix some store dirs
886        o seems to work somewhat, i.e. using ifort but not g77
887        o likely cause are incomplete init. or recomputation
888        o start verification/global_ocean.cs32x15/input_ad.thsice
889    o pkg/obcs: add support for exch2
890      - the position of the boundary and prescribed values are specified using
891        a global domain with exch2 facets stacked
892        - in x for N,S boundaries (like W2_mapIO=-1)
893        - in y for E,W boundaries (so E,W boundaries do not overlap)
894    o pkg/mdsio: add support for writing global sections with exch2
895        file layout is as for obcs described above:
896        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
897        - for y-z sections, facets are stacked in y
898    o pkg/thsice:
899       - change a few routines for better vectorization: thsice_albedo.F,
900         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
901         not affected, but in particular the latter routine has changed
902         dramatically (not necessarily easier to read now).
903       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
904       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
905    o verification/lab_sea:
906      - overhaul of the forward model experiments. The main motivation
907        for this revision is that lab_sea has proven quite fragile (when
908        changing the sea-ice code, and switching platforms) to a point
909        when failures were very hard to attribute to specific code problems.
910      - the suspected reason for this fragility is noise amplification by evp so,
911        to start with, we decided to replace evp with lsr in the main experiment.
912      - the input.lsr experiment thus became obsolete and was removed.
913      - it was replaced with the input.fd experiment that uses an
914        analytical "free drift" solution as the ice velocity field.
915      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
916        will hopefully allow us to discriminate problems due to dynamic solvers
917        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
918        us to test additional options, along with the salt plume package.
919      - Finally a pickup was generated (at the end of a one year run) to
920        make the tests more representative of an actual model run. Previously
921        the tests starting point was a 1m thickness of ice everywhere.
922    o pkg/seaice:
923      - introducing S\R seaice_freedrift.F that compute the
924        analytical solution to an approximate ice momentum
925        equation (i.e. the simple stress/coriolis balance).
926      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
927        of the free drift velocity field, and enable its use.
928        To actually use the free drift solution as the model ice
929        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
930    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
931    
932    checkpoint62l (2010/10/04)
933    o pkg/seaice:
934      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
935      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
936       version (with USE_ORIGINAL_SBI undef);
937  o add hooks for new packages OASIS, the package will follow  o add hooks for new packages OASIS, the package will follow
938    (hooks exclude the seaice pkg for now)    (hooks exclude the seaice pkg for now)
939  o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO  o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
940    Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,    Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
941    rather than mdsio_readvector.F/mdsio_writevector.F, within    rather than mdsio_readvector.F/mdsio_writevector.F, within
942    adread_adwrite.F to read/write adjoint-related tapes to disk.    adread_adwrite.F to read/write adjoint-related tapes to disk.
943  o eesup and pkg/mdsio: ALLOW_WHIO  o eesupp and pkg/mdsio: ALLOW_WHIO
944      Option to write/read 2D fields to files including tiles halos.
945    Option to write/read 2D fields to files including tiles halos.    The main purpose is for adjoint related "tape I/O".
   The main purpose is for adjoint related "tape I/O".  
946    The secondary purpose is for debugging phases.    The secondary purpose is for debugging phases.
   
947    A word on those rather specifically intended purposes.    A word on those rather specifically intended purposes.
948    The code was meant to be stripped down to the bare minimum.    The code was meant to be stripped down to the bare minimum.
949    Typically, there is a unique and basic mapping to the global    Typically, there is a unique and basic mapping to the global
950    buffer (tile by tile, then proc by proc, then level by level), and    buffer (tile by tile, then proc by proc, then level by level), and
951    byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not    byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
952    meant to generate user friendly outputs of various shapes and forms.    meant to generate user friendly outputs of various shapes and forms.
953    Rather it is intended, for the knowledgeabale developers,    Rather it is intended, for the knowledgeabale developers,
954    to be largely independent of the many mdsio options, to allow    to be largely independent of the many mdsio options, to allow
955    outputs of tiles+halos in debugging phases and in adjoint runs,    outputs of tiles+halos in debugging phases and in adjoint runs,
956    and to allow some flexibility in tuning (adoint) I/O depending on each    and to allow some flexibility in tuning (adoint) I/O depending on each
957    file system behavior. With regard to tuning, most of the potential knobs    file system behavior. With regard to tuning, most of the potential knobs
958    (to leave files open, to allocate the I/O indep. of usesinglecpuio,    (to leave files open, to allocate the I/O indep. of usesinglecpuio,
959    to specify directories, to specify the typical size of I/O calls, etc.)    to specify directories, to specify the typical size of I/O calls, etc.)
960    are not yet included, and will be added if they prove useful.    are not yet included, and will be added if they prove useful.
# Line 319  o tools/build_options: Line 1247  o tools/build_options:
1247      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1248  o pkg/ecco  o pkg/ecco
1249    - allow user defined cost function contributions    - allow user defined cost function contributions
1250          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1251          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1252    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1253        the two options are complementary.        the two options are complementary.
1254  o pkg/smooth  o pkg/smooth
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