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revision 1.1274 by jmc, Wed May 19 02:12:10 2010 UTC revision 1.1480 by mlosch, Mon Jul 25 08:21:46 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/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
8    o pkg/diagnostics (velocity potential):
9      - fix mask for OBCS (still problems in stream-function with OBCS);
10      - add specific parameter (default = main code CG2D params) for solver;
11      - in case of poor convergence, use solution corresponding to lowest residual.
12    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
13      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
14      and should be avoided where possible.
15    o model/src (rStar):
16      - include r* effect on reference-state (PhiRef) in totPhiHyd
17        (so that it's really the potential anomaly at the cell center);
18        affect solution only if z* with full pressure in EOS.
19      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
20        update output (because of z* in totPhiHyd and viscA4 changes);
21      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
22        @ constant r) until interpolation at constant r is implemented.
23    o pkg/diagnostics
24      - fix RCENTER diagnostics in case cell center is not at interface middle
25    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
26      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
27      that THETA and SALT are "conservative temperature" and "absolute
28      salinity"
29    o pkg/ctrl
30      - fix computation of endrec in s/r ctrl_init_rec
31      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
32    o pkg/seaice/seaice_growth.F
33      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
34        remove then obsolete STORE directives
35      - fix STORE directives for tice and tices, so that only the
36        appropriate part of the fields are stored (and not the entire
37        field); update global_ocean.cs32x15.seaice AD output.
38      - cosmetic changes: adjust CPP flags and indentation for better
39        legibilty
40    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
41      Chris Wilson)
42    o pkg/gmredi:
43       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
44       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
45    
46    checkpoint63 (2011/07/11)
47    o pkg/exch2:
48     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
49     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
50       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
51       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
52    o pkg/diagnostics:
53     - deal with pairs of post-processed diags which are computed together; in
54       particular, re-order list of diags within 1 file to save 2nd computation.
55     - add S/R to compute velocity stream-function (called after velocity-potential
56       calculation) from divergence free transport -> new diagnostics "PsiVEL".
57     - add parameter to select grid-point location where PsiVEL == 0.
58    o eesupp/src:
59       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
60       (specific S/R needed with exch2 topology - for now, just print an error msg)
61    o pkg/shelfice
62     - Implement friction velocity-dependent transfer coefficients following
63       Holland and Jenkins, JPO, 1999
64       Original code by M. Losch with small modifs.
65       Enable with CPP option SHI_ALLOW_GAMMAFRICT
66       and runtime flag SHELFICEuseGammaFrict
67    o verification lab_sea & global_ocean.cs32x15:
68     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
69       does not miss some dependencies (but is slower) and also works with many files
70       (default makedepend limitation for AD built).
71     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
72    o pkg/diagnostics:
73     - add run-time parameter "useMissingValue" (def=False) to fill land-point
74        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
75       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
76     - Extend the use of "missing_value" setting from data.diagnostics for the case
77       of counter-diagnostics (where fraction-weight is zero). This applies both to
78       MNC and MDS output files.
79    o pkg/seaice/seaice_growth.F:
80      - add 'a priori' cap of latent heat flux based on actual mass considerations
81        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
82        non-legacy seaice_solve4temp.
83      - add diagnostic of the residual sublimation freshwater flux (the freshwater
84        flux taken from the ocean if the total actual latent heat fluxes exceed
85        the maximum)
86      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
87       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
88      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
89       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
90      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
91      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
92    o verification 1D_ocean_ice_column:
93       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
94       update results
95    o pkg/diagnostics:
96     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
97       which are not filled-up but computed from other diags ; In this case, the mate
98       diag points to the primary (filled-up) diag to used for post processing.
99     - Update Velocity-potential computation using post-processed diag framework.
100     ==> Change the ordering of fields and time-periods in MDS output file
101       when using periodic averaging: now writes one time record with the full set
102       of fields for this time period, then the next time reccord (it used to be
103       one field with the full set of time records then the next field).
104         Note: this is now similar to NetCDF (MNC) output file. <==
105    
106    checkpoint62z (2011/06/21)
107    o adjoint monitor:
108     - Add adjoint monitor output for packages exf, seaice
109       and update relevant testreport output
110    o pkg/seaice:
111     - re-order diags inits so that they appear in order in available_diagnostics.log
112     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
113       area/heff/hsnow preceeding thermodynamic growth/melt.
114     - modified diag: SIdA; output actual effect, as the description states.
115     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
116     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
117       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
118        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
119     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
120     - added diagnostics for seaice generic tracers (SItr*).
121     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
122     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
123     I. Fenty: 18-Jun-2011:
124     Minor changes to seaice package:
125     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
126        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
127       - Differentiated "regularization variables" from "floor variables"
128        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
129        * hiceMin became SEAICE_hice_reg (old hiceMin)
130          (with _reg meaning regularization variable)
131       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
132        so as to ensure energy conservation when going between phases
133      - A22 was not used anywhere
134     2) Changed regularization procedure for heffActual and hsnowActual to ensure
135        well-boundedness and smooth adjoint in seaice_growth.F
136     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
137        because the old regularization always set heffActual >= 0.05 cm
138     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
139        on AREA when HEFF > 0.
140      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
141        requiring that DISABLE_AREA_FLOOR *not* be defined
142     Affected verifications:
143      - 1D_ocean_ice_column (output.txt output_adm.txt)
144      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
145    o pkg/diagnostics:
146      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
147      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
148        (was _RL, now integer) with option = 0 to retrieve all levels.
149      - add pieces of code to compute velocity potential at each level (new diagnostics
150        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
151        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
152      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
153        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
154        and in diagnostics_fract_fill.F (do not need a valid pointer for the
155        diagnostics counter-mate); check that definition of counter-diagnostic
156        includes a valid counter-mate (in diagnostics_set_levels.F).
157    o model/src (rStar):
158      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
159        affect solution only if z* with full pressure in EOS;
160        update output of test-exp global_ocean.90x40x15.
161    o pkg/seaice:
162      - introduce siEps=1e-5 parameter
163      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
164      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
165      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
166        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
167        as well as ice cover age and ridging index (attached to AREA).
168        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
169        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
170        Up to SItrMaxNum=3 tracers can be used simultaneously.
171    o pkg/salt_plume:
172      -introduce SPsalFRAC run time parameter that sets the fraction of the
173       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
174       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
175    o model debug options:
176      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
177        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
178      - Refine debug-msg printing selection (3 new levels):
179        debugMode  : controls printing of debug messages (sequence of S/R calls).
180        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
181         debLevZero =  0 ; /* level of disabled aux. msg printing */
182         debLevA =  1 ; /* level of minimum  aux. msg printing */
183         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
184         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
185         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
186         debLevE =  5 ; /* level of extensive debug printing */
187        New debugLevel default: with default debugMode value (=F),
188          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
189          and if debugMode=T, default debugLevel = 4 (debLevD).
190        Relation with previous settings:
191         debLevB (=2) corresponds to former debLevA (=1)
192         debLevD (=4) corresponds to former debLevB (=2)
193        Note:
194         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
195         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
196            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
197      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
198        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
199    o pkg/obcs:
200      - change OBCSfixTopo default from True to False (should not change the results);
201        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
202    o pkg/thsice:
203      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
204        2nd layer seaice sublimation (unlikely to happen)
205      - use Interior mask for OBCS in thsice_advection.F (similar to what is
206        done in gad_advection & seaice_advection).
207    o adjoint:
208      bug fix spotted by Gael Forget:
209      seaice_advection and thsice_advection still had
210      legacy CPP options to avoid CS corner updates for adjoint
211    o pkg/seaice:
212      => Change some of the defaults (2011/05/29):
213         - change SEAICEuseFluxForm default (from False to True)
214         - change DIFF1 default (from 0.004 m/s to 0. m/s)
215         And print warnings if DIFF1 is not set in data.seaice and centered
216          avection scheme is used without any diffusion.
217      also:
218      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
219      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
220      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
221        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
222        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
223      update results of test exp.:
224         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
225             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
226             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
227         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
228         seaice_obcs: output (SEAICEuseFluxForm=T)
229      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
230          for standard fwd & AD lab_sea tests (to keep the same output).
231    o pkg/seaice/seaice_growth.F:
232      - use Ian Fenty's capping formulas for actual ice
233      thickness thoughout EVOLUTION branch.
234      - put treatment pathological case #2) in CPP brackets
235      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
236      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
237    o pkg/seaice:
238      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
239      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
240      also pass fac as a param, which can be 1. (to update the tendency
241      field) or the time step (to update the field itself).
242      - seaice_advdiff.F: for multidim, call seaice_diffusion with
243      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
244      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
245      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
246      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
247    o pkg/seaice:
248      diffusion with centered advection scheme (diffus.F & advect.F):
249      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
250        to just compute the laplacian of input-field.
251      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
252      - fix flux-form version in diffus.F to conserve tracer.
253      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
254       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
255    
256    checkpoint62y (2011/05/26)
257    o pkg/seaice:
258     - seaice_growth.F : in EVOLUTION branch, always include
259       a_QSWbyATM_cover in qnet (as it should be).
260     - verification/global_ocean.cs32x15 : update results accordingly
261       (output.seaice.txt output_adm.seaice.txt).
262    o pkg/seaice + obcs:
263     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
264       equivalent of assuming no tracer gradient outside the OB region.
265       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
266     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
267       after changes above);
268     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
269       only at OB location (instead of over a band of OLx width).
270    o pkg/seaice:
271     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
272       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
273    o pkg/obcs:
274      - split header file "OBCS.h" into 4 separated files:
275        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
276       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
277         (contain no conditional statement which depends on OBCS options).
278      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
279        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
280    o ctrl, cost, grdchk & autodiff pkgs:
281      - make options file more standard (like other {PKG}_OPTIONS.h file but
282        with AD_CONFIG.h); clean-up some of the included header files.
283    o pkg/obcs:
284      - do not mask tracer when applying OB (tracer == 0 could generate problems)
285      - apply tracer OB values to tracer field only at OB location (instead of
286        over a band of OLx width)
287      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
288      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
289        obcs_apply_tloc.F & obcs_apply_sloc.F
290    o obcs in model/src:
291      - call OBCS_APPLY_W only if NonHydrostatic.
292      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
293      - reset dEtaHdt and wVel to zero outside OB interior region ;
294      - leave tracer unchanged outside OB interior region: This has no effect
295        on the solution but just to prevent unrealistic tracer value outside OB.
296      - zero out velocity outside OB interior region: This has no effect on
297        the solution but just to prevent unrealistic velocity outside OB.
298    o obcs and non-lin free-surf:
299       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
300       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
301       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
302       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
303       update results of test-exp. exp4(nlfs).
304    o exp4 (nlfs) test-exp:
305       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
306       with NonLin-FreeSurf); update output.nlfs.txt
307    o obcs and 2d/3d solver norm:
308       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
309       and outside OB interior region (will allow to place OB further inside the
310       domain). Depending on the domain, can affects cg2d-Norm (previous
311       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
312       and cg3d-Norm (previous Norm was computed before canceling OB terms),
313       e.g. in tutorial_plume_on_slope.
314      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
315    o pkg rbcs:
316      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
317      - add capability to apply relaxation to horizontal velocity uVel & vVel.
318    o pkg/grdchk: add gradient check for control variable xx_shifwflx
319    o pkg/shelfice/shelfice_init_fixed.F
320      fix CPP-flag combinations
321    o pkg/seaice: Merge iceage code of Pierre Rampal
322      * update/change/correct ice age calculations
323      * add age updates for pathological cases
324      Probably needs more testing...
325    
326    checkpoint62x (2011/05/13)
327    o pkg/mom_vecinv:
328       high-order vorticity scheme: use interior masks (maskInW & S)
329       to zero-out (outside OB) gradient of vorticity.
330    o verification exp.:
331       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
332       hs94.128x64x5 and seaice_obcs ; update results.
333    o pkg/obcs:
334      fix bug in OBeta for YZ sections in obcs_exf_load.F
335    o pkg/ctrl, pkg/shelfice, and optim:
336      - add new control variable xx_shifwflx (fresh water flux underneath ice
337        shelves). This is almost as tedious as obcs-ctrl, because the
338        variables needs its own mask.
339      - add a cost function term that penalizes the deviation of xx_shifwflx
340        from the first guess (zero) in analogy to other control variables
341    o pkg/shelfice:
342      - start basic adjoint
343    o pkg/ctrl:
344      - remove extra 2D field "for good measure" when initializing in
345        ctrl_set_globfld_[xy/xz/yz].F
346      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
347      - improve error messages in ctrl_set_unpack_*
348    o OBC implementation in momentum:
349       use interior masks (maskInC,W & S) in momentum S/R:
350       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
351       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
352       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
353       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
354       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
355        (and also with Leith/Smagorinsky harmonic-viscosity).
356       Update output of experiment dome and exp4 (+nlfs).
357    o exp4 test-exp:
358      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
359        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
360        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
361        time-varying OB at Western-side for wVel (NonHyd); update output.
362      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
363        and biharmonic-viscosity ; also use prescribed time varying OB.
364    o pkg/obcs:
365      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
366    o model/src:
367      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
368      - initialise startTime & nIter0 with unlikely values: allows to set one
369        from the other without ambiguity.
370    o seaice_obcs test-exp.:
371      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
372    o pkg/obcs:
373      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
374        no longer needed with maskInC,W,S in pkg/generic_advdiff.
375    o pkg/seaice:
376      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
377        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
378      - fixed bug in the initialization of sea ice salinity variable HSALT
379        in seaice_init_varia.F  (removed dependence on ICE2WATR)
380    o fizhi-cs test exp.:
381       switch reference output convention for these 2 non-standard test-exp,
382        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
383          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
384       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
385    o model/inc:
386      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
387        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
388    o pkg/seaice:
389      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
390    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
391      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
392        and initial HSALT
393    
394    checkpoint62w (2011/04/26)
395    o pkg/mom_fluxform:
396      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
397      - use parameter "sideDragFactor" in no-slip BC side-drag part.
398      - update output of exp. global_ocean.90x40x15
399    o pkg/mom_vecinv:
400      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
401    o update seaice exp.:
402      use more consistent parameter values (remove "backward compatability only":
403       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
404      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
405       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
406    o update test-exp global_ocean.90x40x15:
407      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
408      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
409      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
410      o turn on zStar & viscA4 in standard set-up (dir input/)
411        and update output files: output.txt & output.dwnslp.txt
412    o new AD-test experiment: obcs_ctrl
413      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
414    o pkg/dic:
415      fix two bugs in handling water vapour pressure in carbonate chemistry
416      and air-sea fluxes. Found by Val Bennington and Galen McKinley
417      (add DIC Option = WATERVAP_BUG to recover old results)
418      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
419    o adding allowInteriorFreezing option to check for water below freezing point
420      at depth and bring the negative heat anomaly to the surface level
421    o pkgs _fields_load:
422      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
423      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
424        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
425        rbcs to get interpolation weights and time reccord number.
426      - fix multi-threading in aim_fields_load.F
427      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
428    o external_fields_load:
429      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
430       interpolation weights) to use in a periodic time-series ; do not divide by
431       time-step to convert to integer:
432       - this fixes case where externForcingPeriod is not multiple of time-step
433          (Thanks to Christopher L. Wolfe)
434       - this fixes case where externForcingPeriod is an odd multiple of time-step
435         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
436      store index of time-record which is currently loaded:
437       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
438       - needed for the adjoint but not yet used because of extensive recomputations;
439         (to be fixed soon)
440    
441    checkpoint62v (2011/04/02)
442    o verification/1D_ocean_ice_column added to test Ian Fenty's
443      pkg/seaice_growth.F modifications for improving sea ice code differentiability
444    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
445      (new velocity statistics after changing maskInW & maskInS definition)
446    o pkg/generic_advdiff with OBCS:
447      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
448      equivalent to assumption of no tracer gradient outside the OB region.
449      This will affect the results if using obcs+biharmonic diffusion.
450      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
451    o pkg/obcs:
452      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
453      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
454      in Interior region. No impact on solution but affects Velocity monitor stats.
455    o pkg/ptracers (adjoint)
456      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
457      tape file for each tracer
458    o model/inc/src and pkg/autodiff: add parameters that allow to turn
459      of parts of the adjoint code at run time. For now, there are only
460      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
461      parameters are set in data.pkg.
462      This is the lazy coward's version of doing this, but still useful for
463      debugging. In order to do it right, everything needs to be moved to
464      pkg/autodiff.
465    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
466      the end; this fixes the adjoint balancing code for open boundaries.
467    o pkg/ctrl:
468      - change behavior of xx_${varname}period to be analogous to exf-conventions:
469        xx_${varname}period =   0.,  means time-independent control part
470        xx_${varname}period = -12., means one-year-periodic monthly control part
471      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
472        clean up ctrl_init a little, remove unused variables
473      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
474      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
475    
476    checkpoint62u (2011/03/15)
477    o model/src:
478      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
479        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
480      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
481        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
482    o pkg/ctrl/obcs/ecco:
483      - remove obsolete, unused, and partially broken code:
484        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
485        ALLOW_CTRL_OBCS_BALANCE
486      - put a stop statement into ecco/cost_obcsvol.F, but also add
487        cost_obcsvol to ecco_ad_diff.list
488    o pkg/ecco: fix counting cost function contributions for obcs (code
489      by Matt M.) and diffkr for diagnostics
490    o pkg/ecco, pkg/ctrl, pkg/grdchk:
491      add cost penalty terms for initial uvel, vvel, eta controls
492      and I/O for prior error files
493    o pkg/mdsio:
494       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
495       (new argument) to check for tiled file in mdsioLocalDir : this fix the
496       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
497    o pkg/ctrl:
498     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
499       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
500       unused and superfluous variables
501     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
502    o pkg/ecco
503     - enable adjoint of Stevens OB
504    o pkg/ctrl/ecco/grdchk:
505      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
506        Fortunately, we do not have any tests for the numerous cpp-flagged
507        option of "obcs as control parameters" so we will never know
508        if this is an improvement (but at least now things compile).
509      - remove an obsolete initialization from ecco_cost_init_barfiles.F
510      - fix some problems within never used ifdefs to make the code compile
511    o pkg/obcs:
512     - Refine Interior mask definition to work with more complex OB (e.g.
513       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
514       read in Interior mask from file. Check if Interior mask is consistent
515       with OB list of indices.
516    o pkg/seaice
517     - beginning code for a seaice tracer package,
518       but currently only used for seaice age: SEAICE_AGE
519       SEAICE_num = 4
520       iTracer = 1: area-weighted ice age
521               = 2: volume-weighted ice age
522               = 3, 4: template for one-year vs. multi-year ice
523       data.seaice has new namelist SEAICE_PARM03 for arrays related to
524       SEAICE_num
525    
526    checkpoint62t (2011/03/05)
527    o pkg/obcs:
528     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
529       then normal component. This ensures that the normal component is set
530       correctly even when it conficts with tangential setting from an other OB.
531       Affects results of test-experiment seaice_obcs: update the output.txt
532    o pkg/obcs:
533     - add code to monitor statistics of dynamical fields at OB.
534     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
535       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
536       - change default: balance the Net inflow through all OB (instead of balancing
537         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
538     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
539       to match Nortern OB inflow (OBCS_balanceFacN=0).
540    o pkg/seaice:
541     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
542    o pkg/seaice (seaice_growth v 1.113):
543     - reverting seaice_growth to v 1.111 in order to have code with exact bit
544       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
545       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
546       runtime flag SEAICEareaFormula is kept but is inactive
547    o model/src:
548     - add new param to scale curvilinear grid distance and area when using
549       a different sphere radius from the grid-files.
550     - test/check multi-threads EXCH applied to local variable (cg2d_x)
551    o adjoint:
552     - enable adjoint of Stevens OB
553     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
554       (a bit delicate because of potentially modified adj. common block structure;
555       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
556    
557    checkpoint62s (2011/02/15)
558    o pkg/seaice (seaice_growth v 1.112):
559     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
560       computing the ice cover tendency from effective thickness tendencies. Include
561       Ian Fenty's formula.
562     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
563       SEAICEareaFormula.
564     - simplify notations for the various d_HEFF/d_AREA terms.
565    o pkg/gmredi:
566     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
567       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
568       add a verification test-run (front_relax.bvp) to test GM_useBVP.
569    o pkg/seaice (seaice_growth v 1.111):
570     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
571     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
572       also melt ice.
573    o pkg/seaice:
574     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
575     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
576    o pkg/cheapaml:
577     - from Nico Wienders: New version of this package.
578    o pkg/flt:
579     - add CPP options to prevent floats to re-enter the opposite side of
580       a periodic domain (default: keep periodicity)
581    o pkg/gmredi:
582     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
583       (needed for multi-dim advection).
584     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
585    o model/src:
586     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
587    o tutorial_tracer_adjsens
588     - extend to NLFS and replace maskC by hFacC
589       (change reference output accordingly)
590    
591    checkpoint62r (2011/01/24)
592    o testreport:
593     - add option -deloutp (-do) to remove output file after successful run
594     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
595       extract exact list of procs from this file ; adjust COMMAND by
596       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
597    o pkg/ecco: replace old ineffective way of penalizing deviations from
598      first guess (of obcs) with code by Matt Mazloff
599    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
600      exf/cal
601      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
602        and handle case of obcs?period == 0
603        Not affected by these changes: There is still an inconsistency in
604        the computation of start/endrec for the obcs variables for ALLOW_CAL
605        defined (see comment by Menemenlis, 7-Mar-2003)
606      - make S/R ctrl_get_gen_rec return something meaningful even if
607        ALLOW_CAL is not defined
608      - ctrl_getobcs?: simplify code so that it does not need to use
609                       S/R exf_swapfields
610    o testreport:
611       allow to test MPI with different number of processors for each experiment:
612       create file "SIZE.h.mpi" in each build dir.
613       Note: update of "-command" argument not yet implemented.
614    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
615      alleviate the need for additional 3D tapes when using
616      the non-inear free surface in the adjoint. This is done
617      by adding an 'update' of hfacc etc. to their current
618      value at the beginning of forward_step.F.
619    o pkg/seaice
620      seaice_lsr: move stress-divergence computations out of outer pseudo-
621      timestepping loop
622    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
623      up, so that the calls of the ctrl_* subroutines are really at the end
624      of the routine.
625    o pkg/gmredi:
626      allow to specify a 2-D horizontal map and a 1-D vertical profil
627      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
628    o pkg/seaice:
629      move lsr iterations from seaice_dynsolver to seaice_lsr.
630    o pkg/seaice:
631      reduce memory footprint of seaice mutldim advection tapes,
632      by using a 2D tape independent of the generic_advdiff ones,
633      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
634    
635    checkpoint62q (2010/12/29)
636    o model/src:
637      - check horizontal grid-spacing for unset or zero/negative values.
638      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
639    o pkg/flt:
640      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
641      - precision of input and output files set according to readBinaryPrec
642        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
643      - initial float position from tiled file was not converted to index space
644        (looks like a bug): fixed to make it similar to initial pos. global file.
645    o global_ocean.cs32x15:
646       change SIZE.h of AD set-up to get same tiling as with MPI.
647       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
648    o model/src:
649       add flag to control printing of domain fields (bathymetry, hFac ...) in
650       ini_mask_etc (call to plot_fieds_xy*).
651    o pkg/thsice:
652       if useEXF, some forcing fields are not valid in overlap: fixed by computing
653       over the interior only + apply EXCH at the end (like with SEAICE advection).
654    o pkg/mdsio:
655      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
656        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
657      - change barrier call for safe multi-threads access to 3-D shared buffer.
658      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
659      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
660        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
661    o pkg/flt:
662      - add fourth-order Runge-Kutta integration
663      - add basic exch2 support (only 1 facet supported so far!)
664    o pkg/mdsio+rw:
665      new S/R to read local (or tile independent) vector (read counterpart of
666       mds_writevec_loc, and front-end write_glvec_rl/rs).
667    o global_ocean.cs32x15: additional input_ad.seaice experiment
668        that uses pkg/seaice rather than pkg/thsice.
669        (using multidim advection for seaice)
670    o towards more F95 syntax for array specification in namelist:
671      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
672        of all verification experiments.
673           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
674          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
675      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
676    o global_ocean.cs32x15: additional input.seaice experiment
677        that uses pkg/seaice rather than pkg/thsice.
678    
679    checkpoint62p (2010/12/17)
680    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
681        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
682    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
683        allow for use of multim. advection in seaice adjoint.
684    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
685      - first attempt to close budgets by taking into account the freshwater
686        flux implied by the sublimation of snow and ice. So far only the
687        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
688        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
689    o eesupp/src:
690      new S/R with new option (NML_EXTENDED_F77) to change array specification
691      from F95 standard to commonly accepted extended F77 form.
692      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
693      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
694      for less tolerant f77 compiler (e.g., pgf77, g77).
695    o globalFiles:
696      commented out in parameter file "data" since it's not safe with MPI
697      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
698      in this case); no longer commented out in restart test (tst_2+2).
699    o add adTapeDir to specify a special directory where adjoint tapes are
700      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
701      and cannot be used together with mdsioLocalDir.
702    o nesting pkgs:
703      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
704      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
705      - add parameter files + utils dir + output from short run on beagle.
706    o pkg/seaice:
707        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
708    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
709      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
710    
711    checkpoint62o (2010/11/25)
712    o pkg/exf:
713      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
714    o pkg/seaice:
715      - seaice_ocean_stress: split a loop for better vectorization of the
716        adjoint code
717      - seaice_growth.F: fix bug in conservation of freshwater connected to
718        capping of heff, put contribution into d_HEFFbyNEG
719      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
720        by something more sensible (parameters that are what their name implies)
721      - change some defaults, so that by default exf-parameters are used for
722        things like rhoAir, cpAir,latent/sensible heat parameters, in order
723        to reproduce the old results, many data.seaice now contain funny values
724        for cpAir and latent heat of sublimation
725    o packages_readparms.F: move exf_readparms up in line so that
726        exf-parameters are visible for other packages (e.g. seaice)
727    o debugMode & debugLevel=2:
728      - differentiate between debugMode & debugLevel=2:
729        debugMode: controls printing of debug messages (sequence of S/R calls).
730        debugLevel: controls printing of algorithm intermediate results and stats.
731      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
732        => allows to print debug-stats without all sequence of call messages.
733      - switch control of debug print from debugLevel to debugMode in many S/R.
734    o pkg/obcs (obcs-sponge):
735        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
736        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
737    o pkg/generic_advdiff:
738      - record overlap minimum size for each advection scheme;
739      - refine criteria on overlap minimum size;
740      - check and stop (in gad_check) if overlap size is too small.
741    o pkg/obcs:
742      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
743        once, in ptracers_implicit.F)
744      - with seaice: remove test on empty file name in obcs_apply_seaice (always
745        apply OB values when tile has OB)
746    o model/src, coriolis setting:
747      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
748        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
749        files (selectCoriMap=3) with any grid.
750      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
751    o pkg/seaice/seaice_growth.F:
752        a few cosmetic changes that reduce the number of lines of code
753    o pkg/obcs: add boundary conditions following Stevens (1990)
754      - the code follows old MOM/NAOSIM code
755      - so far it is only implemented for the eastern and western boundaries
756        and NOT for pTracers
757    o pkg/rbcs:
758      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
759        beginning of the first rbcs forcing period.
760      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
761        offline package, i.e., one file per time, labeled by iteration number;
762        deltaTrbcs sets the timestep with which the data was generated;
763        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
764      - rbcsForcingCycle=0 makes forcing non-cyclic.
765      - make arithmetic safe for negative times and odd forcing periods.
766    
767    checkpoint62n (2010/11/09)
768    o pkg/seaice:
769        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
770    o pkg/obcs:
771       New S/R to copy tracer value from the OB location to narrow band region
772        (width = same as overlap) beyond the OB: preserve OB value (needed for
773        high-order scheme) which were overwritten by EXCH call if in overlap
774        region. Applied to theta, salt, ptracer and advected seaice variables.
775       With seaice: use maskInC in similar way as in gad_advection.F,
776        in seaice_advection.F and advect.F.
777       Update output of experiment seaice_obcs and change exp4 to test OBCS with
778        4th order Adv.Scheme. for pasive salt and ptracer.
779    o tools/genmake2:
780      - when looking for an optfile (not specified), only search for Fortran compiler
781        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
782      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
783        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
784      - set default for CPP to "cpp -traditional -P" (was the case without specifying
785        an optfile, but otherwise default was just "cpp".
786      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
787      - when "CC" is not set in the optfile, look for possible C compiler
788        (instead of just setting CC=cc)
789      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
790        => add a ".F" to ".o" rule for source files with no "#include" (such as
791           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
792      - move gfortran before g77 in list of possible Fortran compiler (consistent
793        with reference compiler switch from g77 to gfortran)
794    o pkg/seaice:
795      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
796        seaice_check that stops the model, when the CPP flag is used.
797      o seaice_growth.F: make capping of ice volume conserving by returning the
798        capped ice as freshwater to EmPmR. This does not change the verification
799        experiments but will change runs where the capping is acutally active
800    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
801      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
802         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
803         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
804    o tools/genmake2:
805      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
806      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
807      - clean previous genmake log files before anything else.
808      - change Makefile to remove testreport log files (*.tr_log) and genmake log
809        files only with "CLEAN" target (instead of "Clean");
810    o pkg/generic_advdiff:
811      Change OBCS in multiDim advection (gad_advection.F):
812       Use maskInC to prevent intermediate update of tracer-field in OB regions,
813       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
814       which were applying future time-step OB values.
815      This way, all explicit calculations use current-time-step OB values
816       (simpler and more consistent).
817      Affects results when set-up uses time-varying OBC and multi-dim advection;
818       update output of experiment seaice_obcs.
819    o pkg/seaice:
820      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
821       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
822         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
823      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
824       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
825       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
826    o pkg aim (2010/10/26):
827      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
828        formulation with obliquity, eccentricity, ... as run-time parameters,
829      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
830        upward shortwave radition at the surface (all-sky and clear-sky).
831    o pkg/obcs:
832      - writing sections with globalFiles=T does not work: switch to tiled-files
833        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
834      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
835      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
836    
837    checkpoint62m (2010/10/21)
838    o pkg/seaice: vectorize seaice_solve4temp.F
839      - move iterations loops outside of i/j-loops
840      - requires 2D arrays for TB and effConduct
841      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
842        modified in this routine
843      - a little bit of clean up, adjusting indentation, etc.
844      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
845        performance and '**TWO' by '**2' (because TWO is a float),
846        replaced ONE, ZERO
847    o eesupp/src:
848       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
849    o pkg/seaice/seaice_growth.F
850      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
851      merging process. The merged routine has two branches, and one activates the 'evolution'
852      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
853      In summary, here is what the '10/10 revision' did consist of
854        part 1: seaice_growth.F revisions 1.71 to 1.75
855          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
856            The emphasis here was on improving readability (e.g. by trying to use meaningful
857            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
858        part 1.5:
859          - revising the lab_sea experiment to make it a more useful (i.e. stable
860            and representative of an actual model run). This was done by generating a
861            (winter) pickup to start from, switching back the main experiment dynamic
862            solver from evp to lsr, having one of the experiments use the free drift solution.
863        part 2: seaice_growth.F revisions 1.76 to 1.85
864          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
865          - Sorting out the various fields units and sign (set early on and reset at the end)
866            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
867            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
868          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
869            and simplifying logical expressions to further improve readibility.
870        part 3: seaice_growth.F revisions 1.86 to 1.89
871          - Re-organize the blocks of code more logically.
872          - Merging the '_if.F' pieces that add something new.
873    o pkg/thsice:
874      - vectorize thsice_solve4temp and thsice_get_exf.
875        Problem: thsice_solve4temp has an unvectorizable statement that
876        might also be problematic for TAF
877      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
878        does not change the verifcation experiment, but will change all
879        experiments that have this flag undefined (not tested in verification);
880        a little reorganization to save a few 2D fields and recomputations
881      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
882      - 2nd step:  fix some store dirs
883        o seems to work somewhat, i.e. using ifort but not g77
884        o likely cause are incomplete init. or recomputation
885        o start verification/global_ocean.cs32x15/input_ad.thsice
886    o pkg/obcs: add support for exch2
887      - the position of the boundary and prescribed values are specified using
888        a global domain with exch2 facets stacked
889        - in x for N,S boundaries (like W2_mapIO=-1)
890        - in y for E,W boundaries (so E,W boundaries do not overlap)
891    o pkg/mdsio: add support for writing global sections with exch2
892        file layout is as for obcs described above:
893        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
894        - for y-z sections, facets are stacked in y
895    o pkg/thsice:
896       - change a few routines for better vectorization: thsice_albedo.F,
897         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
898         not affected, but in particular the latter routine has changed
899         dramatically (not necessarily easier to read now).
900       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
901       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
902    o verification/lab_sea:
903      - overhaul of the forward model experiments. The main motivation
904        for this revision is that lab_sea has proven quite fragile (when
905        changing the sea-ice code, and switching platforms) to a point
906        when failures were very hard to attribute to specific code problems.
907      - the suspected reason for this fragility is noise amplification by evp so,
908        to start with, we decided to replace evp with lsr in the main experiment.
909      - the input.lsr experiment thus became obsolete and was removed.
910      - it was replaced with the input.fd experiment that uses an
911        analytical "free drift" solution as the ice velocity field.
912      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
913        will hopefully allow us to discriminate problems due to dynamic solvers
914        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
915        us to test additional options, along with the salt plume package.
916      - Finally a pickup was generated (at the end of a one year run) to
917        make the tests more representative of an actual model run. Previously
918        the tests starting point was a 1m thickness of ice everywhere.
919    o pkg/seaice:
920      - introducing S\R seaice_freedrift.F that compute the
921        analytical solution to an approximate ice momentum
922        equation (i.e. the simple stress/coriolis balance).
923      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
924        of the free drift velocity field, and enable its use.
925        To actually use the free drift solution as the model ice
926        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
927    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
928    
929    checkpoint62l (2010/10/04)
930    o pkg/seaice:
931      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
932      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
933       version (with USE_ORIGINAL_SBI undef);
934    o add hooks for new packages OASIS, the package will follow
935      (hooks exclude the seaice pkg for now)
936    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
937      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
938      rather than mdsio_readvector.F/mdsio_writevector.F, within
939      adread_adwrite.F to read/write adjoint-related tapes to disk.
940    o eesupp and pkg/mdsio: ALLOW_WHIO
941      Option to write/read 2D fields to files including tiles halos.
942      The main purpose is for adjoint related "tape I/O".
943      The secondary purpose is for debugging phases.
944      A word on those rather specifically intended purposes.
945      The code was meant to be stripped down to the bare minimum.
946      Typically, there is a unique and basic mapping to the global
947      buffer (tile by tile, then proc by proc, then level by level), and
948      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
949      meant to generate user friendly outputs of various shapes and forms.
950      Rather it is intended, for the knowledgeabale developers,
951      to be largely independent of the many mdsio options, to allow
952      outputs of tiles+halos in debugging phases and in adjoint runs,
953      and to allow some flexibility in tuning (adoint) I/O depending on each
954      file system behavior. With regard to tuning, most of the potential knobs
955      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
956      to specify directories, to specify the typical size of I/O calls, etc.)
957      are not yet included, and will be added if they prove useful.
958    o pkg/seaice:
959       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
960    o pkg/seaice:
961       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
962       code (seaice_budget_ice_if.F) which enable to recover old standard
963       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
964       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
965    o model/src (rStar):
966       use simple average (not area weighted) of rStarFac at U,V point when using
967       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
968       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
969    
970    checkpoint62k (2010/09/17)
971    o adjoint
972       * changed verification/global_ocean.cs32x15 ; adjoint now tests
973         Adams-Bashforth 3 + NLFS + RSTAR
974       * some more modifs required for ECCO-GODAE v4
975    o pkg/seaice
976       add SEAICE_AGE_VOL option to use volume instead of area for
977       integrating SEAICE_AGE
978    o model/src:
979       first check-in of sigma & hybrid-sigma coordinate code ; also includes
980       non-linear free-surface parts ; but pressure-gradient not yet coded.
981    o pkg/ptracers:
982       option for ptracer to convert Salt Relax into additional EmP.
983        tested in exp. global_ocean.90x40x15.dwnslp (update output)
984    
985    checkpoint62j (2010/08/25)
986    o pkg/ggl90:
987       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
988    o pkg/dic: car_flux.F, phos_flux.F
989      - reduce number of exp-calls in order to improve performance
990      - clean up a little (replace fields by their macros, etc., fix
991        typo in CPP-flag)
992    o pkg/ggl90: minor changes
993      - GGL90diffKrS was removed --> always use GGL90diffKr
994      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
995      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
996        (commented out for now)
997      - change in max/min operations to ensure that smoothing is ok
998      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
999      - always use diffKrNrT as background profile (i.e. never use diffKr field)
1000    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1001    o pkg/dic:
1002      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1003        vectorization
1004      - small bug fix in insol for the unlikely case of a cartesian grid
1005      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1006        + now vectorize, which also removes adjoint recomputations;
1007        + replace integer maksp1 by _RL maskp1
1008        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1009    
1010    checkpoint62i (2010/07/21)
1011    o pkg/flt:
1012      - with OBCS: stop floats which enter the OB region
1013    o model/src:
1014      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1015        for implicit vertical advection.
1016    o pkg/seaice:
1017     - account for melting in seaice age evolution.
1018     - remove double counting of seaice ridging effect on seaice age.
1019    
1020    checkpoint62h (2010/06/18)
1021    o pkg/exch2:
1022     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1023    o tools/genmake2
1024      - remove "-pdefault" option: redundant with the use of "packages.conf";
1025      - remove file pkg/pkg_default : set the default as a pkg group
1026        ("default_pkg_list") defined in pkg/pkg_groups;
1027      - fix for case pkg/pkg_depend is missing (was hanging before);
1028      - add option "-pgroups" to specify a different pkg_groups than the default.
1029    o verification/adjustment.cs-32x32x1:
1030       add a "minimal" set-up test (code_min & input_min) which only compiles
1031       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1032    o tools/genmake2
1033      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1034      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1035    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1036      files are nearly the same anyway.
1037      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1038       - redefinition of tau(i,i) (by a factor of ustar)
1039       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1040       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1041       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1042       - replace
1043         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1044         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1045         by
1046         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1047         (changes results)
1048       -> exf_bulkformulae v1.22,
1049          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1050          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1051                    output.txt 1.63
1052           offline_exf_seaice: output.seaicetd.txt 1.7
1053           seaice_obcs: output.txt 1.10)
1054      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1055       -> exf_bulkformulae v1.23,
1056          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1057          and global_ocean.cs32x15.icedyn (only 11 matching digits)
1058      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1059    o adjoint of exch-1:
1060     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1061       (note: was already like this when using EXCH-2) and remove flow dir
1062       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1063     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1064     - update pkg/exch2 diff list.
1065    
1066    checkpoint62g (2010/05/19)
1067  o eesupp/src (exch-1):  o eesupp/src (exch-1):
1068   - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)   - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1069     and remove argument "simulationMode"; same thing for all exch_*rx_cube.F     and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
# Line 184  o tools/build_options: Line 1244  o tools/build_options:
1244      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1245  o pkg/ecco  o pkg/ecco
1246    - allow user defined cost function contributions    - allow user defined cost function contributions
1247          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1248          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1249    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1250        the two options are complementary.        the two options are complementary.
1251  o pkg/smooth  o pkg/smooth
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