/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1273 by jmc, Tue May 18 22:53:25 2010 UTC revision 1.1473 by jmc, Mon Jul 11 12:03:37 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63 (2011/07/11)
8    o pkg/exch2:
9     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
10     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
11       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
12       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
13    o pkg/diagnostics:
14     - deal with pairs of post-processed diags which are computed together; in
15       particular, re-order list of diags within 1 file to save 2nd computation.
16     - add S/R to compute velocity stream-function (called after velocity-potential
17       calculation) from divergence free transport -> new diagnostics "PsiVEL".
18     - add parameter to select grid-point location where PsiVEL == 0.
19    o eesupp/src:
20       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
21       (specific S/R needed with exch2 topology - for now, just print an error msg)
22    o pkg/shelfice
23     - Implement friction velocity-dependent transfer coefficients following
24       Holland and Jenkins, JPO, 1999
25       Original code by M. Losch with small modifs.
26       Enable with CPP option SHI_ALLOW_GAMMAFRICT
27       and runtime flag SHELFICEuseGammaFrict
28    o verification lab_sea & global_ocean.cs32x15:
29     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
30       does not miss some dependencies (but is slower) and also works with many files
31       (default makedepend limitation for AD built).
32     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
33    o pkg/diagnostics:
34     - add run-time parameter "useMissingValue" (def=False) to fill land-point
35        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
36       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
37     - Extend the use of "missing_value" setting from data.diagnostics for the case
38       of counter-diagnostics (where fraction-weight is zero). This applies both to
39       MNC and MDS output files.
40    o pkg/seaice/seaice_growth.F:
41      - add 'a priori' cap of latent heat flux based on actual mass considerations
42        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
43        non-legacy seaice_solve4temp.
44      - add diagnostic of the residual sublimation freshwater flux (the freshwater
45        flux taken from the ocean if the total actual latent heat fluxes exceed
46        the maximum)
47      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
48       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
49      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
50       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
51      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
52      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
53    o verification 1D_ocean_ice_column:
54       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
55       update results
56    o pkg/diagnostics:
57     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
58       which are not filled-up but computed from other diags ; In this case, the mate
59       diag points to the primary (filled-up) diag to used for post processing.
60     - Update Velocity-potential computation using post-processed diag framework.
61     ==> Change the ordering of fields and time-periods in MDS output file
62       when using periodic averaging: now writes one time record with the full set
63       of fields for this time period, then the next time reccord (it used to be
64       one field with the full set of time records then the next field).
65         Note: this is now similar to NetCDF (MNC) output file. <==
66    
67    checkpoint62z (2011/06/21)
68    o adjoint monitor:
69     - Add adjoint monitor output for packages exf, seaice
70       and update relevant testreport output
71    o pkg/seaice:
72     - re-order diags inits so that they appear in order in available_diagnostics.log
73     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
74       area/heff/hsnow preceeding thermodynamic growth/melt.
75     - modified diag: SIdA; output actual effect, as the description states.
76     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
77     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
78       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
79        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
80     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
81     - added diagnostics for seaice generic tracers (SItr*).
82     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
83     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
84     I. Fenty: 18-Jun-2011:
85     Minor changes to seaice package:
86     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
87        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
88       - Differentiated "regularization variables" from "floor variables"
89        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
90        * hiceMin became SEAICE_hice_reg (old hiceMin)
91          (with _reg meaning regularization variable)
92       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
93        so as to ensure energy conservation when going between phases
94      - A22 was not used anywhere
95     2) Changed regularization procedure for heffActual and hsnowActual to ensure
96        well-boundedness and smooth adjoint in seaice_growth.F
97     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
98        because the old regularization always set heffActual >= 0.05 cm
99     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
100        on AREA when HEFF > 0.
101      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
102        requiring that DISABLE_AREA_FLOOR *not* be defined
103     Affected verifications:
104      - 1D_ocean_ice_column (output.txt output_adm.txt)
105      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
106    o pkg/diagnostics:
107      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
108      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
109        (was _RL, now integer) with option = 0 to retrieve all levels.
110      - add pieces of code to compute velocity potential at each level (new diagnostics
111        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
112        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
113      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
114        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
115        and in diagnostics_fract_fill.F (do not need a valid pointer for the
116        diagnostics counter-mate); check that definition of counter-diagnostic
117        includes a valid counter-mate (in diagnostics_set_levels.F).
118    o model/src (rStar):
119      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
120        affect solution only if z* with full pressure in EOS;
121        update output of test-exp global_ocean.90x40x15.
122    o pkg/seaice:
123      - introduce siEps=1e-5 parameter
124      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
125      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
126      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
127        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
128        as well as ice cover age and ridging index (attached to AREA).
129        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
130        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
131        Up to SItrMaxNum=3 tracers can be used simultaneously.
132    o pkg/salt_plume:
133      -introduce SPsalFRAC run time parameter that sets the fraction of the
134       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
135       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
136    o model debug options:
137      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
138        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
139      - Refine debug-msg printing selection (3 new levels):
140        debugMode  : controls printing of debug messages (sequence of S/R calls).
141        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
142         debLevZero =  0 ; /* level of disabled aux. msg printing */
143         debLevA =  1 ; /* level of minimum  aux. msg printing */
144         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
145         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
146         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
147         debLevE =  5 ; /* level of extensive debug printing */
148        New debugLevel default: with default debugMode value (=F),
149          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
150          and if debugMode=T, default debugLevel = 4 (debLevD).
151        Relation with previous settings:
152         debLevB (=2) corresponds to former debLevA (=1)
153         debLevD (=4) corresponds to former debLevB (=2)
154        Note:
155         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
156         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
157            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
158      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
159        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
160    o pkg/obcs:
161      - change OBCSfixTopo default from True to False (should not change the results);
162        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
163    o pkg/thsice:
164      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
165        2nd layer seaice sublimation (unlikely to happen)
166      - use Interior mask for OBCS in thsice_advection.F (similar to what is
167        done in gad_advection & seaice_advection).
168    o adjoint:
169      bug fix spotted by Gael Forget:
170      seaice_advection and thsice_advection still had
171      legacy CPP options to avoid CS corner updates for adjoint
172    o pkg/seaice:
173      => Change some of the defaults (2011/05/29):
174         - change SEAICEuseFluxForm default (from False to True)
175         - change DIFF1 default (from 0.004 m/s to 0. m/s)
176         And print warnings if DIFF1 is not set in data.seaice and centered
177          avection scheme is used without any diffusion.
178      also:
179      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
180      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
181      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
182        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
183        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
184      update results of test exp.:
185         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
186             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
187             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
188         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
189         seaice_obcs: output (SEAICEuseFluxForm=T)
190      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
191          for standard fwd & AD lab_sea tests (to keep the same output).
192    o pkg/seaice/seaice_growth.F:
193      - use Ian Fenty's capping formulas for actual ice
194      thickness thoughout EVOLUTION branch.
195      - put treatment pathological case #2) in CPP brackets
196      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
197      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
198    o pkg/seaice:
199      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
200      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
201      also pass fac as a param, which can be 1. (to update the tendency
202      field) or the time step (to update the field itself).
203      - seaice_advdiff.F: for multidim, call seaice_diffusion with
204      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
205      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
206      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
207      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
208    o pkg/seaice:
209      diffusion with centered advection scheme (diffus.F & advect.F):
210      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
211        to just compute the laplacian of input-field.
212      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
213      - fix flux-form version in diffus.F to conserve tracer.
214      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
215       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
216    
217    checkpoint62y (2011/05/26)
218    o pkg/seaice:
219     - seaice_growth.F : in EVOLUTION branch, always include
220       a_QSWbyATM_cover in qnet (as it should be).
221     - verification/global_ocean.cs32x15 : update results accordingly
222       (output.seaice.txt output_adm.seaice.txt).
223    o pkg/seaice + obcs:
224     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
225       equivalent of assuming no tracer gradient outside the OB region.
226       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
227     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
228       after changes above);
229     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
230       only at OB location (instead of over a band of OLx width).
231    o pkg/seaice:
232     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
233       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
234    o pkg/obcs:
235      - split header file "OBCS.h" into 4 separated files:
236        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
237       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
238         (contain no conditional statement which depends on OBCS options).
239      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
240        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
241    o ctrl, cost, grdchk & autodiff pkgs:
242      - make options file more standard (like other {PKG}_OPTIONS.h file but
243        with AD_CONFIG.h); clean-up some of the included header files.
244    o pkg/obcs:
245      - do not mask tracer when applying OB (tracer == 0 could generate problems)
246      - apply tracer OB values to tracer field only at OB location (instead of
247        over a band of OLx width)
248      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
249      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
250        obcs_apply_tloc.F & obcs_apply_sloc.F
251    o obcs in model/src:
252      - call OBCS_APPLY_W only if NonHydrostatic.
253      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
254      - reset dEtaHdt and wVel to zero outside OB interior region ;
255      - leave tracer unchanged outside OB interior region: This has no effect
256        on the solution but just to prevent unrealistic tracer value outside OB.
257      - zero out velocity outside OB interior region: This has no effect on
258        the solution but just to prevent unrealistic velocity outside OB.
259    o obcs and non-lin free-surf:
260       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
261       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
262       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
263       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
264       update results of test-exp. exp4(nlfs).
265    o exp4 (nlfs) test-exp:
266       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
267       with NonLin-FreeSurf); update output.nlfs.txt
268    o obcs and 2d/3d solver norm:
269       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
270       and outside OB interior region (will allow to place OB further inside the
271       domain). Depending on the domain, can affects cg2d-Norm (previous
272       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
273       and cg3d-Norm (previous Norm was computed before canceling OB terms),
274       e.g. in tutorial_plume_on_slope.
275      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
276    o pkg rbcs:
277      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
278      - add capability to apply relaxation to horizontal velocity uVel & vVel.
279    o pkg/grdchk: add gradient check for control variable xx_shifwflx
280    o pkg/shelfice/shelfice_init_fixed.F
281      fix CPP-flag combinations
282    o pkg/seaice: Merge iceage code of Pierre Rampal
283      * update/change/correct ice age calculations
284      * add age updates for pathological cases
285      Probably needs more testing...
286    
287    checkpoint62x (2011/05/13)
288    o pkg/mom_vecinv:
289       high-order vorticity scheme: use interior masks (maskInW & S)
290       to zero-out (outside OB) gradient of vorticity.
291    o verification exp.:
292       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
293       hs94.128x64x5 and seaice_obcs ; update results.
294    o pkg/obcs:
295      fix bug in OBeta for YZ sections in obcs_exf_load.F
296    o pkg/ctrl, pkg/shelfice, and optim:
297      - add new control variable xx_shifwflx (fresh water flux underneath ice
298        shelves). This is almost as tedious as obcs-ctrl, because the
299        variables needs its own mask.
300      - add a cost function term that penalizes the deviation of xx_shifwflx
301        from the first guess (zero) in analogy to other control variables
302    o pkg/shelfice:
303      - start basic adjoint
304    o pkg/ctrl:
305      - remove extra 2D field "for good measure" when initializing in
306        ctrl_set_globfld_[xy/xz/yz].F
307      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
308      - improve error messages in ctrl_set_unpack_*
309    o OBC implementation in momentum:
310       use interior masks (maskInC,W & S) in momentum S/R:
311       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
312       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
313       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
314       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
315       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
316        (and also with Leith/Smagorinsky harmonic-viscosity).
317       Update output of experiment dome and exp4 (+nlfs).
318    o exp4 test-exp:
319      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
320        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
321        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
322        time-varying OB at Western-side for wVel (NonHyd); update output.
323      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
324        and biharmonic-viscosity ; also use prescribed time varying OB.
325    o pkg/obcs:
326      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
327    o model/src:
328      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
329      - initialise startTime & nIter0 with unlikely values: allows to set one
330        from the other without ambiguity.
331    o seaice_obcs test-exp.:
332      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
333    o pkg/obcs:
334      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
335        no longer needed with maskInC,W,S in pkg/generic_advdiff.
336    o pkg/seaice:
337      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
338        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
339      - fixed bug in the initialization of sea ice salinity variable HSALT
340        in seaice_init_varia.F  (removed dependence on ICE2WATR)
341    o fizhi-cs test exp.:
342       switch reference output convention for these 2 non-standard test-exp,
343        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
344          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
345       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
346    o model/inc:
347      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
348        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
349    o pkg/seaice:
350      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
351    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
352      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
353        and initial HSALT
354    
355    checkpoint62w (2011/04/26)
356    o pkg/mom_fluxform:
357      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
358      - use parameter "sideDragFactor" in no-slip BC side-drag part.
359      - update output of exp. global_ocean.90x40x15
360    o pkg/mom_vecinv:
361      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
362    o update seaice exp.:
363      use more consistent parameter values (remove "backward compatability only":
364       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
365      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
366       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
367    o update test-exp global_ocean.90x40x15:
368      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
369      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
370      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
371      o turn on zStar & viscA4 in standard set-up (dir input/)
372        and update output files: output.txt & output.dwnslp.txt
373    o new AD-test experiment: obcs_ctrl
374      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
375    o pkg/dic:
376      fix two bugs in handling water vapour pressure in carbonate chemistry
377      and air-sea fluxes. Found by Val Bennington and Galen McKinley
378      (add DIC Option = WATERVAP_BUG to recover old results)
379      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
380    o adding allowInteriorFreezing option to check for water below freezing point
381      at depth and bring the negative heat anomaly to the surface level
382    o pkgs _fields_load:
383      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
384      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
385        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
386        rbcs to get interpolation weights and time reccord number.
387      - fix multi-threading in aim_fields_load.F
388      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
389    o external_fields_load:
390      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
391       interpolation weights) to use in a periodic time-series ; do not divide by
392       time-step to convert to integer:
393       - this fixes case where externForcingPeriod is not multiple of time-step
394          (Thanks to Christopher L. Wolfe)
395       - this fixes case where externForcingPeriod is an odd multiple of time-step
396         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
397      store index of time-record which is currently loaded:
398       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
399       - needed for the adjoint but not yet used because of extensive recomputations;
400         (to be fixed soon)
401    
402    checkpoint62v (2011/04/02)
403    o verification/1D_ocean_ice_column added to test Ian Fenty's
404      pkg/seaice_growth.F modifications for improving sea ice code differentiability
405    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
406      (new velocity statistics after changing maskInW & maskInS definition)
407    o pkg/generic_advdiff with OBCS:
408      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
409      equivalent to assumption of no tracer gradient outside the OB region.
410      This will affect the results if using obcs+biharmonic diffusion.
411      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
412    o pkg/obcs:
413      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
414      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
415      in Interior region. No impact on solution but affects Velocity monitor stats.
416    o pkg/ptracers (adjoint)
417      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
418      tape file for each tracer
419    o model/inc/src and pkg/autodiff: add parameters that allow to turn
420      of parts of the adjoint code at run time. For now, there are only
421      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
422      parameters are set in data.pkg.
423      This is the lazy coward's version of doing this, but still useful for
424      debugging. In order to do it right, everything needs to be moved to
425      pkg/autodiff.
426    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
427      the end; this fixes the adjoint balancing code for open boundaries.
428    o pkg/ctrl:
429      - change behavior of xx_${varname}period to be analogous to exf-conventions:
430        xx_${varname}period =   0.,  means time-independent control part
431        xx_${varname}period = -12., means one-year-periodic monthly control part
432      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
433        clean up ctrl_init a little, remove unused variables
434      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
435      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
436    
437    checkpoint62u (2011/03/15)
438    o model/src:
439      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
440        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
441      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
442        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
443    o pkg/ctrl/obcs/ecco:
444      - remove obsolete, unused, and partially broken code:
445        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
446        ALLOW_CTRL_OBCS_BALANCE
447      - put a stop statement into ecco/cost_obcsvol.F, but also add
448        cost_obcsvol to ecco_ad_diff.list
449    o pkg/ecco: fix counting cost function contributions for obcs (code
450      by Matt M.) and diffkr for diagnostics
451    o pkg/ecco, pkg/ctrl, pkg/grdchk:
452      add cost penalty terms for initial uvel, vvel, eta controls
453      and I/O for prior error files
454    o pkg/mdsio:
455       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
456       (new argument) to check for tiled file in mdsioLocalDir : this fix the
457       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
458    o pkg/ctrl:
459     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
460       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
461       unused and superfluous variables
462     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
463    o pkg/ecco
464     - enable adjoint of Stevens OB
465    o pkg/ctrl/ecco/grdchk:
466      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
467        Fortunately, we do not have any tests for the numerous cpp-flagged
468        option of "obcs as control parameters" so we will never know
469        if this is an improvement (but at least now things compile).
470      - remove an obsolete initialization from ecco_cost_init_barfiles.F
471      - fix some problems within never used ifdefs to make the code compile
472    o pkg/obcs:
473     - Refine Interior mask definition to work with more complex OB (e.g.
474       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
475       read in Interior mask from file. Check if Interior mask is consistent
476       with OB list of indices.
477    o pkg/seaice
478     - beginning code for a seaice tracer package,
479       but currently only used for seaice age: SEAICE_AGE
480       SEAICE_num = 4
481       iTracer = 1: area-weighted ice age
482               = 2: volume-weighted ice age
483               = 3, 4: template for one-year vs. multi-year ice
484       data.seaice has new namelist SEAICE_PARM03 for arrays related to
485       SEAICE_num
486    
487    checkpoint62t (2011/03/05)
488    o pkg/obcs:
489     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
490       then normal component. This ensures that the normal component is set
491       correctly even when it conficts with tangential setting from an other OB.
492       Affects results of test-experiment seaice_obcs: update the output.txt
493    o pkg/obcs:
494     - add code to monitor statistics of dynamical fields at OB.
495     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
496       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
497       - change default: balance the Net inflow through all OB (instead of balancing
498         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
499     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
500       to match Nortern OB inflow (OBCS_balanceFacN=0).
501    o pkg/seaice:
502     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
503    o pkg/seaice (seaice_growth v 1.113):
504     - reverting seaice_growth to v 1.111 in order to have code with exact bit
505       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
506       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
507       runtime flag SEAICEareaFormula is kept but is inactive
508    o model/src:
509     - add new param to scale curvilinear grid distance and area when using
510       a different sphere radius from the grid-files.
511     - test/check multi-threads EXCH applied to local variable (cg2d_x)
512    o adjoint:
513     - enable adjoint of Stevens OB
514     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
515       (a bit delicate because of potentially modified adj. common block structure;
516       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
517    
518    checkpoint62s (2011/02/15)
519    o pkg/seaice (seaice_growth v 1.112):
520     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
521       computing the ice cover tendency from effective thickness tendencies. Include
522       Ian Fenty's formula.
523     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
524       SEAICEareaFormula.
525     - simplify notations for the various d_HEFF/d_AREA terms.
526    o pkg/gmredi:
527     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
528       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
529       add a verification test-run (front_relax.bvp) to test GM_useBVP.
530    o pkg/seaice (seaice_growth v 1.111):
531     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
532     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
533       also melt ice.
534    o pkg/seaice:
535     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
536     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
537    o pkg/cheapaml:
538     - from Nico Wienders: New version of this package.
539    o pkg/flt:
540     - add CPP options to prevent floats to re-enter the opposite side of
541       a periodic domain (default: keep periodicity)
542    o pkg/gmredi:
543     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
544       (needed for multi-dim advection).
545     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
546    o model/src:
547     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
548    o tutorial_tracer_adjsens
549     - extend to NLFS and replace maskC by hFacC
550       (change reference output accordingly)
551    
552    checkpoint62r (2011/01/24)
553    o testreport:
554     - add option -deloutp (-do) to remove output file after successful run
555     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
556       extract exact list of procs from this file ; adjust COMMAND by
557       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
558    o pkg/ecco: replace old ineffective way of penalizing deviations from
559      first guess (of obcs) with code by Matt Mazloff
560    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
561      exf/cal
562      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
563        and handle case of obcs?period == 0
564        Not affected by these changes: There is still an inconsistency in
565        the computation of start/endrec for the obcs variables for ALLOW_CAL
566        defined (see comment by Menemenlis, 7-Mar-2003)
567      - make S/R ctrl_get_gen_rec return something meaningful even if
568        ALLOW_CAL is not defined
569      - ctrl_getobcs?: simplify code so that it does not need to use
570                       S/R exf_swapfields
571    o testreport:
572       allow to test MPI with different number of processors for each experiment:
573       create file "SIZE.h.mpi" in each build dir.
574       Note: update of "-command" argument not yet implemented.
575    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
576      alleviate the need for additional 3D tapes when using
577      the non-inear free surface in the adjoint. This is done
578      by adding an 'update' of hfacc etc. to their current
579      value at the beginning of forward_step.F.
580    o pkg/seaice
581      seaice_lsr: move stress-divergence computations out of outer pseudo-
582      timestepping loop
583    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
584      up, so that the calls of the ctrl_* subroutines are really at the end
585      of the routine.
586    o pkg/gmredi:
587      allow to specify a 2-D horizontal map and a 1-D vertical profil
588      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
589    o pkg/seaice:
590      move lsr iterations from seaice_dynsolver to seaice_lsr.
591    o pkg/seaice:
592      reduce memory footprint of seaice mutldim advection tapes,
593      by using a 2D tape independent of the generic_advdiff ones,
594      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
595    
596    checkpoint62q (2010/12/29)
597    o model/src:
598      - check horizontal grid-spacing for unset or zero/negative values.
599      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
600    o pkg/flt:
601      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
602      - precision of input and output files set according to readBinaryPrec
603        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
604      - initial float position from tiled file was not converted to index space
605        (looks like a bug): fixed to make it similar to initial pos. global file.
606    o global_ocean.cs32x15:
607       change SIZE.h of AD set-up to get same tiling as with MPI.
608       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
609    o model/src:
610       add flag to control printing of domain fields (bathymetry, hFac ...) in
611       ini_mask_etc (call to plot_fieds_xy*).
612    o pkg/thsice:
613       if useEXF, some forcing fields are not valid in overlap: fixed by computing
614       over the interior only + apply EXCH at the end (like with SEAICE advection).
615    o pkg/mdsio:
616      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
617        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
618      - change barrier call for safe multi-threads access to 3-D shared buffer.
619      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
620      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
621        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
622    o pkg/flt:
623      - add fourth-order Runge-Kutta integration
624      - add basic exch2 support (only 1 facet supported so far!)
625    o pkg/mdsio+rw:
626      new S/R to read local (or tile independent) vector (read counterpart of
627       mds_writevec_loc, and front-end write_glvec_rl/rs).
628    o global_ocean.cs32x15: additional input_ad.seaice experiment
629        that uses pkg/seaice rather than pkg/thsice.
630        (using multidim advection for seaice)
631    o towards more F95 syntax for array specification in namelist:
632      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
633        of all verification experiments.
634           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
635          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
636      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
637    o global_ocean.cs32x15: additional input.seaice experiment
638        that uses pkg/seaice rather than pkg/thsice.
639    
640    checkpoint62p (2010/12/17)
641    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
642        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
643    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
644        allow for use of multim. advection in seaice adjoint.
645    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
646      - first attempt to close budgets by taking into account the freshwater
647        flux implied by the sublimation of snow and ice. So far only the
648        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
649        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
650    o eesupp/src:
651      new S/R with new option (NML_EXTENDED_F77) to change array specification
652      from F95 standard to commonly accepted extended F77 form.
653      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
654      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
655      for less tolerant f77 compiler (e.g., pgf77, g77).
656    o globalFiles:
657      commented out in parameter file "data" since it's not safe with MPI
658      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
659      in this case); no longer commented out in restart test (tst_2+2).
660    o add adTapeDir to specify a special directory where adjoint tapes are
661      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
662      and cannot be used together with mdsioLocalDir.
663    o nesting pkgs:
664      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
665      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
666      - add parameter files + utils dir + output from short run on beagle.
667    o pkg/seaice:
668        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
669    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
670      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
671    
672    checkpoint62o (2010/11/25)
673    o pkg/exf:
674      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
675    o pkg/seaice:
676      - seaice_ocean_stress: split a loop for better vectorization of the
677        adjoint code
678      - seaice_growth.F: fix bug in conservation of freshwater connected to
679        capping of heff, put contribution into d_HEFFbyNEG
680      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
681        by something more sensible (parameters that are what their name implies)
682      - change some defaults, so that by default exf-parameters are used for
683        things like rhoAir, cpAir,latent/sensible heat parameters, in order
684        to reproduce the old results, many data.seaice now contain funny values
685        for cpAir and latent heat of sublimation
686    o packages_readparms.F: move exf_readparms up in line so that
687        exf-parameters are visible for other packages (e.g. seaice)
688    o debugMode & debugLevel=2:
689      - differentiate between debugMode & debugLevel=2:
690        debugMode: controls printing of debug messages (sequence of S/R calls).
691        debugLevel: controls printing of algorithm intermediate results and stats.
692      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
693        => allows to print debug-stats without all sequence of call messages.
694      - switch control of debug print from debugLevel to debugMode in many S/R.
695    o pkg/obcs (obcs-sponge):
696        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
697        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
698    o pkg/generic_advdiff:
699      - record overlap minimum size for each advection scheme;
700      - refine criteria on overlap minimum size;
701      - check and stop (in gad_check) if overlap size is too small.
702    o pkg/obcs:
703      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
704        once, in ptracers_implicit.F)
705      - with seaice: remove test on empty file name in obcs_apply_seaice (always
706        apply OB values when tile has OB)
707    o model/src, coriolis setting:
708      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
709        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
710        files (selectCoriMap=3) with any grid.
711      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
712    o pkg/seaice/seaice_growth.F:
713        a few cosmetic changes that reduce the number of lines of code
714    o pkg/obcs: add boundary conditions following Stevens (1990)
715      - the code follows old MOM/NAOSIM code
716      - so far it is only implemented for the eastern and western boundaries
717        and NOT for pTracers
718    o pkg/rbcs:
719      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
720        beginning of the first rbcs forcing period.
721      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
722        offline package, i.e., one file per time, labeled by iteration number;
723        deltaTrbcs sets the timestep with which the data was generated;
724        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
725      - rbcsForcingCycle=0 makes forcing non-cyclic.
726      - make arithmetic safe for negative times and odd forcing periods.
727    
728    checkpoint62n (2010/11/09)
729    o pkg/seaice:
730        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
731    o pkg/obcs:
732       New S/R to copy tracer value from the OB location to narrow band region
733        (width = same as overlap) beyond the OB: preserve OB value (needed for
734        high-order scheme) which were overwritten by EXCH call if in overlap
735        region. Applied to theta, salt, ptracer and advected seaice variables.
736       With seaice: use maskInC in similar way as in gad_advection.F,
737        in seaice_advection.F and advect.F.
738       Update output of experiment seaice_obcs and change exp4 to test OBCS with
739        4th order Adv.Scheme. for pasive salt and ptracer.
740    o tools/genmake2:
741      - when looking for an optfile (not specified), only search for Fortran compiler
742        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
743      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
744        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
745      - set default for CPP to "cpp -traditional -P" (was the case without specifying
746        an optfile, but otherwise default was just "cpp".
747      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
748      - when "CC" is not set in the optfile, look for possible C compiler
749        (instead of just setting CC=cc)
750      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
751        => add a ".F" to ".o" rule for source files with no "#include" (such as
752           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
753      - move gfortran before g77 in list of possible Fortran compiler (consistent
754        with reference compiler switch from g77 to gfortran)
755    o pkg/seaice:
756      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
757        seaice_check that stops the model, when the CPP flag is used.
758      o seaice_growth.F: make capping of ice volume conserving by returning the
759        capped ice as freshwater to EmPmR. This does not change the verification
760        experiments but will change runs where the capping is acutally active
761    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
762      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
763         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
764         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
765    o tools/genmake2:
766      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
767      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
768      - clean previous genmake log files before anything else.
769      - change Makefile to remove testreport log files (*.tr_log) and genmake log
770        files only with "CLEAN" target (instead of "Clean");
771    o pkg/generic_advdiff:
772      Change OBCS in multiDim advection (gad_advection.F):
773       Use maskInC to prevent intermediate update of tracer-field in OB regions,
774       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
775       which were applying future time-step OB values.
776      This way, all explicit calculations use current-time-step OB values
777       (simpler and more consistent).
778      Affects results when set-up uses time-varying OBC and multi-dim advection;
779       update output of experiment seaice_obcs.
780    o pkg/seaice:
781      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
782       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
783         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
784      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
785       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
786       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
787    o pkg aim (2010/10/26):
788      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
789        formulation with obliquity, eccentricity, ... as run-time parameters,
790      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
791        upward shortwave radition at the surface (all-sky and clear-sky).
792    o pkg/obcs:
793      - writing sections with globalFiles=T does not work: switch to tiled-files
794        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
795      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
796      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
797    
798    checkpoint62m (2010/10/21)
799    o pkg/seaice: vectorize seaice_solve4temp.F
800      - move iterations loops outside of i/j-loops
801      - requires 2D arrays for TB and effConduct
802      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
803        modified in this routine
804      - a little bit of clean up, adjusting indentation, etc.
805      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
806        performance and '**TWO' by '**2' (because TWO is a float),
807        replaced ONE, ZERO
808    o eesupp/src:
809       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
810    o pkg/seaice/seaice_growth.F
811      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
812      merging process. The merged routine has two branches, and one activates the 'evolution'
813      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
814      In summary, here is what the '10/10 revision' did consist of
815        part 1: seaice_growth.F revisions 1.71 to 1.75
816          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
817            The emphasis here was on improving readability (e.g. by trying to use meaningful
818            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
819        part 1.5:
820          - revising the lab_sea experiment to make it a more useful (i.e. stable
821            and representative of an actual model run). This was done by generating a
822            (winter) pickup to start from, switching back the main experiment dynamic
823            solver from evp to lsr, having one of the experiments use the free drift solution.
824        part 2: seaice_growth.F revisions 1.76 to 1.85
825          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
826          - Sorting out the various fields units and sign (set early on and reset at the end)
827            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
828            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
829          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
830            and simplifying logical expressions to further improve readibility.
831        part 3: seaice_growth.F revisions 1.86 to 1.89
832          - Re-organize the blocks of code more logically.
833          - Merging the '_if.F' pieces that add something new.
834    o pkg/thsice:
835      - vectorize thsice_solve4temp and thsice_get_exf.
836        Problem: thsice_solve4temp has an unvectorizable statement that
837        might also be problematic for TAF
838      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
839        does not change the verifcation experiment, but will change all
840        experiments that have this flag undefined (not tested in verification);
841        a little reorganization to save a few 2D fields and recomputations
842      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
843      - 2nd step:  fix some store dirs
844        o seems to work somewhat, i.e. using ifort but not g77
845        o likely cause are incomplete init. or recomputation
846        o start verification/global_ocean.cs32x15/input_ad.thsice
847    o pkg/obcs: add support for exch2
848      - the position of the boundary and prescribed values are specified using
849        a global domain with exch2 facets stacked
850        - in x for N,S boundaries (like W2_mapIO=-1)
851        - in y for E,W boundaries (so E,W boundaries do not overlap)
852    o pkg/mdsio: add support for writing global sections with exch2
853        file layout is as for obcs described above:
854        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
855        - for y-z sections, facets are stacked in y
856    o pkg/thsice:
857       - change a few routines for better vectorization: thsice_albedo.F,
858         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
859         not affected, but in particular the latter routine has changed
860         dramatically (not necessarily easier to read now).
861       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
862       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
863    o verification/lab_sea:
864      - overhaul of the forward model experiments. The main motivation
865        for this revision is that lab_sea has proven quite fragile (when
866        changing the sea-ice code, and switching platforms) to a point
867        when failures were very hard to attribute to specific code problems.
868      - the suspected reason for this fragility is noise amplification by evp so,
869        to start with, we decided to replace evp with lsr in the main experiment.
870      - the input.lsr experiment thus became obsolete and was removed.
871      - it was replaced with the input.fd experiment that uses an
872        analytical "free drift" solution as the ice velocity field.
873      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
874        will hopefully allow us to discriminate problems due to dynamic solvers
875        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
876        us to test additional options, along with the salt plume package.
877      - Finally a pickup was generated (at the end of a one year run) to
878        make the tests more representative of an actual model run. Previously
879        the tests starting point was a 1m thickness of ice everywhere.
880    o pkg/seaice:
881      - introducing S\R seaice_freedrift.F that compute the
882        analytical solution to an approximate ice momentum
883        equation (i.e. the simple stress/coriolis balance).
884      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
885        of the free drift velocity field, and enable its use.
886        To actually use the free drift solution as the model ice
887        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
888    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
889    
890    checkpoint62l (2010/10/04)
891    o pkg/seaice:
892      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
893      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
894       version (with USE_ORIGINAL_SBI undef);
895    o add hooks for new packages OASIS, the package will follow
896      (hooks exclude the seaice pkg for now)
897    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
898      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
899      rather than mdsio_readvector.F/mdsio_writevector.F, within
900      adread_adwrite.F to read/write adjoint-related tapes to disk.
901    o eesupp and pkg/mdsio: ALLOW_WHIO
902      Option to write/read 2D fields to files including tiles halos.
903      The main purpose is for adjoint related "tape I/O".
904      The secondary purpose is for debugging phases.
905      A word on those rather specifically intended purposes.
906      The code was meant to be stripped down to the bare minimum.
907      Typically, there is a unique and basic mapping to the global
908      buffer (tile by tile, then proc by proc, then level by level), and
909      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
910      meant to generate user friendly outputs of various shapes and forms.
911      Rather it is intended, for the knowledgeabale developers,
912      to be largely independent of the many mdsio options, to allow
913      outputs of tiles+halos in debugging phases and in adjoint runs,
914      and to allow some flexibility in tuning (adoint) I/O depending on each
915      file system behavior. With regard to tuning, most of the potential knobs
916      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
917      to specify directories, to specify the typical size of I/O calls, etc.)
918      are not yet included, and will be added if they prove useful.
919    o pkg/seaice:
920       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
921    o pkg/seaice:
922       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
923       code (seaice_budget_ice_if.F) which enable to recover old standard
924       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
925       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
926    o model/src (rStar):
927       use simple average (not area weighted) of rStarFac at U,V point when using
928       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
929       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
930    
931    checkpoint62k (2010/09/17)
932    o adjoint
933       * changed verification/global_ocean.cs32x15 ; adjoint now tests
934         Adams-Bashforth 3 + NLFS + RSTAR
935       * some more modifs required for ECCO-GODAE v4
936    o pkg/seaice
937       add SEAICE_AGE_VOL option to use volume instead of area for
938       integrating SEAICE_AGE
939    o model/src:
940       first check-in of sigma & hybrid-sigma coordinate code ; also includes
941       non-linear free-surface parts ; but pressure-gradient not yet coded.
942    o pkg/ptracers:
943       option for ptracer to convert Salt Relax into additional EmP.
944        tested in exp. global_ocean.90x40x15.dwnslp (update output)
945    
946    checkpoint62j (2010/08/25)
947    o pkg/ggl90:
948       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
949    o pkg/dic: car_flux.F, phos_flux.F
950      - reduce number of exp-calls in order to improve performance
951      - clean up a little (replace fields by their macros, etc., fix
952        typo in CPP-flag)
953    o pkg/ggl90: minor changes
954      - GGL90diffKrS was removed --> always use GGL90diffKr
955      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
956      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
957        (commented out for now)
958      - change in max/min operations to ensure that smoothing is ok
959      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
960      - always use diffKrNrT as background profile (i.e. never use diffKr field)
961    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
962    o pkg/dic:
963      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
964        vectorization
965      - small bug fix in insol for the unlikely case of a cartesian grid
966      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
967        + now vectorize, which also removes adjoint recomputations;
968        + replace integer maksp1 by _RL maskp1
969        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
970    
971    checkpoint62i (2010/07/21)
972    o pkg/flt:
973      - with OBCS: stop floats which enter the OB region
974    o model/src:
975      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
976        for implicit vertical advection.
977    o pkg/seaice:
978     - account for melting in seaice age evolution.
979     - remove double counting of seaice ridging effect on seaice age.
980    
981    checkpoint62h (2010/06/18)
982    o pkg/exch2:
983     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
984    o tools/genmake2
985      - remove "-pdefault" option: redundant with the use of "packages.conf";
986      - remove file pkg/pkg_default : set the default as a pkg group
987        ("default_pkg_list") defined in pkg/pkg_groups;
988      - fix for case pkg/pkg_depend is missing (was hanging before);
989      - add option "-pgroups" to specify a different pkg_groups than the default.
990    o verification/adjustment.cs-32x32x1:
991       add a "minimal" set-up test (code_min & input_min) which only compiles
992       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
993    o tools/genmake2
994      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
995      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
996    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
997      files are nearly the same anyway.
998      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
999       - redefinition of tau(i,i) (by a factor of ustar)
1000       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1001       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1002       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1003       - replace
1004         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1005         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1006         by
1007         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1008         (changes results)
1009       -> exf_bulkformulae v1.22,
1010          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1011          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1012                    output.txt 1.63
1013           offline_exf_seaice: output.seaicetd.txt 1.7
1014           seaice_obcs: output.txt 1.10)
1015      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1016       -> exf_bulkformulae v1.23,
1017          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1018          and global_ocean.cs32x15.icedyn (only 11 matching digits)
1019      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1020    o adjoint of exch-1:
1021     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1022       (note: was already like this when using EXCH-2) and remove flow dir
1023       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1024     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1025     - update pkg/exch2 diff list.
1026    
1027    checkpoint62g (2010/05/19)
1028    o eesupp/src (exch-1):
1029     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1030       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1031       (renamed to exch1_*rx_cube.F).
1032     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1033       to call new exch1 S/R ; update Makefile and .cvsignore.
1034     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1035       exch2_xy_rx later)
1036      Note: after updating your code, need to run "make clean" in eesupp/src
1037  o test experiment bottom_ctrl_5x5:  o test experiment bottom_ctrl_5x5:
1038     new output_adm.txt with fewer grdchk & less monitor output.     new output_adm.txt with fewer grdchk & less monitor output.
1039  o model/src:  o model/src:
1040    remove the call to ini_cori in initialise_varia.F (just keep the usual one    remove the call to ini_cori in initialise_varia.F (just keep the usual one
1041     in initialise_fixed.F). More consistent with coriolis & horizontal grid     in initialise_fixed.F). More consistent with coriolis & horizontal grid
1042     beeing treated in the same way (ini_grid is not called a 2nd time).     beeing treated in the same way (ini_grid is not called a 2nd time).
1043  o pkg/exf:  o pkg/exf:
1044    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1045    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1046    - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)    - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
# Line 175  o tools/build_options: Line 1205  o tools/build_options:
1205      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1206  o pkg/ecco  o pkg/ecco
1207    - allow user defined cost function contributions    - allow user defined cost function contributions
1208          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1209          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1210    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1211        the two options are complementary.        the two options are complementary.
1212  o pkg/smooth  o pkg/smooth
Legend:
Removed from v.1.1273  
changed lines
  Added in v.1.1473
  ViewVC Help
Powered by ViewVC 1.1.22