/[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 1.1458 by heimbach, Sun Jun 19 18:21:32 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o adjoint monitor:
8     - Add adjoint monitor output for packages exf, seaice
9       and update relevant testreport output
10    o pkg/seaice:
11     - re-order diags inits so that they appear in order in available_diagnostics.log
12     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
13       area/heff/hsnow preceeding thermodynamic growth/melt.
14     - modified diag: SIdA; output actual effect, as the description states.
15     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
16     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
17       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
18        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
19     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
20     - added diagnostics for seaice genereic tracers (SItr*).
21     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
22     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
23     I. Fenty: 18-Jun-2011:
24     Minor changes to seaice package:
25     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
26        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
27       - Differentiated "regularization variables" from "floor variables"
28        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
29        * hiceMin became SEAICE_hice_reg (old hiceMin)
30          (with _reg meaning regularization variable)
31       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
32        so as to ensure energy conservation when going between phases
33      - A22 was not used anywhere
34     2) Changed regularization procedure for heffActual and hsnowActual to ensure
35        well-boundedness and smooth adjoint in seaice_growth.F
36     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
37        because the old regularization always set heffActual >= 0.05 cm
38     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
39        on AREA when HEFF > 0.  
40      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
41        requiring that DISABLE_AREA_FLOOR *not* be defined    
42     Affected verifications:
43      - 1D_ocean_ice_column (output.txt output_adm.txt)
44      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
45    o pkg/diagnostics:
46      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
47      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
48        (was _RL, now integer) with option = 0 to retrieve all levels.
49      - add pieces of code to compute velocity potential at each level (new diagnostics
50        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
51        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
52    o model/src (rStar):
53      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
54        affect solution only if z* with full pressure in EOS;
55        update output of test-exp global_ocean.90x40x15.
56    o pkg/seaice:
57      - introduce siEps=1e-5 parameter
58      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
59      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
60      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
61        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
62        as well as ice cover age and ridging index (attached to AREA).
63        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
64        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
65        Up to SItrMaxNum=3 tracers can be used simultaneously.
66    o pkg/salt_plume:
67      -introduce SPsalFRAC run time parameter that sets the fraction of the
68       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
69       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
70    o model debug options:
71      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
72        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
73      - Refine debug-msg printing selection (3 new levels):
74        debugMode  : controls printing of debug messages (sequence of S/R calls).
75        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
76         debLevZero =  0 ; /* level of disabled aux. msg printing */
77         debLevA =  1 ; /* level of minimum  aux. msg printing */
78         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
79         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
80         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
81         debLevE =  5 ; /* level of extensive debug printing */
82        New debugLevel default: with default debugMode value (=F),
83          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
84          and if debugMode=T, default debugLevel = 4 (debLevD).
85        Relation with previous settings:
86         debLevB (=2) corresponds to former debLevA (=1)
87         debLevD (=4) corresponds to former debLevB (=2)
88        Note:
89         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
90         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
91            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
92      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
93        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
94    o pkg/obcs:
95      - change OBCSfixTopo default from True to False (should not change the results);
96        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
97    o pkg/thsice:
98      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
99        2nd layer seaice sublimation (unlikely to happen)
100      - use Interior mask for OBCS in thsice_advection.F (similar to what is
101        done in gad_advection & seaice_advection).
102    o adjoint:
103      bug fix spotted by Gael Forget:
104      seaice_advection and thsice_advection still had
105      legacy CPP options to avoid CS corner updates for adjoint
106    o pkg/seaice:
107      => Change some of the defaults (2011/05/29):
108         - change SEAICEuseFluxForm default (from False to True)
109         - change DIFF1 default (from 0.004 m/s to 0. m/s)
110         And print warnings if DIFF1 is not set in data.seaice and centered
111          avection scheme is used without any diffusion.
112      also:
113      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
114      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
115      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
116        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
117        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
118      update results of test exp.:
119         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
120             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
121             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
122         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
123         seaice_obcs: output (SEAICEuseFluxForm=T)
124      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
125          for standard fwd & AD lab_sea tests (to keep the same output).
126    o pkg/seaice/seaice_growth.F:
127      - use Ian Fenty's capping formulas for actual ice
128      thickness thoughout EVOLUTION branch.
129      - put treatment pathological case #2) in CPP brackets
130      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
131      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
132    o pkg/seaice:
133      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
134      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
135      also pass fac as a param, which can be 1. (to update the tendency
136      field) or the time step (to update the field itself).
137      - seaice_advdiff.F: for multidim, call seaice_diffusion with
138      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
139      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
140      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
141      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
142    o pkg/seaice:
143      diffusion with centered advection scheme (diffus.F & advect.F):
144      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
145        to just compute the laplacian of input-field.
146      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
147      - fix flux-form version in diffus.F to conserve tracer.
148      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
149       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
150    
151    checkpoint62y (2011/05/26)
152    o pkg/seaice:
153     - seaice_growth.F : in EVOLUTION branch, always include
154       a_QSWbyATM_cover in qnet (as it should be).
155     - verification/global_ocean.cs32x15 : update results accordingly
156       (output.seaice.txt output_adm.seaice.txt).
157    o pkg/seaice + obcs:
158     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
159       equivalent of assuming no tracer gradient outside the OB region.
160       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
161     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
162       after changes above);
163     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
164       only at OB location (instead of over a band of OLx width).
165    o pkg/seaice:
166     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
167       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
168    o pkg/obcs:
169      - split header file "OBCS.h" into 4 separated files:
170        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
171       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
172         (contain no conditional statement which depends on OBCS options).
173      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
174        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
175    o ctrl, cost, grdchk & autodiff pkgs:
176      - make options file more standard (like other {PKG}_OPTIONS.h file but
177        with AD_CONFIG.h); clean-up some of the included header files.
178    o pkg/obcs:
179      - do not mask tracer when applying OB (tracer == 0 could generate problems)
180      - apply tracer OB values to tracer field only at OB location (instead of
181        over a band of OLx width)
182      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
183      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
184        obcs_apply_tloc.F & obcs_apply_sloc.F
185    o obcs in model/src:
186      - call OBCS_APPLY_W only if NonHydrostatic.
187      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
188      - reset dEtaHdt and wVel to zero outside OB interior region ;
189      - leave tracer unchanged outside OB interior region: This has no effect
190        on the solution but just to prevent unrealistic tracer value outside OB.
191      - zero out velocity outside OB interior region: This has no effect on
192        the solution but just to prevent unrealistic velocity outside OB.
193    o obcs and non-lin free-surf:
194       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
195       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
196       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
197       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
198       update results of test-exp. exp4(nlfs).
199    o exp4 (nlfs) test-exp:
200       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
201       with NonLin-FreeSurf); update output.nlfs.txt
202    o obcs and 2d/3d solver norm:
203       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
204       and outside OB interior region (will allow to place OB further inside the
205       domain). Depending on the domain, can affects cg2d-Norm (previous
206       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
207       and cg3d-Norm (previous Norm was computed before canceling OB terms),
208       e.g. in tutorial_plume_on_slope.
209      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
210    o pkg rbcs:
211      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
212      - add capability to apply relaxation to horizontal velocity uVel & vVel.
213    o pkg/grdchk: add gradient check for control variable xx_shifwflx
214    o pkg/shelfice/shelfice_init_fixed.F
215      fix CPP-flag combinations
216    o pkg/seaice: Merge iceage code of Pierre Rampal
217      * update/change/correct ice age calculations
218      * add age updates for pathological cases
219      Probably needs more testing...
220    
221    checkpoint62x (2011/05/13)
222    o pkg/mom_vecinv:
223       high-order vorticity scheme: use interior masks (maskInW & S)
224       to zero-out (outside OB) gradient of vorticity.
225    o verification exp.:
226       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
227       hs94.128x64x5 and seaice_obcs ; update results.
228    o pkg/obcs:
229      fix bug in OBeta for YZ sections in obcs_exf_load.F
230    o pkg/ctrl, pkg/shelfice, and optim:
231      - add new control variable xx_shifwflx (fresh water flux underneath ice
232        shelves). This is almost as tedious as obcs-ctrl, because the
233        variables needs its own mask.
234      - add a cost function term that penalizes the deviation of xx_shifwflx
235        from the first guess (zero) in analogy to other control variables
236    o pkg/shelfice:
237      - start basic adjoint
238    o pkg/ctrl:
239      - remove extra 2D field "for good measure" when initializing in
240        ctrl_set_globfld_[xy/xz/yz].F
241      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
242      - improve error messages in ctrl_set_unpack_*
243    o OBC implementation in momentum:
244       use interior masks (maskInC,W & S) in momentum S/R:
245       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
246       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
247       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
248       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
249       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
250        (and also with Leith/Smagorinsky harmonic-viscosity).
251       Update output of experiment dome and exp4 (+nlfs).
252    o exp4 test-exp:
253      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
254        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
255        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
256        time-varying OB at Western-side for wVel (NonHyd); update output.
257      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
258        and biharmonic-viscosity ; also use prescribed time varying OB.
259    o pkg/obcs:
260      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
261    o model/src:
262      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
263      - initialise startTime & nIter0 with unlikely values: allows to set one
264        from the other without ambiguity.
265    o seaice_obcs test-exp.:
266      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
267    o pkg/obcs:
268      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
269        no longer needed with maskInC,W,S in pkg/generic_advdiff.
270    o pkg/seaice:
271      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
272        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
273      - fixed bug in the initialization of sea ice salinity variable HSALT
274        in seaice_init_varia.F  (removed dependence on ICE2WATR)
275    o fizhi-cs test exp.:
276       switch reference output convention for these 2 non-standard test-exp,
277        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
278          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
279       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
280    o model/inc:
281      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
282        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
283    o pkg/seaice:
284      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
285    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
286      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
287        and initial HSALT
288    
289    checkpoint62w (2011/04/26)
290    o pkg/mom_fluxform:
291      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
292      - use parameter "sideDragFactor" in no-slip BC side-drag part.
293      - update output of exp. global_ocean.90x40x15
294    o pkg/mom_vecinv:
295      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
296    o update seaice exp.:
297      use more consistent parameter values (remove "backward compatability only":
298       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
299      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
300       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
301    o update test-exp global_ocean.90x40x15:
302      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
303      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
304      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
305      o turn on zStar & viscA4 in standard set-up (dir input/)
306        and update output files: output.txt & output.dwnslp.txt
307    o new AD-test experiment: obcs_ctrl
308      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
309    o pkg/dic:
310      fix two bugs in handling water vapour pressure in carbonate chemistry
311      and air-sea fluxes. Found by Val Bennington and Galen McKinley
312      (add DIC Option = WATERVAP_BUG to recover old results)
313      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
314    o adding allowInteriorFreezing option to check for water below freezing point
315      at depth and bring the negative heat anomaly to the surface level
316    o pkgs _fields_load:
317      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
318      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
319        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
320        rbcs to get interpolation weights and time reccord number.
321      - fix multi-threading in aim_fields_load.F
322      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
323    o external_fields_load:
324      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
325       interpolation weights) to use in a periodic time-series ; do not divide by
326       time-step to convert to integer:
327       - this fixes case where externForcingPeriod is not multiple of time-step
328          (Thanks to Christopher L. Wolfe)
329       - this fixes case where externForcingPeriod is an odd multiple of time-step
330         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
331      store index of time-record which is currently loaded:
332       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
333       - needed for the adjoint but not yet used because of extensive recomputations;
334         (to be fixed soon)
335    
336    checkpoint62v (2011/04/02)
337    o verification/1D_ocean_ice_column added to test Ian Fenty's
338      pkg/seaice_growth.F modifications for improving sea ice code differentiability
339    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
340      (new velocity statistics after changing maskInW & maskInS definition)
341    o pkg/generic_advdiff with OBCS:
342      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
343      equivalent to assumption of no tracer gradient outside the OB region.
344      This will affect the results if using obcs+biharmonic diffusion.
345      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
346    o pkg/obcs:
347      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
348      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
349      in Interior region. No impact on solution but affects Velocity monitor stats.
350    o pkg/ptracers (adjoint)
351      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
352      tape file for each tracer
353    o model/inc/src and pkg/autodiff: add parameters that allow to turn
354      of parts of the adjoint code at run time. For now, there are only
355      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
356      parameters are set in data.pkg.
357      This is the lazy coward's version of doing this, but still useful for
358      debugging. In order to do it right, everything needs to be moved to
359      pkg/autodiff.
360    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
361      the end; this fixes the adjoint balancing code for open boundaries.
362    o pkg/ctrl:
363      - change behavior of xx_${varname}period to be analogous to exf-conventions:
364        xx_${varname}period =   0.,  means time-independent control part
365        xx_${varname}period = -12., means one-year-periodic monthly control part
366      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
367        clean up ctrl_init a little, remove unused variables
368      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
369      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
370    
371    checkpoint62u (2011/03/15)
372    o model/src:
373      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
374        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
375      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
376        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
377    o pkg/ctrl/obcs/ecco:
378      - remove obsolete, unused, and partially broken code:
379        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
380        ALLOW_CTRL_OBCS_BALANCE
381      - put a stop statement into ecco/cost_obcsvol.F, but also add
382        cost_obcsvol to ecco_ad_diff.list
383    o pkg/ecco: fix counting cost function contributions for obcs (code
384      by Matt M.) and diffkr for diagnostics
385    o pkg/ecco, pkg/ctrl, pkg/grdchk:
386      add cost penalty terms for initial uvel, vvel, eta controls
387      and I/O for prior error files
388    o pkg/mdsio:
389       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
390       (new argument) to check for tiled file in mdsioLocalDir : this fix the
391       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
392    o pkg/ctrl:
393     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
394       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
395       unused and superfluous variables
396     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
397    o pkg/ecco
398     - enable adjoint of Stevens OB
399    o pkg/ctrl/ecco/grdchk:
400      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
401        Fortunately, we do not have any tests for the numerous cpp-flagged
402        option of "obcs as control parameters" so we will never know
403        if this is an improvement (but at least now things compile).
404      - remove an obsolete initialization from ecco_cost_init_barfiles.F
405      - fix some problems within never used ifdefs to make the code compile
406    o pkg/obcs:
407     - Refine Interior mask definition to work with more complex OB (e.g.
408       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
409       read in Interior mask from file. Check if Interior mask is consistent
410       with OB list of indices.
411    o pkg/seaice
412     - beginning code for a seaice tracer package,
413       but currently only used for seaice age: SEAICE_AGE
414       SEAICE_num = 4
415       iTracer = 1: area-weighted ice age
416               = 2: volume-weighted ice age
417               = 3, 4: template for one-year vs. multi-year ice
418       data.seaice has new namelist SEAICE_PARM03 for arrays related to
419       SEAICE_num
420    
421    checkpoint62t (2011/03/05)
422    o pkg/obcs:
423     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
424       then normal component. This ensures that the normal component is set
425       correctly even when it conficts with tangential setting from an other OB.
426       Affects results of test-experiment seaice_obcs: update the output.txt
427    o pkg/obcs:
428     - add code to monitor statistics of dynamical fields at OB.
429     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
430       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
431       - change default: balance the Net inflow through all OB (instead of balancing
432         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
433     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
434       to match Nortern OB inflow (OBCS_balanceFacN=0).
435    o pkg/seaice:
436     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
437    o pkg/seaice (seaice_growth v 1.113):
438     - reverting seaice_growth to v 1.111 in order to have code with exact bit
439       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
440       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
441       runtime flag SEAICEareaFormula is kept but is inactive
442    o model/src:
443     - add new param to scale curvilinear grid distance and area when using
444       a different sphere radius from the grid-files.
445     - test/check multi-threads EXCH applied to local variable (cg2d_x)
446    o adjoint:
447     - enable adjoint of Stevens OB
448     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
449       (a bit delicate because of potentially modified adj. common block structure;
450       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
451    
452    checkpoint62s (2011/02/15)
453    o pkg/seaice (seaice_growth v 1.112):
454     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
455       computing the ice cover tendency from effective thickness tendencies. Include
456       Ian Fenty's formula.
457     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
458       SEAICEareaFormula.
459     - simplify notations for the various d_HEFF/d_AREA terms.
460    o pkg/gmredi:
461     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
462       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
463       add a verification test-run (front_relax.bvp) to test GM_useBVP.
464    o pkg/seaice (seaice_growth v 1.111):
465     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
466     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
467       also melt ice.
468    o pkg/seaice:
469     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
470     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
471    o pkg/cheapaml:
472     - from Nico Wienders: New version of this package.
473    o pkg/flt:
474     - add CPP options to prevent floats to re-enter the opposite side of
475       a periodic domain (default: keep periodicity)
476    o pkg/gmredi:
477     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
478       (needed for multi-dim advection).
479     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
480    o model/src:
481     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
482    o tutorial_tracer_adjsens
483     - extend to NLFS and replace maskC by hFacC
484       (change reference output accordingly)
485    
486    checkpoint62r (2011/01/24)
487    o testreport:
488     - add option -deloutp (-do) to remove output file after successful run
489     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
490       extract exact list of procs from this file ; adjust COMMAND by
491       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
492    o pkg/ecco: replace old ineffective way of penalizing deviations from
493      first guess (of obcs) with code by Matt Mazloff
494    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
495      exf/cal
496      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
497        and handle case of obcs?period == 0
498        Not affected by these changes: There is still an inconsistency in
499        the computation of start/endrec for the obcs variables for ALLOW_CAL
500        defined (see comment by Menemenlis, 7-Mar-2003)
501      - make S/R ctrl_get_gen_rec return something meaningful even if
502        ALLOW_CAL is not defined
503      - ctrl_getobcs?: simplify code so that it does not need to use
504                       S/R exf_swapfields
505    o testreport:
506       allow to test MPI with different number of processors for each experiment:
507       create file "SIZE.h.mpi" in each build dir.
508       Note: update of "-command" argument not yet implemented.
509    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
510      alleviate the need for additional 3D tapes when using
511      the non-inear free surface in the adjoint. This is done
512      by adding an 'update' of hfacc etc. to their current
513      value at the beginning of forward_step.F.
514    o pkg/seaice
515      seaice_lsr: move stress-divergence computations out of outer pseudo-
516      timestepping loop
517    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
518      up, so that the calls of the ctrl_* subroutines are really at the end
519      of the routine.
520    o pkg/gmredi:
521      allow to specify a 2-D horizontal map and a 1-D vertical profil
522      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
523    o pkg/seaice:
524      move lsr iterations from seaice_dynsolver to seaice_lsr.
525    o pkg/seaice:
526      reduce memory footprint of seaice mutldim advection tapes,
527      by using a 2D tape independent of the generic_advdiff ones,
528      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
529    
530    checkpoint62q (2010/12/29)
531    o model/src:
532      - check horizontal grid-spacing for unset or zero/negative values.
533      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
534    o pkg/flt:
535      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
536      - precision of input and output files set according to readBinaryPrec
537        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
538      - initial float position from tiled file was not converted to index space
539        (looks like a bug): fixed to make it similar to initial pos. global file.
540    o global_ocean.cs32x15:
541       change SIZE.h of AD set-up to get same tiling as with MPI.
542       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
543    o model/src:
544       add flag to control printing of domain fields (bathymetry, hFac ...) in
545       ini_mask_etc (call to plot_fieds_xy*).
546    o pkg/thsice:
547       if useEXF, some forcing fields are not valid in overlap: fixed by computing
548       over the interior only + apply EXCH at the end (like with SEAICE advection).
549    o pkg/mdsio:
550      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
551        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
552      - change barrier call for safe multi-threads access to 3-D shared buffer.
553      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
554      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
555        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
556    o pkg/flt:
557      - add fourth-order Runge-Kutta integration
558      - add basic exch2 support (only 1 facet supported so far!)
559    o pkg/mdsio+rw:
560      new S/R to read local (or tile independent) vector (read counterpart of
561       mds_writevec_loc, and front-end write_glvec_rl/rs).
562    o global_ocean.cs32x15: additional input_ad.seaice experiment
563        that uses pkg/seaice rather than pkg/thsice.
564        (using multidim advection for seaice)
565    o towards more F95 syntax for array specification in namelist:
566      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
567        of all verification experiments.
568           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
569          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
570      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
571    o global_ocean.cs32x15: additional input.seaice experiment
572        that uses pkg/seaice rather than pkg/thsice.
573    
574    checkpoint62p (2010/12/17)
575    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
576        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
577    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
578        allow for use of multim. advection in seaice adjoint.
579    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
580      - first attempt to close budgets by taking into account the freshwater
581        flux implied by the sublimation of snow and ice. So far only the
582        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
583        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
584    o eesupp/src:
585      new S/R with new option (NML_EXTENDED_F77) to change array specification
586      from F95 standard to commonly accepted extended F77 form.
587      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
588      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
589      for less tolerant f77 compiler (e.g., pgf77, g77).
590    o globalFiles:
591      commented out in parameter file "data" since it's not safe with MPI
592      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
593      in this case); no longer commented out in restart test (tst_2+2).
594    o add adTapeDir to specify a special directory where adjoint tapes are
595      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
596      and cannot be used together with mdsioLocalDir.
597    o nesting pkgs:
598      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
599      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
600      - add parameter files + utils dir + output from short run on beagle.
601    o pkg/seaice:
602        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
603    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
604      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
605    
606    checkpoint62o (2010/11/25)
607    o pkg/exf:
608      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
609    o pkg/seaice:
610      - seaice_ocean_stress: split a loop for better vectorization of the
611        adjoint code
612      - seaice_growth.F: fix bug in conservation of freshwater connected to
613        capping of heff, put contribution into d_HEFFbyNEG
614      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
615        by something more sensible (parameters that are what their name implies)
616      - change some defaults, so that by default exf-parameters are used for
617        things like rhoAir, cpAir,latent/sensible heat parameters, in order
618        to reproduce the old results, many data.seaice now contain funny values
619        for cpAir and latent heat of sublimation
620    o packages_readparms.F: move exf_readparms up in line so that
621        exf-parameters are visible for other packages (e.g. seaice)
622    o debugMode & debugLevel=2:
623      - differentiate between debugMode & debugLevel=2:
624        debugMode: controls printing of debug messages (sequence of S/R calls).
625        debugLevel: controls printing of algorithm intermediate results and stats.
626      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
627        => allows to print debug-stats without all sequence of call messages.
628      - switch control of debug print from debugLevel to debugMode in many S/R.
629    o pkg/obcs (obcs-sponge):
630        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
631        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
632    o pkg/generic_advdiff:
633      - record overlap minimum size for each advection scheme;
634      - refine criteria on overlap minimum size;
635      - check and stop (in gad_check) if overlap size is too small.
636    o pkg/obcs:
637      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
638        once, in ptracers_implicit.F)
639      - with seaice: remove test on empty file name in obcs_apply_seaice (always
640        apply OB values when tile has OB)
641    o model/src, coriolis setting:
642      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
643        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
644        files (selectCoriMap=3) with any grid.
645      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
646    o pkg/seaice/seaice_growth.F:
647        a few cosmetic changes that reduce the number of lines of code
648    o pkg/obcs: add boundary conditions following Stevens (1990)
649      - the code follows old MOM/NAOSIM code
650      - so far it is only implemented for the eastern and western boundaries
651        and NOT for pTracers
652    o pkg/rbcs:
653      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
654        beginning of the first rbcs forcing period.
655      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
656        offline package, i.e., one file per time, labeled by iteration number;
657        deltaTrbcs sets the timestep with which the data was generated;
658        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
659      - rbcsForcingCycle=0 makes forcing non-cyclic.
660      - make arithmetic safe for negative times and odd forcing periods.
661    
662    checkpoint62n (2010/11/09)
663    o pkg/seaice:
664        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
665    o pkg/obcs:
666       New S/R to copy tracer value from the OB location to narrow band region
667        (width = same as overlap) beyond the OB: preserve OB value (needed for
668        high-order scheme) which were overwritten by EXCH call if in overlap
669        region. Applied to theta, salt, ptracer and advected seaice variables.
670       With seaice: use maskInC in similar way as in gad_advection.F,
671        in seaice_advection.F and advect.F.
672       Update output of experiment seaice_obcs and change exp4 to test OBCS with
673        4th order Adv.Scheme. for pasive salt and ptracer.
674    o tools/genmake2:
675      - when looking for an optfile (not specified), only search for Fortran compiler
676        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
677      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
678        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
679      - set default for CPP to "cpp -traditional -P" (was the case without specifying
680        an optfile, but otherwise default was just "cpp".
681      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
682      - when "CC" is not set in the optfile, look for possible C compiler
683        (instead of just setting CC=cc)
684      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
685        => add a ".F" to ".o" rule for source files with no "#include" (such as
686           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
687      - move gfortran before g77 in list of possible Fortran compiler (consistent
688        with reference compiler switch from g77 to gfortran)
689    o pkg/seaice:
690      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
691        seaice_check that stops the model, when the CPP flag is used.
692      o seaice_growth.F: make capping of ice volume conserving by returning the
693        capped ice as freshwater to EmPmR. This does not change the verification
694        experiments but will change runs where the capping is acutally active
695    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
696      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
697         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
698         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
699    o tools/genmake2:
700      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
701      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
702      - clean previous genmake log files before anything else.
703      - change Makefile to remove testreport log files (*.tr_log) and genmake log
704        files only with "CLEAN" target (instead of "Clean");
705    o pkg/generic_advdiff:
706      Change OBCS in multiDim advection (gad_advection.F):
707       Use maskInC to prevent intermediate update of tracer-field in OB regions,
708       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
709       which were applying future time-step OB values.
710      This way, all explicit calculations use current-time-step OB values
711       (simpler and more consistent).
712      Affects results when set-up uses time-varying OBC and multi-dim advection;
713       update output of experiment seaice_obcs.
714    o pkg/seaice:
715      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
716       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
717         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
718      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
719       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
720       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
721    o pkg aim (2010/10/26):
722      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
723        formulation with obliquity, eccentricity, ... as run-time parameters,
724      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
725        upward shortwave radition at the surface (all-sky and clear-sky).
726    o pkg/obcs:
727      - writing sections with globalFiles=T does not work: switch to tiled-files
728        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
729      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
730      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
731    
732    checkpoint62m (2010/10/21)
733    o pkg/seaice: vectorize seaice_solve4temp.F
734      - move iterations loops outside of i/j-loops
735      - requires 2D arrays for TB and effConduct
736      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
737        modified in this routine
738      - a little bit of clean up, adjusting indentation, etc.
739      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
740        performance and '**TWO' by '**2' (because TWO is a float),
741        replaced ONE, ZERO
742    o eesupp/src:
743       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
744    o pkg/seaice/seaice_growth.F
745      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
746      merging process. The merged routine has two branches, and one activates the 'evolution'
747      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
748      In summary, here is what the '10/10 revision' did consist of
749        part 1: seaice_growth.F revisions 1.71 to 1.75
750          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
751            The emphasis here was on improving readability (e.g. by trying to use meaningful
752            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
753        part 1.5:
754          - revising the lab_sea experiment to make it a more useful (i.e. stable
755            and representative of an actual model run). This was done by generating a
756            (winter) pickup to start from, switching back the main experiment dynamic
757            solver from evp to lsr, having one of the experiments use the free drift solution.
758        part 2: seaice_growth.F revisions 1.76 to 1.85
759          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
760          - Sorting out the various fields units and sign (set early on and reset at the end)
761            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
762            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
763          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
764            and simplifying logical expressions to further improve readibility.
765        part 3: seaice_growth.F revisions 1.86 to 1.89
766          - Re-organize the blocks of code more logically.
767          - Merging the '_if.F' pieces that add something new.
768    o pkg/thsice:
769      - vectorize thsice_solve4temp and thsice_get_exf.
770        Problem: thsice_solve4temp has an unvectorizable statement that
771        might also be problematic for TAF
772      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
773        does not change the verifcation experiment, but will change all
774        experiments that have this flag undefined (not tested in verification);
775        a little reorganization to save a few 2D fields and recomputations
776      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
777      - 2nd step:  fix some store dirs
778        o seems to work somewhat, i.e. using ifort but not g77
779        o likely cause are incomplete init. or recomputation
780        o start verification/global_ocean.cs32x15/input_ad.thsice
781    o pkg/obcs: add support for exch2
782      - the position of the boundary and prescribed values are specified using
783        a global domain with exch2 facets stacked
784        - in x for N,S boundaries (like W2_mapIO=-1)
785        - in y for E,W boundaries (so E,W boundaries do not overlap)
786    o pkg/mdsio: add support for writing global sections with exch2
787        file layout is as for obcs described above:
788        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
789        - for y-z sections, facets are stacked in y
790    o pkg/thsice:
791       - change a few routines for better vectorization: thsice_albedo.F,
792         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
793         not affected, but in particular the latter routine has changed
794         dramatically (not necessarily easier to read now).
795       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
796       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
797    o verification/lab_sea:
798      - overhaul of the forward model experiments. The main motivation
799        for this revision is that lab_sea has proven quite fragile (when
800        changing the sea-ice code, and switching platforms) to a point
801        when failures were very hard to attribute to specific code problems.
802      - the suspected reason for this fragility is noise amplification by evp so,
803        to start with, we decided to replace evp with lsr in the main experiment.
804      - the input.lsr experiment thus became obsolete and was removed.
805      - it was replaced with the input.fd experiment that uses an
806        analytical "free drift" solution as the ice velocity field.
807      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
808        will hopefully allow us to discriminate problems due to dynamic solvers
809        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
810        us to test additional options, along with the salt plume package.
811      - Finally a pickup was generated (at the end of a one year run) to
812        make the tests more representative of an actual model run. Previously
813        the tests starting point was a 1m thickness of ice everywhere.
814    o pkg/seaice:
815      - introducing S\R seaice_freedrift.F that compute the
816        analytical solution to an approximate ice momentum
817        equation (i.e. the simple stress/coriolis balance).
818      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
819        of the free drift velocity field, and enable its use.
820        To actually use the free drift solution as the model ice
821        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
822    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
823    
824    checkpoint62l (2010/10/04)
825    o pkg/seaice:
826      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
827      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
828       version (with USE_ORIGINAL_SBI undef);
829    o add hooks for new packages OASIS, the package will follow
830      (hooks exclude the seaice pkg for now)
831    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
832      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
833      rather than mdsio_readvector.F/mdsio_writevector.F, within
834      adread_adwrite.F to read/write adjoint-related tapes to disk.
835    o eesupp and pkg/mdsio: ALLOW_WHIO
836      Option to write/read 2D fields to files including tiles halos.
837      The main purpose is for adjoint related "tape I/O".
838      The secondary purpose is for debugging phases.
839      A word on those rather specifically intended purposes.
840      The code was meant to be stripped down to the bare minimum.
841      Typically, there is a unique and basic mapping to the global
842      buffer (tile by tile, then proc by proc, then level by level), and
843      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
844      meant to generate user friendly outputs of various shapes and forms.
845      Rather it is intended, for the knowledgeabale developers,
846      to be largely independent of the many mdsio options, to allow
847      outputs of tiles+halos in debugging phases and in adjoint runs,
848      and to allow some flexibility in tuning (adoint) I/O depending on each
849      file system behavior. With regard to tuning, most of the potential knobs
850      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
851      to specify directories, to specify the typical size of I/O calls, etc.)
852      are not yet included, and will be added if they prove useful.
853    o pkg/seaice:
854       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
855    o pkg/seaice:
856       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
857       code (seaice_budget_ice_if.F) which enable to recover old standard
858       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
859       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
860    o model/src (rStar):
861       use simple average (not area weighted) of rStarFac at U,V point when using
862       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
863       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
864    
865    checkpoint62k (2010/09/17)
866    o adjoint
867       * changed verification/global_ocean.cs32x15 ; adjoint now tests
868         Adams-Bashforth 3 + NLFS + RSTAR
869       * some more modifs required for ECCO-GODAE v4
870    o pkg/seaice
871       add SEAICE_AGE_VOL option to use volume instead of area for
872       integrating SEAICE_AGE
873    o model/src:
874       first check-in of sigma & hybrid-sigma coordinate code ; also includes
875       non-linear free-surface parts ; but pressure-gradient not yet coded.
876    o pkg/ptracers:
877       option for ptracer to convert Salt Relax into additional EmP.
878        tested in exp. global_ocean.90x40x15.dwnslp (update output)
879    
880    checkpoint62j (2010/08/25)
881    o pkg/ggl90:
882       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
883    o pkg/dic: car_flux.F, phos_flux.F
884      - reduce number of exp-calls in order to improve performance
885      - clean up a little (replace fields by their macros, etc., fix
886        typo in CPP-flag)
887    o pkg/ggl90: minor changes
888      - GGL90diffKrS was removed --> always use GGL90diffKr
889      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
890      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
891        (commented out for now)
892      - change in max/min operations to ensure that smoothing is ok
893      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
894      - always use diffKrNrT as background profile (i.e. never use diffKr field)
895    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
896    o pkg/dic:
897      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
898        vectorization
899      - small bug fix in insol for the unlikely case of a cartesian grid
900      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
901        + now vectorize, which also removes adjoint recomputations;
902        + replace integer maksp1 by _RL maskp1
903        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
904    
905    checkpoint62i (2010/07/21)
906    o pkg/flt:
907      - with OBCS: stop floats which enter the OB region
908    o model/src:
909      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
910        for implicit vertical advection.
911    o pkg/seaice:
912     - account for melting in seaice age evolution.
913     - remove double counting of seaice ridging effect on seaice age.
914    
915    checkpoint62h (2010/06/18)
916    o pkg/exch2:
917     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
918    o tools/genmake2
919      - remove "-pdefault" option: redundant with the use of "packages.conf";
920      - remove file pkg/pkg_default : set the default as a pkg group
921        ("default_pkg_list") defined in pkg/pkg_groups;
922      - fix for case pkg/pkg_depend is missing (was hanging before);
923      - add option "-pgroups" to specify a different pkg_groups than the default.
924    o verification/adjustment.cs-32x32x1:
925       add a "minimal" set-up test (code_min & input_min) which only compiles
926       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
927    o tools/genmake2
928      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
929      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
930    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
931      files are nearly the same anyway.
932      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
933       - redefinition of tau(i,i) (by a factor of ustar)
934       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
935       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
936       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
937       - replace
938         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
939         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
940         by
941         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
942         (changes results)
943       -> exf_bulkformulae v1.22,
944          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
945          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
946                    output.txt 1.63
947           offline_exf_seaice: output.seaicetd.txt 1.7
948           seaice_obcs: output.txt 1.10)
949      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
950       -> exf_bulkformulae v1.23,
951          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
952          and global_ocean.cs32x15.icedyn (only 11 matching digits)
953      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
954    o adjoint of exch-1:
955     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
956       (note: was already like this when using EXCH-2) and remove flow dir
957       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
958     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
959     - update pkg/exch2 diff list.
960    
961    checkpoint62g (2010/05/19)
962    o eesupp/src (exch-1):
963     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
964       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
965       (renamed to exch1_*rx_cube.F).
966     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
967       to call new exch1 S/R ; update Makefile and .cvsignore.
968     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
969       exch2_xy_rx later)
970      Note: after updating your code, need to run "make clean" in eesupp/src
971  o test experiment bottom_ctrl_5x5:  o test experiment bottom_ctrl_5x5:
972     new output_adm.txt with fewer grdchk & less monitor output.     new output_adm.txt with fewer grdchk & less monitor output.
973  o model/src:  o model/src:
974    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
975     in initialise_fixed.F). More consistent with coriolis & horizontal grid     in initialise_fixed.F). More consistent with coriolis & horizontal grid
976     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).
977  o pkg/exf:  o pkg/exf:
978    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes    - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
979    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated    global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
980    - 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 1139  o tools/build_options:
1139      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1140  o pkg/ecco  o pkg/ecco
1141    - allow user defined cost function contributions    - allow user defined cost function contributions
1142          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1143          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1144    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1145        the two options are complementary.        the two options are complementary.
1146  o pkg/smooth  o pkg/smooth
Legend:
Removed from v.1.1273  
changed lines
  Added in v.1.1458
  ViewVC Help
Powered by ViewVC 1.1.22