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revision 1.1232 by jmc, Thu Feb 18 17:06:02 2010 UTC revision 1.1461 by jmc, Wed Jun 22 02:31:29 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/diagnostics:
8     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
9       which are not filled-up but computed from other diags ; In this case, the mate
10       diag points to the primary (filled-up) diag to used for post processing.
11     - Update Velocity-potential computation using post-processed diag framework.
12    
13    checkpoint62z (2011/06/21)
14    o adjoint monitor:
15     - Add adjoint monitor output for packages exf, seaice
16       and update relevant testreport output
17    o pkg/seaice:
18     - re-order diags inits so that they appear in order in available_diagnostics.log
19     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
20       area/heff/hsnow preceeding thermodynamic growth/melt.
21     - modified diag: SIdA; output actual effect, as the description states.
22     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
23     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
24       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
25        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
26     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
27     - added diagnostics for seaice generic tracers (SItr*).
28     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
29     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
30     I. Fenty: 18-Jun-2011:
31     Minor changes to seaice package:
32     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
33        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
34       - Differentiated "regularization variables" from "floor variables"
35        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
36        * hiceMin became SEAICE_hice_reg (old hiceMin)
37          (with _reg meaning regularization variable)
38       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
39        so as to ensure energy conservation when going between phases
40      - A22 was not used anywhere
41     2) Changed regularization procedure for heffActual and hsnowActual to ensure
42        well-boundedness and smooth adjoint in seaice_growth.F
43     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
44        because the old regularization always set heffActual >= 0.05 cm
45     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
46        on AREA when HEFF > 0.
47      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
48        requiring that DISABLE_AREA_FLOOR *not* be defined
49     Affected verifications:
50      - 1D_ocean_ice_column (output.txt output_adm.txt)
51      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
52    o pkg/diagnostics:
53      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
54      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
55        (was _RL, now integer) with option = 0 to retrieve all levels.
56      - add pieces of code to compute velocity potential at each level (new diagnostics
57        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
58        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
59      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
60        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
61        and in diagnostics_fract_fill.F (do not need a valid pointer for the
62        diagnostics counter-mate); check that definition of counter-diagnostic
63        includes a valid counter-mate (in diagnostics_set_levels.F).
64    o model/src (rStar):
65      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
66        affect solution only if z* with full pressure in EOS;
67        update output of test-exp global_ocean.90x40x15.
68    o pkg/seaice:
69      - introduce siEps=1e-5 parameter
70      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
71      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
72      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
73        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
74        as well as ice cover age and ridging index (attached to AREA).
75        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
76        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
77        Up to SItrMaxNum=3 tracers can be used simultaneously.
78    o pkg/salt_plume:
79      -introduce SPsalFRAC run time parameter that sets the fraction of the
80       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
81       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
82    o model debug options:
83      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
84        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
85      - Refine debug-msg printing selection (3 new levels):
86        debugMode  : controls printing of debug messages (sequence of S/R calls).
87        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
88         debLevZero =  0 ; /* level of disabled aux. msg printing */
89         debLevA =  1 ; /* level of minimum  aux. msg printing */
90         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
91         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
92         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
93         debLevE =  5 ; /* level of extensive debug printing */
94        New debugLevel default: with default debugMode value (=F),
95          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
96          and if debugMode=T, default debugLevel = 4 (debLevD).
97        Relation with previous settings:
98         debLevB (=2) corresponds to former debLevA (=1)
99         debLevD (=4) corresponds to former debLevB (=2)
100        Note:
101         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
102         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
103            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
104      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
105        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
106    o pkg/obcs:
107      - change OBCSfixTopo default from True to False (should not change the results);
108        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
109    o pkg/thsice:
110      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
111        2nd layer seaice sublimation (unlikely to happen)
112      - use Interior mask for OBCS in thsice_advection.F (similar to what is
113        done in gad_advection & seaice_advection).
114    o adjoint:
115      bug fix spotted by Gael Forget:
116      seaice_advection and thsice_advection still had
117      legacy CPP options to avoid CS corner updates for adjoint
118    o pkg/seaice:
119      => Change some of the defaults (2011/05/29):
120         - change SEAICEuseFluxForm default (from False to True)
121         - change DIFF1 default (from 0.004 m/s to 0. m/s)
122         And print warnings if DIFF1 is not set in data.seaice and centered
123          avection scheme is used without any diffusion.
124      also:
125      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
126      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
127      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
128        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
129        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
130      update results of test exp.:
131         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
132             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
133             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
134         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
135         seaice_obcs: output (SEAICEuseFluxForm=T)
136      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
137          for standard fwd & AD lab_sea tests (to keep the same output).
138    o pkg/seaice/seaice_growth.F:
139      - use Ian Fenty's capping formulas for actual ice
140      thickness thoughout EVOLUTION branch.
141      - put treatment pathological case #2) in CPP brackets
142      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
143      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
144    o pkg/seaice:
145      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
146      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
147      also pass fac as a param, which can be 1. (to update the tendency
148      field) or the time step (to update the field itself).
149      - seaice_advdiff.F: for multidim, call seaice_diffusion with
150      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
151      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
152      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
153      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
154    o pkg/seaice:
155      diffusion with centered advection scheme (diffus.F & advect.F):
156      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
157        to just compute the laplacian of input-field.
158      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
159      - fix flux-form version in diffus.F to conserve tracer.
160      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
161       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
162    
163    checkpoint62y (2011/05/26)
164    o pkg/seaice:
165     - seaice_growth.F : in EVOLUTION branch, always include
166       a_QSWbyATM_cover in qnet (as it should be).
167     - verification/global_ocean.cs32x15 : update results accordingly
168       (output.seaice.txt output_adm.seaice.txt).
169    o pkg/seaice + obcs:
170     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
171       equivalent of assuming no tracer gradient outside the OB region.
172       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
173     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
174       after changes above);
175     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
176       only at OB location (instead of over a band of OLx width).
177    o pkg/seaice:
178     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
179       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
180    o pkg/obcs:
181      - split header file "OBCS.h" into 4 separated files:
182        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
183       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
184         (contain no conditional statement which depends on OBCS options).
185      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
186        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
187    o ctrl, cost, grdchk & autodiff pkgs:
188      - make options file more standard (like other {PKG}_OPTIONS.h file but
189        with AD_CONFIG.h); clean-up some of the included header files.
190    o pkg/obcs:
191      - do not mask tracer when applying OB (tracer == 0 could generate problems)
192      - apply tracer OB values to tracer field only at OB location (instead of
193        over a band of OLx width)
194      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
195      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
196        obcs_apply_tloc.F & obcs_apply_sloc.F
197    o obcs in model/src:
198      - call OBCS_APPLY_W only if NonHydrostatic.
199      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
200      - reset dEtaHdt and wVel to zero outside OB interior region ;
201      - leave tracer unchanged outside OB interior region: This has no effect
202        on the solution but just to prevent unrealistic tracer value outside OB.
203      - zero out velocity outside OB interior region: This has no effect on
204        the solution but just to prevent unrealistic velocity outside OB.
205    o obcs and non-lin free-surf:
206       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
207       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
208       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
209       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
210       update results of test-exp. exp4(nlfs).
211    o exp4 (nlfs) test-exp:
212       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
213       with NonLin-FreeSurf); update output.nlfs.txt
214    o obcs and 2d/3d solver norm:
215       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
216       and outside OB interior region (will allow to place OB further inside the
217       domain). Depending on the domain, can affects cg2d-Norm (previous
218       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
219       and cg3d-Norm (previous Norm was computed before canceling OB terms),
220       e.g. in tutorial_plume_on_slope.
221      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
222    o pkg rbcs:
223      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
224      - add capability to apply relaxation to horizontal velocity uVel & vVel.
225    o pkg/grdchk: add gradient check for control variable xx_shifwflx
226    o pkg/shelfice/shelfice_init_fixed.F
227      fix CPP-flag combinations
228    o pkg/seaice: Merge iceage code of Pierre Rampal
229      * update/change/correct ice age calculations
230      * add age updates for pathological cases
231      Probably needs more testing...
232    
233    checkpoint62x (2011/05/13)
234    o pkg/mom_vecinv:
235       high-order vorticity scheme: use interior masks (maskInW & S)
236       to zero-out (outside OB) gradient of vorticity.
237    o verification exp.:
238       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
239       hs94.128x64x5 and seaice_obcs ; update results.
240    o pkg/obcs:
241      fix bug in OBeta for YZ sections in obcs_exf_load.F
242    o pkg/ctrl, pkg/shelfice, and optim:
243      - add new control variable xx_shifwflx (fresh water flux underneath ice
244        shelves). This is almost as tedious as obcs-ctrl, because the
245        variables needs its own mask.
246      - add a cost function term that penalizes the deviation of xx_shifwflx
247        from the first guess (zero) in analogy to other control variables
248    o pkg/shelfice:
249      - start basic adjoint
250    o pkg/ctrl:
251      - remove extra 2D field "for good measure" when initializing in
252        ctrl_set_globfld_[xy/xz/yz].F
253      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
254      - improve error messages in ctrl_set_unpack_*
255    o OBC implementation in momentum:
256       use interior masks (maskInC,W & S) in momentum S/R:
257       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
258       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
259       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
260       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
261       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
262        (and also with Leith/Smagorinsky harmonic-viscosity).
263       Update output of experiment dome and exp4 (+nlfs).
264    o exp4 test-exp:
265      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
266        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
267        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
268        time-varying OB at Western-side for wVel (NonHyd); update output.
269      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
270        and biharmonic-viscosity ; also use prescribed time varying OB.
271    o pkg/obcs:
272      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
273    o model/src:
274      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
275      - initialise startTime & nIter0 with unlikely values: allows to set one
276        from the other without ambiguity.
277    o seaice_obcs test-exp.:
278      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
279    o pkg/obcs:
280      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
281        no longer needed with maskInC,W,S in pkg/generic_advdiff.
282    o pkg/seaice:
283      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
284        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
285      - fixed bug in the initialization of sea ice salinity variable HSALT
286        in seaice_init_varia.F  (removed dependence on ICE2WATR)
287    o fizhi-cs test exp.:
288       switch reference output convention for these 2 non-standard test-exp,
289        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
290          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
291       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
292    o model/inc:
293      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
294        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
295    o pkg/seaice:
296      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
297    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
298      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
299        and initial HSALT
300    
301    checkpoint62w (2011/04/26)
302    o pkg/mom_fluxform:
303      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
304      - use parameter "sideDragFactor" in no-slip BC side-drag part.
305      - update output of exp. global_ocean.90x40x15
306    o pkg/mom_vecinv:
307      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
308    o update seaice exp.:
309      use more consistent parameter values (remove "backward compatability only":
310       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
311      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
312       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
313    o update test-exp global_ocean.90x40x15:
314      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
315      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
316      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
317      o turn on zStar & viscA4 in standard set-up (dir input/)
318        and update output files: output.txt & output.dwnslp.txt
319    o new AD-test experiment: obcs_ctrl
320      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
321    o pkg/dic:
322      fix two bugs in handling water vapour pressure in carbonate chemistry
323      and air-sea fluxes. Found by Val Bennington and Galen McKinley
324      (add DIC Option = WATERVAP_BUG to recover old results)
325      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
326    o adding allowInteriorFreezing option to check for water below freezing point
327      at depth and bring the negative heat anomaly to the surface level
328    o pkgs _fields_load:
329      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
330      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
331        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
332        rbcs to get interpolation weights and time reccord number.
333      - fix multi-threading in aim_fields_load.F
334      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
335    o external_fields_load:
336      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
337       interpolation weights) to use in a periodic time-series ; do not divide by
338       time-step to convert to integer:
339       - this fixes case where externForcingPeriod is not multiple of time-step
340          (Thanks to Christopher L. Wolfe)
341       - this fixes case where externForcingPeriod is an odd multiple of time-step
342         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
343      store index of time-record which is currently loaded:
344       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
345       - needed for the adjoint but not yet used because of extensive recomputations;
346         (to be fixed soon)
347    
348    checkpoint62v (2011/04/02)
349    o verification/1D_ocean_ice_column added to test Ian Fenty's
350      pkg/seaice_growth.F modifications for improving sea ice code differentiability
351    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
352      (new velocity statistics after changing maskInW & maskInS definition)
353    o pkg/generic_advdiff with OBCS:
354      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
355      equivalent to assumption of no tracer gradient outside the OB region.
356      This will affect the results if using obcs+biharmonic diffusion.
357      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
358    o pkg/obcs:
359      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
360      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
361      in Interior region. No impact on solution but affects Velocity monitor stats.
362    o pkg/ptracers (adjoint)
363      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
364      tape file for each tracer
365    o model/inc/src and pkg/autodiff: add parameters that allow to turn
366      of parts of the adjoint code at run time. For now, there are only
367      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
368      parameters are set in data.pkg.
369      This is the lazy coward's version of doing this, but still useful for
370      debugging. In order to do it right, everything needs to be moved to
371      pkg/autodiff.
372    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
373      the end; this fixes the adjoint balancing code for open boundaries.
374    o pkg/ctrl:
375      - change behavior of xx_${varname}period to be analogous to exf-conventions:
376        xx_${varname}period =   0.,  means time-independent control part
377        xx_${varname}period = -12., means one-year-periodic monthly control part
378      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
379        clean up ctrl_init a little, remove unused variables
380      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
381      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
382    
383    checkpoint62u (2011/03/15)
384    o model/src:
385      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
386        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
387      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
388        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
389    o pkg/ctrl/obcs/ecco:
390      - remove obsolete, unused, and partially broken code:
391        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
392        ALLOW_CTRL_OBCS_BALANCE
393      - put a stop statement into ecco/cost_obcsvol.F, but also add
394        cost_obcsvol to ecco_ad_diff.list
395    o pkg/ecco: fix counting cost function contributions for obcs (code
396      by Matt M.) and diffkr for diagnostics
397    o pkg/ecco, pkg/ctrl, pkg/grdchk:
398      add cost penalty terms for initial uvel, vvel, eta controls
399      and I/O for prior error files
400    o pkg/mdsio:
401       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
402       (new argument) to check for tiled file in mdsioLocalDir : this fix the
403       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
404    o pkg/ctrl:
405     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
406       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
407       unused and superfluous variables
408     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
409    o pkg/ecco
410     - enable adjoint of Stevens OB
411    o pkg/ctrl/ecco/grdchk:
412      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
413        Fortunately, we do not have any tests for the numerous cpp-flagged
414        option of "obcs as control parameters" so we will never know
415        if this is an improvement (but at least now things compile).
416      - remove an obsolete initialization from ecco_cost_init_barfiles.F
417      - fix some problems within never used ifdefs to make the code compile
418    o pkg/obcs:
419     - Refine Interior mask definition to work with more complex OB (e.g.
420       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
421       read in Interior mask from file. Check if Interior mask is consistent
422       with OB list of indices.
423    o pkg/seaice
424     - beginning code for a seaice tracer package,
425       but currently only used for seaice age: SEAICE_AGE
426       SEAICE_num = 4
427       iTracer = 1: area-weighted ice age
428               = 2: volume-weighted ice age
429               = 3, 4: template for one-year vs. multi-year ice
430       data.seaice has new namelist SEAICE_PARM03 for arrays related to
431       SEAICE_num
432    
433    checkpoint62t (2011/03/05)
434    o pkg/obcs:
435     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
436       then normal component. This ensures that the normal component is set
437       correctly even when it conficts with tangential setting from an other OB.
438       Affects results of test-experiment seaice_obcs: update the output.txt
439    o pkg/obcs:
440     - add code to monitor statistics of dynamical fields at OB.
441     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
442       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
443       - change default: balance the Net inflow through all OB (instead of balancing
444         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
445     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
446       to match Nortern OB inflow (OBCS_balanceFacN=0).
447    o pkg/seaice:
448     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
449    o pkg/seaice (seaice_growth v 1.113):
450     - reverting seaice_growth to v 1.111 in order to have code with exact bit
451       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
452       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
453       runtime flag SEAICEareaFormula is kept but is inactive
454    o model/src:
455     - add new param to scale curvilinear grid distance and area when using
456       a different sphere radius from the grid-files.
457     - test/check multi-threads EXCH applied to local variable (cg2d_x)
458    o adjoint:
459     - enable adjoint of Stevens OB
460     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
461       (a bit delicate because of potentially modified adj. common block structure;
462       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
463    
464    checkpoint62s (2011/02/15)
465    o pkg/seaice (seaice_growth v 1.112):
466     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
467       computing the ice cover tendency from effective thickness tendencies. Include
468       Ian Fenty's formula.
469     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
470       SEAICEareaFormula.
471     - simplify notations for the various d_HEFF/d_AREA terms.
472    o pkg/gmredi:
473     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
474       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
475       add a verification test-run (front_relax.bvp) to test GM_useBVP.
476    o pkg/seaice (seaice_growth v 1.111):
477     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
478     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
479       also melt ice.
480    o pkg/seaice:
481     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
482     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
483    o pkg/cheapaml:
484     - from Nico Wienders: New version of this package.
485    o pkg/flt:
486     - add CPP options to prevent floats to re-enter the opposite side of
487       a periodic domain (default: keep periodicity)
488    o pkg/gmredi:
489     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
490       (needed for multi-dim advection).
491     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
492    o model/src:
493     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
494    o tutorial_tracer_adjsens
495     - extend to NLFS and replace maskC by hFacC
496       (change reference output accordingly)
497    
498    checkpoint62r (2011/01/24)
499    o testreport:
500     - add option -deloutp (-do) to remove output file after successful run
501     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
502       extract exact list of procs from this file ; adjust COMMAND by
503       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
504    o pkg/ecco: replace old ineffective way of penalizing deviations from
505      first guess (of obcs) with code by Matt Mazloff
506    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
507      exf/cal
508      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
509        and handle case of obcs?period == 0
510        Not affected by these changes: There is still an inconsistency in
511        the computation of start/endrec for the obcs variables for ALLOW_CAL
512        defined (see comment by Menemenlis, 7-Mar-2003)
513      - make S/R ctrl_get_gen_rec return something meaningful even if
514        ALLOW_CAL is not defined
515      - ctrl_getobcs?: simplify code so that it does not need to use
516                       S/R exf_swapfields
517    o testreport:
518       allow to test MPI with different number of processors for each experiment:
519       create file "SIZE.h.mpi" in each build dir.
520       Note: update of "-command" argument not yet implemented.
521    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
522      alleviate the need for additional 3D tapes when using
523      the non-inear free surface in the adjoint. This is done
524      by adding an 'update' of hfacc etc. to their current
525      value at the beginning of forward_step.F.
526    o pkg/seaice
527      seaice_lsr: move stress-divergence computations out of outer pseudo-
528      timestepping loop
529    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
530      up, so that the calls of the ctrl_* subroutines are really at the end
531      of the routine.
532    o pkg/gmredi:
533      allow to specify a 2-D horizontal map and a 1-D vertical profil
534      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
535    o pkg/seaice:
536      move lsr iterations from seaice_dynsolver to seaice_lsr.
537    o pkg/seaice:
538      reduce memory footprint of seaice mutldim advection tapes,
539      by using a 2D tape independent of the generic_advdiff ones,
540      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
541    
542    checkpoint62q (2010/12/29)
543    o model/src:
544      - check horizontal grid-spacing for unset or zero/negative values.
545      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
546    o pkg/flt:
547      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
548      - precision of input and output files set according to readBinaryPrec
549        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
550      - initial float position from tiled file was not converted to index space
551        (looks like a bug): fixed to make it similar to initial pos. global file.
552    o global_ocean.cs32x15:
553       change SIZE.h of AD set-up to get same tiling as with MPI.
554       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
555    o model/src:
556       add flag to control printing of domain fields (bathymetry, hFac ...) in
557       ini_mask_etc (call to plot_fieds_xy*).
558    o pkg/thsice:
559       if useEXF, some forcing fields are not valid in overlap: fixed by computing
560       over the interior only + apply EXCH at the end (like with SEAICE advection).
561    o pkg/mdsio:
562      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
563        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
564      - change barrier call for safe multi-threads access to 3-D shared buffer.
565      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
566      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
567        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
568    o pkg/flt:
569      - add fourth-order Runge-Kutta integration
570      - add basic exch2 support (only 1 facet supported so far!)
571    o pkg/mdsio+rw:
572      new S/R to read local (or tile independent) vector (read counterpart of
573       mds_writevec_loc, and front-end write_glvec_rl/rs).
574    o global_ocean.cs32x15: additional input_ad.seaice experiment
575        that uses pkg/seaice rather than pkg/thsice.
576        (using multidim advection for seaice)
577    o towards more F95 syntax for array specification in namelist:
578      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
579        of all verification experiments.
580           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
581          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
582      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
583    o global_ocean.cs32x15: additional input.seaice experiment
584        that uses pkg/seaice rather than pkg/thsice.
585    
586    checkpoint62p (2010/12/17)
587    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
588        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
589    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
590        allow for use of multim. advection in seaice adjoint.
591    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
592      - first attempt to close budgets by taking into account the freshwater
593        flux implied by the sublimation of snow and ice. So far only the
594        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
595        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
596    o eesupp/src:
597      new S/R with new option (NML_EXTENDED_F77) to change array specification
598      from F95 standard to commonly accepted extended F77 form.
599      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
600      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
601      for less tolerant f77 compiler (e.g., pgf77, g77).
602    o globalFiles:
603      commented out in parameter file "data" since it's not safe with MPI
604      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
605      in this case); no longer commented out in restart test (tst_2+2).
606    o add adTapeDir to specify a special directory where adjoint tapes are
607      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
608      and cannot be used together with mdsioLocalDir.
609    o nesting pkgs:
610      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
611      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
612      - add parameter files + utils dir + output from short run on beagle.
613    o pkg/seaice:
614        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
615    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
616      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
617    
618    checkpoint62o (2010/11/25)
619    o pkg/exf:
620      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
621    o pkg/seaice:
622      - seaice_ocean_stress: split a loop for better vectorization of the
623        adjoint code
624      - seaice_growth.F: fix bug in conservation of freshwater connected to
625        capping of heff, put contribution into d_HEFFbyNEG
626      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
627        by something more sensible (parameters that are what their name implies)
628      - change some defaults, so that by default exf-parameters are used for
629        things like rhoAir, cpAir,latent/sensible heat parameters, in order
630        to reproduce the old results, many data.seaice now contain funny values
631        for cpAir and latent heat of sublimation
632    o packages_readparms.F: move exf_readparms up in line so that
633        exf-parameters are visible for other packages (e.g. seaice)
634    o debugMode & debugLevel=2:
635      - differentiate between debugMode & debugLevel=2:
636        debugMode: controls printing of debug messages (sequence of S/R calls).
637        debugLevel: controls printing of algorithm intermediate results and stats.
638      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
639        => allows to print debug-stats without all sequence of call messages.
640      - switch control of debug print from debugLevel to debugMode in many S/R.
641    o pkg/obcs (obcs-sponge):
642        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
643        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
644    o pkg/generic_advdiff:
645      - record overlap minimum size for each advection scheme;
646      - refine criteria on overlap minimum size;
647      - check and stop (in gad_check) if overlap size is too small.
648    o pkg/obcs:
649      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
650        once, in ptracers_implicit.F)
651      - with seaice: remove test on empty file name in obcs_apply_seaice (always
652        apply OB values when tile has OB)
653    o model/src, coriolis setting:
654      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
655        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
656        files (selectCoriMap=3) with any grid.
657      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
658    o pkg/seaice/seaice_growth.F:
659        a few cosmetic changes that reduce the number of lines of code
660    o pkg/obcs: add boundary conditions following Stevens (1990)
661      - the code follows old MOM/NAOSIM code
662      - so far it is only implemented for the eastern and western boundaries
663        and NOT for pTracers
664    o pkg/rbcs:
665      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
666        beginning of the first rbcs forcing period.
667      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
668        offline package, i.e., one file per time, labeled by iteration number;
669        deltaTrbcs sets the timestep with which the data was generated;
670        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
671      - rbcsForcingCycle=0 makes forcing non-cyclic.
672      - make arithmetic safe for negative times and odd forcing periods.
673    
674    checkpoint62n (2010/11/09)
675    o pkg/seaice:
676        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
677    o pkg/obcs:
678       New S/R to copy tracer value from the OB location to narrow band region
679        (width = same as overlap) beyond the OB: preserve OB value (needed for
680        high-order scheme) which were overwritten by EXCH call if in overlap
681        region. Applied to theta, salt, ptracer and advected seaice variables.
682       With seaice: use maskInC in similar way as in gad_advection.F,
683        in seaice_advection.F and advect.F.
684       Update output of experiment seaice_obcs and change exp4 to test OBCS with
685        4th order Adv.Scheme. for pasive salt and ptracer.
686    o tools/genmake2:
687      - when looking for an optfile (not specified), only search for Fortran compiler
688        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
689      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
690        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
691      - set default for CPP to "cpp -traditional -P" (was the case without specifying
692        an optfile, but otherwise default was just "cpp".
693      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
694      - when "CC" is not set in the optfile, look for possible C compiler
695        (instead of just setting CC=cc)
696      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
697        => add a ".F" to ".o" rule for source files with no "#include" (such as
698           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
699      - move gfortran before g77 in list of possible Fortran compiler (consistent
700        with reference compiler switch from g77 to gfortran)
701    o pkg/seaice:
702      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
703        seaice_check that stops the model, when the CPP flag is used.
704      o seaice_growth.F: make capping of ice volume conserving by returning the
705        capped ice as freshwater to EmPmR. This does not change the verification
706        experiments but will change runs where the capping is acutally active
707    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
708      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
709         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
710         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
711    o tools/genmake2:
712      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
713      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
714      - clean previous genmake log files before anything else.
715      - change Makefile to remove testreport log files (*.tr_log) and genmake log
716        files only with "CLEAN" target (instead of "Clean");
717    o pkg/generic_advdiff:
718      Change OBCS in multiDim advection (gad_advection.F):
719       Use maskInC to prevent intermediate update of tracer-field in OB regions,
720       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
721       which were applying future time-step OB values.
722      This way, all explicit calculations use current-time-step OB values
723       (simpler and more consistent).
724      Affects results when set-up uses time-varying OBC and multi-dim advection;
725       update output of experiment seaice_obcs.
726    o pkg/seaice:
727      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
728       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
729         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
730      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
731       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
732       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
733    o pkg aim (2010/10/26):
734      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
735        formulation with obliquity, eccentricity, ... as run-time parameters,
736      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
737        upward shortwave radition at the surface (all-sky and clear-sky).
738    o pkg/obcs:
739      - writing sections with globalFiles=T does not work: switch to tiled-files
740        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
741      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
742      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
743    
744    checkpoint62m (2010/10/21)
745    o pkg/seaice: vectorize seaice_solve4temp.F
746      - move iterations loops outside of i/j-loops
747      - requires 2D arrays for TB and effConduct
748      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
749        modified in this routine
750      - a little bit of clean up, adjusting indentation, etc.
751      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
752        performance and '**TWO' by '**2' (because TWO is a float),
753        replaced ONE, ZERO
754    o eesupp/src:
755       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
756    o pkg/seaice/seaice_growth.F
757      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
758      merging process. The merged routine has two branches, and one activates the 'evolution'
759      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
760      In summary, here is what the '10/10 revision' did consist of
761        part 1: seaice_growth.F revisions 1.71 to 1.75
762          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
763            The emphasis here was on improving readability (e.g. by trying to use meaningful
764            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
765        part 1.5:
766          - revising the lab_sea experiment to make it a more useful (i.e. stable
767            and representative of an actual model run). This was done by generating a
768            (winter) pickup to start from, switching back the main experiment dynamic
769            solver from evp to lsr, having one of the experiments use the free drift solution.
770        part 2: seaice_growth.F revisions 1.76 to 1.85
771          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
772          - Sorting out the various fields units and sign (set early on and reset at the end)
773            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
774            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
775          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
776            and simplifying logical expressions to further improve readibility.
777        part 3: seaice_growth.F revisions 1.86 to 1.89
778          - Re-organize the blocks of code more logically.
779          - Merging the '_if.F' pieces that add something new.
780    o pkg/thsice:
781      - vectorize thsice_solve4temp and thsice_get_exf.
782        Problem: thsice_solve4temp has an unvectorizable statement that
783        might also be problematic for TAF
784      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
785        does not change the verifcation experiment, but will change all
786        experiments that have this flag undefined (not tested in verification);
787        a little reorganization to save a few 2D fields and recomputations
788      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
789      - 2nd step:  fix some store dirs
790        o seems to work somewhat, i.e. using ifort but not g77
791        o likely cause are incomplete init. or recomputation
792        o start verification/global_ocean.cs32x15/input_ad.thsice
793    o pkg/obcs: add support for exch2
794      - the position of the boundary and prescribed values are specified using
795        a global domain with exch2 facets stacked
796        - in x for N,S boundaries (like W2_mapIO=-1)
797        - in y for E,W boundaries (so E,W boundaries do not overlap)
798    o pkg/mdsio: add support for writing global sections with exch2
799        file layout is as for obcs described above:
800        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
801        - for y-z sections, facets are stacked in y
802    o pkg/thsice:
803       - change a few routines for better vectorization: thsice_albedo.F,
804         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
805         not affected, but in particular the latter routine has changed
806         dramatically (not necessarily easier to read now).
807       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
808       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
809    o verification/lab_sea:
810      - overhaul of the forward model experiments. The main motivation
811        for this revision is that lab_sea has proven quite fragile (when
812        changing the sea-ice code, and switching platforms) to a point
813        when failures were very hard to attribute to specific code problems.
814      - the suspected reason for this fragility is noise amplification by evp so,
815        to start with, we decided to replace evp with lsr in the main experiment.
816      - the input.lsr experiment thus became obsolete and was removed.
817      - it was replaced with the input.fd experiment that uses an
818        analytical "free drift" solution as the ice velocity field.
819      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
820        will hopefully allow us to discriminate problems due to dynamic solvers
821        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
822        us to test additional options, along with the salt plume package.
823      - Finally a pickup was generated (at the end of a one year run) to
824        make the tests more representative of an actual model run. Previously
825        the tests starting point was a 1m thickness of ice everywhere.
826    o pkg/seaice:
827      - introducing S\R seaice_freedrift.F that compute the
828        analytical solution to an approximate ice momentum
829        equation (i.e. the simple stress/coriolis balance).
830      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
831        of the free drift velocity field, and enable its use.
832        To actually use the free drift solution as the model ice
833        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
834    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
835    
836    checkpoint62l (2010/10/04)
837    o pkg/seaice:
838      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
839      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
840       version (with USE_ORIGINAL_SBI undef);
841    o add hooks for new packages OASIS, the package will follow
842      (hooks exclude the seaice pkg for now)
843    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
844      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
845      rather than mdsio_readvector.F/mdsio_writevector.F, within
846      adread_adwrite.F to read/write adjoint-related tapes to disk.
847    o eesupp and pkg/mdsio: ALLOW_WHIO
848      Option to write/read 2D fields to files including tiles halos.
849      The main purpose is for adjoint related "tape I/O".
850      The secondary purpose is for debugging phases.
851      A word on those rather specifically intended purposes.
852      The code was meant to be stripped down to the bare minimum.
853      Typically, there is a unique and basic mapping to the global
854      buffer (tile by tile, then proc by proc, then level by level), and
855      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
856      meant to generate user friendly outputs of various shapes and forms.
857      Rather it is intended, for the knowledgeabale developers,
858      to be largely independent of the many mdsio options, to allow
859      outputs of tiles+halos in debugging phases and in adjoint runs,
860      and to allow some flexibility in tuning (adoint) I/O depending on each
861      file system behavior. With regard to tuning, most of the potential knobs
862      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
863      to specify directories, to specify the typical size of I/O calls, etc.)
864      are not yet included, and will be added if they prove useful.
865    o pkg/seaice:
866       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
867    o pkg/seaice:
868       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
869       code (seaice_budget_ice_if.F) which enable to recover old standard
870       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
871       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
872    o model/src (rStar):
873       use simple average (not area weighted) of rStarFac at U,V point when using
874       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
875       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
876    
877    checkpoint62k (2010/09/17)
878    o adjoint
879       * changed verification/global_ocean.cs32x15 ; adjoint now tests
880         Adams-Bashforth 3 + NLFS + RSTAR
881       * some more modifs required for ECCO-GODAE v4
882    o pkg/seaice
883       add SEAICE_AGE_VOL option to use volume instead of area for
884       integrating SEAICE_AGE
885    o model/src:
886       first check-in of sigma & hybrid-sigma coordinate code ; also includes
887       non-linear free-surface parts ; but pressure-gradient not yet coded.
888    o pkg/ptracers:
889       option for ptracer to convert Salt Relax into additional EmP.
890        tested in exp. global_ocean.90x40x15.dwnslp (update output)
891    
892    checkpoint62j (2010/08/25)
893    o pkg/ggl90:
894       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
895    o pkg/dic: car_flux.F, phos_flux.F
896      - reduce number of exp-calls in order to improve performance
897      - clean up a little (replace fields by their macros, etc., fix
898        typo in CPP-flag)
899    o pkg/ggl90: minor changes
900      - GGL90diffKrS was removed --> always use GGL90diffKr
901      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
902      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
903        (commented out for now)
904      - change in max/min operations to ensure that smoothing is ok
905      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
906      - always use diffKrNrT as background profile (i.e. never use diffKr field)
907    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
908    o pkg/dic:
909      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
910        vectorization
911      - small bug fix in insol for the unlikely case of a cartesian grid
912      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
913        + now vectorize, which also removes adjoint recomputations;
914        + replace integer maksp1 by _RL maskp1
915        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
916    
917    checkpoint62i (2010/07/21)
918    o pkg/flt:
919      - with OBCS: stop floats which enter the OB region
920    o model/src:
921      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
922        for implicit vertical advection.
923    o pkg/seaice:
924     - account for melting in seaice age evolution.
925     - remove double counting of seaice ridging effect on seaice age.
926    
927    checkpoint62h (2010/06/18)
928    o pkg/exch2:
929     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
930    o tools/genmake2
931      - remove "-pdefault" option: redundant with the use of "packages.conf";
932      - remove file pkg/pkg_default : set the default as a pkg group
933        ("default_pkg_list") defined in pkg/pkg_groups;
934      - fix for case pkg/pkg_depend is missing (was hanging before);
935      - add option "-pgroups" to specify a different pkg_groups than the default.
936    o verification/adjustment.cs-32x32x1:
937       add a "minimal" set-up test (code_min & input_min) which only compiles
938       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
939    o tools/genmake2
940      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
941      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
942    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
943      files are nearly the same anyway.
944      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
945       - redefinition of tau(i,i) (by a factor of ustar)
946       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
947       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
948       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
949       - replace
950         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
951         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
952         by
953         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
954         (changes results)
955       -> exf_bulkformulae v1.22,
956          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
957          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
958                    output.txt 1.63
959           offline_exf_seaice: output.seaicetd.txt 1.7
960           seaice_obcs: output.txt 1.10)
961      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
962       -> exf_bulkformulae v1.23,
963          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
964          and global_ocean.cs32x15.icedyn (only 11 matching digits)
965      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
966    o adjoint of exch-1:
967     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
968       (note: was already like this when using EXCH-2) and remove flow dir
969       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
970     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
971     - update pkg/exch2 diff list.
972    
973    checkpoint62g (2010/05/19)
974    o eesupp/src (exch-1):
975     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
976       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
977       (renamed to exch1_*rx_cube.F).
978     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
979       to call new exch1 S/R ; update Makefile and .cvsignore.
980     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
981       exch2_xy_rx later)
982      Note: after updating your code, need to run "make clean" in eesupp/src
983    o test experiment bottom_ctrl_5x5:
984       new output_adm.txt with fewer grdchk & less monitor output.
985    o model/src:
986      remove the call to ini_cori in initialise_varia.F (just keep the usual one
987       in initialise_fixed.F). More consistent with coriolis & horizontal grid
988       beeing treated in the same way (ini_grid is not called a 2nd time).
989    o pkg/exf:
990      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
991      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
992      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
993      - cosmetic changes to exf_bulkformulae.F to make it look more like
994        exf_bulk_largeyeager04.F
995    o eesupp/src (exch-1):
996      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
997      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
998        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
999        (even without using MPI).
1000      - Message mode: move RecvAck setting (indicator of buffer being ready)
1001        from send_put to recv_get S/R (was useless before, but not sure if
1002        it's much more useful now);
1003      - Switch the order of sync: MPI-proc 1rst and then threads;
1004      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1005      - fix AD code for communication mode ='get' (but not used).
1006    o model/src:
1007      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1008      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1009    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1010    o pkg/ctrl: require a specific set of control variables and exf-flags for
1011      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1012    o model/src:
1013     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1014       1rst forward sweep, to avoid over-writing output files during recomputations
1015       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1016     b) 2nd version:
1017      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1018      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1019         writePickupAtEnd) + seaice & ptracers output;
1020      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1021    o model/src:
1022      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1023    o pkg/exch2:
1024      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1025      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1026    o pkg/autodiff & exch2:
1027      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1028      (for now, only if ALLOW_EXCH2 is defined).
1029    o pkg/autodiff:
1030      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1031        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1032       + clean-up comments (_RS is not always real*4)
1033      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1034      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1035        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1036    o testreport (AD-tests):
1037      no longer link files from dir "../input" (1rst link files from
1038      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1039    
1040    checkpoint62f (2010/04/29)
1041    o model/src/the_main_loop.F:
1042      adjust store directives for seaice evp and multicategory according to
1043      pkg/ecco/the_main_loop.F
1044    o adjoint:
1045      global_sum_ad was incomplete (noted many times by many people ;)
1046      nice description by Jean U. as follows:
1047      * allreduce(var) in global_sum.F can be interpreted as
1048        reduce(sum) followed by broadcast of sum.
1049      * The adjoint of that is
1050        sum(adjoint) followed by broadcast(summed adjoint value)
1051        or in other words, allreduce(sum, adjoint vars)
1052      We were missing the sum(adjoint)!
1053      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1054      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1055      The fix should produce 16-digit accuracy between
1056      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1057      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1058      We'll probably change this yet again shortly
1059    o eesupp/src:
1060      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1061    o pkg/icefront
1062      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1063        specification of addmass array based on a 2D field, which is added
1064        at bottommost wet level at each horizontal location.
1065    o model/src:
1066     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1067     layout; (not always compatible with delX,delY setting; commented out for now).
1068    o pkg/exch2:
1069     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1070     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1071    
1072    checkpoint62e (2010/04/15)
1073    o pkg/obcs:
1074      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1075    o pkg/dic:
1076      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1077        (note: not presently tested in any forward verification exp.)
1078       update tutorial_global_oce_biogeo AD output file.
1079    o pkg/exf:
1080      - account for the variation of albedo as a function of zenith angle
1081        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1082    o build_options:
1083     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1084    o pkg/dic:
1085      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1086      - use binary pickup file for restart;
1087      - initialise atmos-CO2 box from dic_pCO2 parameter;
1088      - fix multi-threaded.
1089    o pkg/rbcs:
1090     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1091       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1092     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1093       and update output.txt
1094    o pkg/kpp:
1095     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1096     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1097       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1098       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1099     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1100       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1101    o pkg/offline:
1102      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1103      (bug was added in version 1.10 on 2007-08-23).
1104    o pkg/offline:
1105      - no need to specify periodicExternalForcing, etc ... to use offline pack
1106      - offline input files no longer just single prec --> parameter offlineLoadPrec
1107    o verification/lab_sea:
1108      change AD test to multi-tile setup and update all 4 AD output.
1109      NOTE: while cost function values remain very similar,
1110      gradients are very different, although gradient checks are self-consistent
1111      Should try to get to the bottom of this (cost function summation order?)
1112    o pkg/dic:
1113      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1114      a weakness of TAF that drops part of double precision in log10 derivative.
1115      <= changes removed since problem has been fixed in current TAF version 1.9.71
1116      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1117    o pkg/ecco:
1118      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1119      update all 4 lab_sea AD output.
1120    
1121    checkpoint62d (2010/03/22)
1122    o build_options:
1123      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1124    o remove unbalanced quote (single or double) in commented line of source code
1125      (may cause some warning with some preprocessor/makedepend versions).
1126    o pkg/seaice:
1127      fix seaice_model.F for adjoint (gael) and update AD results of experiments
1128       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1129    o testreport:
1130      add option '-runonly' (short: '-ro') to just do the run part (without make).
1131    o eesupp: remove JAM communication code (obsolete).
1132    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1133      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1134      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1135      (update also the output).
1136    
1137    checkpoint62c (2010/03/02)
1138  o tools/build_options :  o tools/build_options :
1139     move (some) old optfiles from build_options/ to build_options/unsupported/     move (some) old optfiles from build_options/ to build_options/unsupported/
1140  o model/src and pkg/exf  o model/src and pkg/exf
# Line 20  o tools/build_options: Line 1151  o tools/build_options:
1151      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
1152  o pkg/ecco  o pkg/ecco
1153    - allow user defined cost function contributions    - allow user defined cost function contributions
1154          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
1155          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
1156    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1157        the two options are complementary.        the two options are complementary.
1158  o pkg/smooth  o pkg/smooth
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