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revision 1.66 by jmc, Tue Mar 5 15:36:06 2002 UTC revision 1.1462 by jmc, Wed Jun 22 19:17:36 2011 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  checkpoint44g_post  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     Change the ordering of fields and time-periods in MDS output file
13       when using periodic averaging: now writes one time record with the full set
14       of fields for this time period, then the next time reccord (it used to be
15       one field with the full set of time records then the next field).
16       Note: this is now similar to NetCDF (MNC) output file.
17    
18    checkpoint62z (2011/06/21)
19    o adjoint monitor:
20     - Add adjoint monitor output for packages exf, seaice
21       and update relevant testreport output
22    o pkg/seaice:
23     - re-order diags inits so that they appear in order in available_diagnostics.log
24     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
25       area/heff/hsnow preceeding thermodynamic growth/melt.
26     - modified diag: SIdA; output actual effect, as the description states.
27     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
28     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
29       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
30        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
31     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
32     - added diagnostics for seaice generic tracers (SItr*).
33     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
34     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
35     I. Fenty: 18-Jun-2011:
36     Minor changes to seaice package:
37     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
38        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
39       - Differentiated "regularization variables" from "floor variables"
40        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
41        * hiceMin became SEAICE_hice_reg (old hiceMin)
42          (with _reg meaning regularization variable)
43       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
44        so as to ensure energy conservation when going between phases
45      - A22 was not used anywhere
46     2) Changed regularization procedure for heffActual and hsnowActual to ensure
47        well-boundedness and smooth adjoint in seaice_growth.F
48     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
49        because the old regularization always set heffActual >= 0.05 cm
50     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
51        on AREA when HEFF > 0.
52      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
53        requiring that DISABLE_AREA_FLOOR *not* be defined
54     Affected verifications:
55      - 1D_ocean_ice_column (output.txt output_adm.txt)
56      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
57    o pkg/diagnostics:
58      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
59      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
60        (was _RL, now integer) with option = 0 to retrieve all levels.
61      - add pieces of code to compute velocity potential at each level (new diagnostics
62        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
63        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
64      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
65        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
66        and in diagnostics_fract_fill.F (do not need a valid pointer for the
67        diagnostics counter-mate); check that definition of counter-diagnostic
68        includes a valid counter-mate (in diagnostics_set_levels.F).
69    o model/src (rStar):
70      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
71        affect solution only if z* with full pressure in EOS;
72        update output of test-exp global_ocean.90x40x15.
73    o pkg/seaice:
74      - introduce siEps=1e-5 parameter
75      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
76      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
77      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
78        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
79        as well as ice cover age and ridging index (attached to AREA).
80        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
81        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
82        Up to SItrMaxNum=3 tracers can be used simultaneously.
83    o pkg/salt_plume:
84      -introduce SPsalFRAC run time parameter that sets the fraction of the
85       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
86       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
87    o model debug options:
88      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
89        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
90      - Refine debug-msg printing selection (3 new levels):
91        debugMode  : controls printing of debug messages (sequence of S/R calls).
92        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
93         debLevZero =  0 ; /* level of disabled aux. msg printing */
94         debLevA =  1 ; /* level of minimum  aux. msg printing */
95         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
96         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
97         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
98         debLevE =  5 ; /* level of extensive debug printing */
99        New debugLevel default: with default debugMode value (=F),
100          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
101          and if debugMode=T, default debugLevel = 4 (debLevD).
102        Relation with previous settings:
103         debLevB (=2) corresponds to former debLevA (=1)
104         debLevD (=4) corresponds to former debLevB (=2)
105        Note:
106         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
107         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
108            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
109      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
110        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
111    o pkg/obcs:
112      - change OBCSfixTopo default from True to False (should not change the results);
113        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
114    o pkg/thsice:
115      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
116        2nd layer seaice sublimation (unlikely to happen)
117      - use Interior mask for OBCS in thsice_advection.F (similar to what is
118        done in gad_advection & seaice_advection).
119    o adjoint:
120      bug fix spotted by Gael Forget:
121      seaice_advection and thsice_advection still had
122      legacy CPP options to avoid CS corner updates for adjoint
123    o pkg/seaice:
124      => Change some of the defaults (2011/05/29):
125         - change SEAICEuseFluxForm default (from False to True)
126         - change DIFF1 default (from 0.004 m/s to 0. m/s)
127         And print warnings if DIFF1 is not set in data.seaice and centered
128          avection scheme is used without any diffusion.
129      also:
130      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
131      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
132      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
133        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
134        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
135      update results of test exp.:
136         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
137             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
138             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
139         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
140         seaice_obcs: output (SEAICEuseFluxForm=T)
141      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
142          for standard fwd & AD lab_sea tests (to keep the same output).
143    o pkg/seaice/seaice_growth.F:
144      - use Ian Fenty's capping formulas for actual ice
145      thickness thoughout EVOLUTION branch.
146      - put treatment pathological case #2) in CPP brackets
147      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
148      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
149    o pkg/seaice:
150      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
151      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
152      also pass fac as a param, which can be 1. (to update the tendency
153      field) or the time step (to update the field itself).
154      - seaice_advdiff.F: for multidim, call seaice_diffusion with
155      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
156      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
157      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
158      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
159    o pkg/seaice:
160      diffusion with centered advection scheme (diffus.F & advect.F):
161      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
162        to just compute the laplacian of input-field.
163      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
164      - fix flux-form version in diffus.F to conserve tracer.
165      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
166       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
167    
168    checkpoint62y (2011/05/26)
169    o pkg/seaice:
170     - seaice_growth.F : in EVOLUTION branch, always include
171       a_QSWbyATM_cover in qnet (as it should be).
172     - verification/global_ocean.cs32x15 : update results accordingly
173       (output.seaice.txt output_adm.seaice.txt).
174    o pkg/seaice + obcs:
175     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
176       equivalent of assuming no tracer gradient outside the OB region.
177       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
178     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
179       after changes above);
180     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
181       only at OB location (instead of over a band of OLx width).
182    o pkg/seaice:
183     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
184       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
185    o pkg/obcs:
186      - split header file "OBCS.h" into 4 separated files:
187        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
188       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
189         (contain no conditional statement which depends on OBCS options).
190      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
191        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
192    o ctrl, cost, grdchk & autodiff pkgs:
193      - make options file more standard (like other {PKG}_OPTIONS.h file but
194        with AD_CONFIG.h); clean-up some of the included header files.
195    o pkg/obcs:
196      - do not mask tracer when applying OB (tracer == 0 could generate problems)
197      - apply tracer OB values to tracer field only at OB location (instead of
198        over a band of OLx width)
199      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
200      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
201        obcs_apply_tloc.F & obcs_apply_sloc.F
202    o obcs in model/src:
203      - call OBCS_APPLY_W only if NonHydrostatic.
204      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
205      - reset dEtaHdt and wVel to zero outside OB interior region ;
206      - leave tracer unchanged outside OB interior region: This has no effect
207        on the solution but just to prevent unrealistic tracer value outside OB.
208      - zero out velocity outside OB interior region: This has no effect on
209        the solution but just to prevent unrealistic velocity outside OB.
210    o obcs and non-lin free-surf:
211       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
212       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
213       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
214       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
215       update results of test-exp. exp4(nlfs).
216    o exp4 (nlfs) test-exp:
217       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
218       with NonLin-FreeSurf); update output.nlfs.txt
219    o obcs and 2d/3d solver norm:
220       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
221       and outside OB interior region (will allow to place OB further inside the
222       domain). Depending on the domain, can affects cg2d-Norm (previous
223       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
224       and cg3d-Norm (previous Norm was computed before canceling OB terms),
225       e.g. in tutorial_plume_on_slope.
226      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
227    o pkg rbcs:
228      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
229      - add capability to apply relaxation to horizontal velocity uVel & vVel.
230    o pkg/grdchk: add gradient check for control variable xx_shifwflx
231    o pkg/shelfice/shelfice_init_fixed.F
232      fix CPP-flag combinations
233    o pkg/seaice: Merge iceage code of Pierre Rampal
234      * update/change/correct ice age calculations
235      * add age updates for pathological cases
236      Probably needs more testing...
237    
238    checkpoint62x (2011/05/13)
239    o pkg/mom_vecinv:
240       high-order vorticity scheme: use interior masks (maskInW & S)
241       to zero-out (outside OB) gradient of vorticity.
242    o verification exp.:
243       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
244       hs94.128x64x5 and seaice_obcs ; update results.
245    o pkg/obcs:
246      fix bug in OBeta for YZ sections in obcs_exf_load.F
247    o pkg/ctrl, pkg/shelfice, and optim:
248      - add new control variable xx_shifwflx (fresh water flux underneath ice
249        shelves). This is almost as tedious as obcs-ctrl, because the
250        variables needs its own mask.
251      - add a cost function term that penalizes the deviation of xx_shifwflx
252        from the first guess (zero) in analogy to other control variables
253    o pkg/shelfice:
254      - start basic adjoint
255    o pkg/ctrl:
256      - remove extra 2D field "for good measure" when initializing in
257        ctrl_set_globfld_[xy/xz/yz].F
258      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
259      - improve error messages in ctrl_set_unpack_*
260    o OBC implementation in momentum:
261       use interior masks (maskInC,W & S) in momentum S/R:
262       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
263       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
264       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
265       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
266       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
267        (and also with Leith/Smagorinsky harmonic-viscosity).
268       Update output of experiment dome and exp4 (+nlfs).
269    o exp4 test-exp:
270      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
271        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
272        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
273        time-varying OB at Western-side for wVel (NonHyd); update output.
274      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
275        and biharmonic-viscosity ; also use prescribed time varying OB.
276    o pkg/obcs:
277      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
278    o model/src:
279      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
280      - initialise startTime & nIter0 with unlikely values: allows to set one
281        from the other without ambiguity.
282    o seaice_obcs test-exp.:
283      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
284    o pkg/obcs:
285      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
286        no longer needed with maskInC,W,S in pkg/generic_advdiff.
287    o pkg/seaice:
288      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
289        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
290      - fixed bug in the initialization of sea ice salinity variable HSALT
291        in seaice_init_varia.F  (removed dependence on ICE2WATR)
292    o fizhi-cs test exp.:
293       switch reference output convention for these 2 non-standard test-exp,
294        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
295          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
296       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
297    o model/inc:
298      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
299        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
300    o pkg/seaice:
301      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
302    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
303      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
304        and initial HSALT
305    
306    checkpoint62w (2011/04/26)
307    o pkg/mom_fluxform:
308      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
309      - use parameter "sideDragFactor" in no-slip BC side-drag part.
310      - update output of exp. global_ocean.90x40x15
311    o pkg/mom_vecinv:
312      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
313    o update seaice exp.:
314      use more consistent parameter values (remove "backward compatability only":
315       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
316      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
317       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
318    o update test-exp global_ocean.90x40x15:
319      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
320      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
321      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
322      o turn on zStar & viscA4 in standard set-up (dir input/)
323        and update output files: output.txt & output.dwnslp.txt
324    o new AD-test experiment: obcs_ctrl
325      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
326    o pkg/dic:
327      fix two bugs in handling water vapour pressure in carbonate chemistry
328      and air-sea fluxes. Found by Val Bennington and Galen McKinley
329      (add DIC Option = WATERVAP_BUG to recover old results)
330      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
331    o adding allowInteriorFreezing option to check for water below freezing point
332      at depth and bring the negative heat anomaly to the surface level
333    o pkgs _fields_load:
334      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
335      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
336        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
337        rbcs to get interpolation weights and time reccord number.
338      - fix multi-threading in aim_fields_load.F
339      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
340    o external_fields_load:
341      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
342       interpolation weights) to use in a periodic time-series ; do not divide by
343       time-step to convert to integer:
344       - this fixes case where externForcingPeriod is not multiple of time-step
345          (Thanks to Christopher L. Wolfe)
346       - this fixes case where externForcingPeriod is an odd multiple of time-step
347         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
348      store index of time-record which is currently loaded:
349       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
350       - needed for the adjoint but not yet used because of extensive recomputations;
351         (to be fixed soon)
352    
353    checkpoint62v (2011/04/02)
354    o verification/1D_ocean_ice_column added to test Ian Fenty's
355      pkg/seaice_growth.F modifications for improving sea ice code differentiability
356    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
357      (new velocity statistics after changing maskInW & maskInS definition)
358    o pkg/generic_advdiff with OBCS:
359      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
360      equivalent to assumption of no tracer gradient outside the OB region.
361      This will affect the results if using obcs+biharmonic diffusion.
362      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
363    o pkg/obcs:
364      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
365      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
366      in Interior region. No impact on solution but affects Velocity monitor stats.
367    o pkg/ptracers (adjoint)
368      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
369      tape file for each tracer
370    o model/inc/src and pkg/autodiff: add parameters that allow to turn
371      of parts of the adjoint code at run time. For now, there are only
372      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
373      parameters are set in data.pkg.
374      This is the lazy coward's version of doing this, but still useful for
375      debugging. In order to do it right, everything needs to be moved to
376      pkg/autodiff.
377    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
378      the end; this fixes the adjoint balancing code for open boundaries.
379    o pkg/ctrl:
380      - change behavior of xx_${varname}period to be analogous to exf-conventions:
381        xx_${varname}period =   0.,  means time-independent control part
382        xx_${varname}period = -12., means one-year-periodic monthly control part
383      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
384        clean up ctrl_init a little, remove unused variables
385      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
386      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
387    
388    checkpoint62u (2011/03/15)
389    o model/src:
390      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
391        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
392      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
393        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
394    o pkg/ctrl/obcs/ecco:
395      - remove obsolete, unused, and partially broken code:
396        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
397        ALLOW_CTRL_OBCS_BALANCE
398      - put a stop statement into ecco/cost_obcsvol.F, but also add
399        cost_obcsvol to ecco_ad_diff.list
400    o pkg/ecco: fix counting cost function contributions for obcs (code
401      by Matt M.) and diffkr for diagnostics
402    o pkg/ecco, pkg/ctrl, pkg/grdchk:
403      add cost penalty terms for initial uvel, vvel, eta controls
404      and I/O for prior error files
405    o pkg/mdsio:
406       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
407       (new argument) to check for tiled file in mdsioLocalDir : this fix the
408       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
409    o pkg/ctrl:
410     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
411       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
412       unused and superfluous variables
413     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
414    o pkg/ecco
415     - enable adjoint of Stevens OB
416    o pkg/ctrl/ecco/grdchk:
417      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
418        Fortunately, we do not have any tests for the numerous cpp-flagged
419        option of "obcs as control parameters" so we will never know
420        if this is an improvement (but at least now things compile).
421      - remove an obsolete initialization from ecco_cost_init_barfiles.F
422      - fix some problems within never used ifdefs to make the code compile
423    o pkg/obcs:
424     - Refine Interior mask definition to work with more complex OB (e.g.
425       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
426       read in Interior mask from file. Check if Interior mask is consistent
427       with OB list of indices.
428    o pkg/seaice
429     - beginning code for a seaice tracer package,
430       but currently only used for seaice age: SEAICE_AGE
431       SEAICE_num = 4
432       iTracer = 1: area-weighted ice age
433               = 2: volume-weighted ice age
434               = 3, 4: template for one-year vs. multi-year ice
435       data.seaice has new namelist SEAICE_PARM03 for arrays related to
436       SEAICE_num
437    
438    checkpoint62t (2011/03/05)
439    o pkg/obcs:
440     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
441       then normal component. This ensures that the normal component is set
442       correctly even when it conficts with tangential setting from an other OB.
443       Affects results of test-experiment seaice_obcs: update the output.txt
444    o pkg/obcs:
445     - add code to monitor statistics of dynamical fields at OB.
446     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
447       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
448       - change default: balance the Net inflow through all OB (instead of balancing
449         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
450     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
451       to match Nortern OB inflow (OBCS_balanceFacN=0).
452    o pkg/seaice:
453     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
454    o pkg/seaice (seaice_growth v 1.113):
455     - reverting seaice_growth to v 1.111 in order to have code with exact bit
456       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
457       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
458       runtime flag SEAICEareaFormula is kept but is inactive
459    o model/src:
460     - add new param to scale curvilinear grid distance and area when using
461       a different sphere radius from the grid-files.
462     - test/check multi-threads EXCH applied to local variable (cg2d_x)
463    o adjoint:
464     - enable adjoint of Stevens OB
465     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
466       (a bit delicate because of potentially modified adj. common block structure;
467       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
468    
469    checkpoint62s (2011/02/15)
470    o pkg/seaice (seaice_growth v 1.112):
471     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
472       computing the ice cover tendency from effective thickness tendencies. Include
473       Ian Fenty's formula.
474     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
475       SEAICEareaFormula.
476     - simplify notations for the various d_HEFF/d_AREA terms.
477    o pkg/gmredi:
478     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
479       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
480       add a verification test-run (front_relax.bvp) to test GM_useBVP.
481    o pkg/seaice (seaice_growth v 1.111):
482     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
483     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
484       also melt ice.
485    o pkg/seaice:
486     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
487     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
488    o pkg/cheapaml:
489     - from Nico Wienders: New version of this package.
490    o pkg/flt:
491     - add CPP options to prevent floats to re-enter the opposite side of
492       a periodic domain (default: keep periodicity)
493    o pkg/gmredi:
494     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
495       (needed for multi-dim advection).
496     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
497    o model/src:
498     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
499    o tutorial_tracer_adjsens
500     - extend to NLFS and replace maskC by hFacC
501       (change reference output accordingly)
502    
503    checkpoint62r (2011/01/24)
504    o testreport:
505     - add option -deloutp (-do) to remove output file after successful run
506     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
507       extract exact list of procs from this file ; adjust COMMAND by
508       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
509    o pkg/ecco: replace old ineffective way of penalizing deviations from
510      first guess (of obcs) with code by Matt Mazloff
511    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
512      exf/cal
513      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
514        and handle case of obcs?period == 0
515        Not affected by these changes: There is still an inconsistency in
516        the computation of start/endrec for the obcs variables for ALLOW_CAL
517        defined (see comment by Menemenlis, 7-Mar-2003)
518      - make S/R ctrl_get_gen_rec return something meaningful even if
519        ALLOW_CAL is not defined
520      - ctrl_getobcs?: simplify code so that it does not need to use
521                       S/R exf_swapfields
522    o testreport:
523       allow to test MPI with different number of processors for each experiment:
524       create file "SIZE.h.mpi" in each build dir.
525       Note: update of "-command" argument not yet implemented.
526    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
527      alleviate the need for additional 3D tapes when using
528      the non-inear free surface in the adjoint. This is done
529      by adding an 'update' of hfacc etc. to their current
530      value at the beginning of forward_step.F.
531    o pkg/seaice
532      seaice_lsr: move stress-divergence computations out of outer pseudo-
533      timestepping loop
534    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
535      up, so that the calls of the ctrl_* subroutines are really at the end
536      of the routine.
537    o pkg/gmredi:
538      allow to specify a 2-D horizontal map and a 1-D vertical profil
539      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
540    o pkg/seaice:
541      move lsr iterations from seaice_dynsolver to seaice_lsr.
542    o pkg/seaice:
543      reduce memory footprint of seaice mutldim advection tapes,
544      by using a 2D tape independent of the generic_advdiff ones,
545      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
546    
547    checkpoint62q (2010/12/29)
548    o model/src:
549      - check horizontal grid-spacing for unset or zero/negative values.
550      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
551    o pkg/flt:
552      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
553      - precision of input and output files set according to readBinaryPrec
554        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
555      - initial float position from tiled file was not converted to index space
556        (looks like a bug): fixed to make it similar to initial pos. global file.
557    o global_ocean.cs32x15:
558       change SIZE.h of AD set-up to get same tiling as with MPI.
559       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
560    o model/src:
561       add flag to control printing of domain fields (bathymetry, hFac ...) in
562       ini_mask_etc (call to plot_fieds_xy*).
563    o pkg/thsice:
564       if useEXF, some forcing fields are not valid in overlap: fixed by computing
565       over the interior only + apply EXCH at the end (like with SEAICE advection).
566    o pkg/mdsio:
567      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
568        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
569      - change barrier call for safe multi-threads access to 3-D shared buffer.
570      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
571      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
572        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
573    o pkg/flt:
574      - add fourth-order Runge-Kutta integration
575      - add basic exch2 support (only 1 facet supported so far!)
576    o pkg/mdsio+rw:
577      new S/R to read local (or tile independent) vector (read counterpart of
578       mds_writevec_loc, and front-end write_glvec_rl/rs).
579    o global_ocean.cs32x15: additional input_ad.seaice experiment
580        that uses pkg/seaice rather than pkg/thsice.
581        (using multidim advection for seaice)
582    o towards more F95 syntax for array specification in namelist:
583      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
584        of all verification experiments.
585           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
586          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
587      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
588    o global_ocean.cs32x15: additional input.seaice experiment
589        that uses pkg/seaice rather than pkg/thsice.
590    
591    checkpoint62p (2010/12/17)
592    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
593        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
594    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
595        allow for use of multim. advection in seaice adjoint.
596    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
597      - first attempt to close budgets by taking into account the freshwater
598        flux implied by the sublimation of snow and ice. So far only the
599        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
600        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
601    o eesupp/src:
602      new S/R with new option (NML_EXTENDED_F77) to change array specification
603      from F95 standard to commonly accepted extended F77 form.
604      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
605      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
606      for less tolerant f77 compiler (e.g., pgf77, g77).
607    o globalFiles:
608      commented out in parameter file "data" since it's not safe with MPI
609      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
610      in this case); no longer commented out in restart test (tst_2+2).
611    o add adTapeDir to specify a special directory where adjoint tapes are
612      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
613      and cannot be used together with mdsioLocalDir.
614    o nesting pkgs:
615      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
616      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
617      - add parameter files + utils dir + output from short run on beagle.
618    o pkg/seaice:
619        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
620    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
621      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
622    
623    checkpoint62o (2010/11/25)
624    o pkg/exf:
625      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
626    o pkg/seaice:
627      - seaice_ocean_stress: split a loop for better vectorization of the
628        adjoint code
629      - seaice_growth.F: fix bug in conservation of freshwater connected to
630        capping of heff, put contribution into d_HEFFbyNEG
631      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
632        by something more sensible (parameters that are what their name implies)
633      - change some defaults, so that by default exf-parameters are used for
634        things like rhoAir, cpAir,latent/sensible heat parameters, in order
635        to reproduce the old results, many data.seaice now contain funny values
636        for cpAir and latent heat of sublimation
637    o packages_readparms.F: move exf_readparms up in line so that
638        exf-parameters are visible for other packages (e.g. seaice)
639    o debugMode & debugLevel=2:
640      - differentiate between debugMode & debugLevel=2:
641        debugMode: controls printing of debug messages (sequence of S/R calls).
642        debugLevel: controls printing of algorithm intermediate results and stats.
643      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
644        => allows to print debug-stats without all sequence of call messages.
645      - switch control of debug print from debugLevel to debugMode in many S/R.
646    o pkg/obcs (obcs-sponge):
647        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
648        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
649    o pkg/generic_advdiff:
650      - record overlap minimum size for each advection scheme;
651      - refine criteria on overlap minimum size;
652      - check and stop (in gad_check) if overlap size is too small.
653    o pkg/obcs:
654      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
655        once, in ptracers_implicit.F)
656      - with seaice: remove test on empty file name in obcs_apply_seaice (always
657        apply OB values when tile has OB)
658    o model/src, coriolis setting:
659      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
660        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
661        files (selectCoriMap=3) with any grid.
662      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
663    o pkg/seaice/seaice_growth.F:
664        a few cosmetic changes that reduce the number of lines of code
665    o pkg/obcs: add boundary conditions following Stevens (1990)
666      - the code follows old MOM/NAOSIM code
667      - so far it is only implemented for the eastern and western boundaries
668        and NOT for pTracers
669    o pkg/rbcs:
670      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
671        beginning of the first rbcs forcing period.
672      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
673        offline package, i.e., one file per time, labeled by iteration number;
674        deltaTrbcs sets the timestep with which the data was generated;
675        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
676      - rbcsForcingCycle=0 makes forcing non-cyclic.
677      - make arithmetic safe for negative times and odd forcing periods.
678    
679    checkpoint62n (2010/11/09)
680    o pkg/seaice:
681        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
682    o pkg/obcs:
683       New S/R to copy tracer value from the OB location to narrow band region
684        (width = same as overlap) beyond the OB: preserve OB value (needed for
685        high-order scheme) which were overwritten by EXCH call if in overlap
686        region. Applied to theta, salt, ptracer and advected seaice variables.
687       With seaice: use maskInC in similar way as in gad_advection.F,
688        in seaice_advection.F and advect.F.
689       Update output of experiment seaice_obcs and change exp4 to test OBCS with
690        4th order Adv.Scheme. for pasive salt and ptracer.
691    o tools/genmake2:
692      - when looking for an optfile (not specified), only search for Fortran compiler
693        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
694      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
695        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
696      - set default for CPP to "cpp -traditional -P" (was the case without specifying
697        an optfile, but otherwise default was just "cpp".
698      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
699      - when "CC" is not set in the optfile, look for possible C compiler
700        (instead of just setting CC=cc)
701      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
702        => add a ".F" to ".o" rule for source files with no "#include" (such as
703           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
704      - move gfortran before g77 in list of possible Fortran compiler (consistent
705        with reference compiler switch from g77 to gfortran)
706    o pkg/seaice:
707      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
708        seaice_check that stops the model, when the CPP flag is used.
709      o seaice_growth.F: make capping of ice volume conserving by returning the
710        capped ice as freshwater to EmPmR. This does not change the verification
711        experiments but will change runs where the capping is acutally active
712    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
713      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
714         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
715         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
716    o tools/genmake2:
717      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
718      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
719      - clean previous genmake log files before anything else.
720      - change Makefile to remove testreport log files (*.tr_log) and genmake log
721        files only with "CLEAN" target (instead of "Clean");
722    o pkg/generic_advdiff:
723      Change OBCS in multiDim advection (gad_advection.F):
724       Use maskInC to prevent intermediate update of tracer-field in OB regions,
725       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
726       which were applying future time-step OB values.
727      This way, all explicit calculations use current-time-step OB values
728       (simpler and more consistent).
729      Affects results when set-up uses time-varying OBC and multi-dim advection;
730       update output of experiment seaice_obcs.
731    o pkg/seaice:
732      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
733       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
734         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
735      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
736       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
737       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
738    o pkg aim (2010/10/26):
739      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
740        formulation with obliquity, eccentricity, ... as run-time parameters,
741      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
742        upward shortwave radition at the surface (all-sky and clear-sky).
743    o pkg/obcs:
744      - writing sections with globalFiles=T does not work: switch to tiled-files
745        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
746      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
747      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
748    
749    checkpoint62m (2010/10/21)
750    o pkg/seaice: vectorize seaice_solve4temp.F
751      - move iterations loops outside of i/j-loops
752      - requires 2D arrays for TB and effConduct
753      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
754        modified in this routine
755      - a little bit of clean up, adjusting indentation, etc.
756      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
757        performance and '**TWO' by '**2' (because TWO is a float),
758        replaced ONE, ZERO
759    o eesupp/src:
760       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
761    o pkg/seaice/seaice_growth.F
762      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
763      merging process. The merged routine has two branches, and one activates the 'evolution'
764      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
765      In summary, here is what the '10/10 revision' did consist of
766        part 1: seaice_growth.F revisions 1.71 to 1.75
767          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
768            The emphasis here was on improving readability (e.g. by trying to use meaningful
769            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
770        part 1.5:
771          - revising the lab_sea experiment to make it a more useful (i.e. stable
772            and representative of an actual model run). This was done by generating a
773            (winter) pickup to start from, switching back the main experiment dynamic
774            solver from evp to lsr, having one of the experiments use the free drift solution.
775        part 2: seaice_growth.F revisions 1.76 to 1.85
776          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
777          - Sorting out the various fields units and sign (set early on and reset at the end)
778            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
779            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
780          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
781            and simplifying logical expressions to further improve readibility.
782        part 3: seaice_growth.F revisions 1.86 to 1.89
783          - Re-organize the blocks of code more logically.
784          - Merging the '_if.F' pieces that add something new.
785    o pkg/thsice:
786      - vectorize thsice_solve4temp and thsice_get_exf.
787        Problem: thsice_solve4temp has an unvectorizable statement that
788        might also be problematic for TAF
789      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
790        does not change the verifcation experiment, but will change all
791        experiments that have this flag undefined (not tested in verification);
792        a little reorganization to save a few 2D fields and recomputations
793      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
794      - 2nd step:  fix some store dirs
795        o seems to work somewhat, i.e. using ifort but not g77
796        o likely cause are incomplete init. or recomputation
797        o start verification/global_ocean.cs32x15/input_ad.thsice
798    o pkg/obcs: add support for exch2
799      - the position of the boundary and prescribed values are specified using
800        a global domain with exch2 facets stacked
801        - in x for N,S boundaries (like W2_mapIO=-1)
802        - in y for E,W boundaries (so E,W boundaries do not overlap)
803    o pkg/mdsio: add support for writing global sections with exch2
804        file layout is as for obcs described above:
805        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
806        - for y-z sections, facets are stacked in y
807    o pkg/thsice:
808       - change a few routines for better vectorization: thsice_albedo.F,
809         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
810         not affected, but in particular the latter routine has changed
811         dramatically (not necessarily easier to read now).
812       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
813       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
814    o verification/lab_sea:
815      - overhaul of the forward model experiments. The main motivation
816        for this revision is that lab_sea has proven quite fragile (when
817        changing the sea-ice code, and switching platforms) to a point
818        when failures were very hard to attribute to specific code problems.
819      - the suspected reason for this fragility is noise amplification by evp so,
820        to start with, we decided to replace evp with lsr in the main experiment.
821      - the input.lsr experiment thus became obsolete and was removed.
822      - it was replaced with the input.fd experiment that uses an
823        analytical "free drift" solution as the ice velocity field.
824      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
825        will hopefully allow us to discriminate problems due to dynamic solvers
826        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
827        us to test additional options, along with the salt plume package.
828      - Finally a pickup was generated (at the end of a one year run) to
829        make the tests more representative of an actual model run. Previously
830        the tests starting point was a 1m thickness of ice everywhere.
831    o pkg/seaice:
832      - introducing S\R seaice_freedrift.F that compute the
833        analytical solution to an approximate ice momentum
834        equation (i.e. the simple stress/coriolis balance).
835      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
836        of the free drift velocity field, and enable its use.
837        To actually use the free drift solution as the model ice
838        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
839    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
840    
841    checkpoint62l (2010/10/04)
842    o pkg/seaice:
843      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
844      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
845       version (with USE_ORIGINAL_SBI undef);
846    o add hooks for new packages OASIS, the package will follow
847      (hooks exclude the seaice pkg for now)
848    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
849      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
850      rather than mdsio_readvector.F/mdsio_writevector.F, within
851      adread_adwrite.F to read/write adjoint-related tapes to disk.
852    o eesupp and pkg/mdsio: ALLOW_WHIO
853      Option to write/read 2D fields to files including tiles halos.
854      The main purpose is for adjoint related "tape I/O".
855      The secondary purpose is for debugging phases.
856      A word on those rather specifically intended purposes.
857      The code was meant to be stripped down to the bare minimum.
858      Typically, there is a unique and basic mapping to the global
859      buffer (tile by tile, then proc by proc, then level by level), and
860      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
861      meant to generate user friendly outputs of various shapes and forms.
862      Rather it is intended, for the knowledgeabale developers,
863      to be largely independent of the many mdsio options, to allow
864      outputs of tiles+halos in debugging phases and in adjoint runs,
865      and to allow some flexibility in tuning (adoint) I/O depending on each
866      file system behavior. With regard to tuning, most of the potential knobs
867      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
868      to specify directories, to specify the typical size of I/O calls, etc.)
869      are not yet included, and will be added if they prove useful.
870    o pkg/seaice:
871       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
872    o pkg/seaice:
873       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
874       code (seaice_budget_ice_if.F) which enable to recover old standard
875       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
876       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
877    o model/src (rStar):
878       use simple average (not area weighted) of rStarFac at U,V point when using
879       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
880       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
881    
882    checkpoint62k (2010/09/17)
883    o adjoint
884       * changed verification/global_ocean.cs32x15 ; adjoint now tests
885         Adams-Bashforth 3 + NLFS + RSTAR
886       * some more modifs required for ECCO-GODAE v4
887    o pkg/seaice
888       add SEAICE_AGE_VOL option to use volume instead of area for
889       integrating SEAICE_AGE
890    o model/src:
891       first check-in of sigma & hybrid-sigma coordinate code ; also includes
892       non-linear free-surface parts ; but pressure-gradient not yet coded.
893    o pkg/ptracers:
894       option for ptracer to convert Salt Relax into additional EmP.
895        tested in exp. global_ocean.90x40x15.dwnslp (update output)
896    
897    checkpoint62j (2010/08/25)
898    o pkg/ggl90:
899       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
900    o pkg/dic: car_flux.F, phos_flux.F
901      - reduce number of exp-calls in order to improve performance
902      - clean up a little (replace fields by their macros, etc., fix
903        typo in CPP-flag)
904    o pkg/ggl90: minor changes
905      - GGL90diffKrS was removed --> always use GGL90diffKr
906      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
907      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
908        (commented out for now)
909      - change in max/min operations to ensure that smoothing is ok
910      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
911      - always use diffKrNrT as background profile (i.e. never use diffKr field)
912    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
913    o pkg/dic:
914      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
915        vectorization
916      - small bug fix in insol for the unlikely case of a cartesian grid
917      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
918        + now vectorize, which also removes adjoint recomputations;
919        + replace integer maksp1 by _RL maskp1
920        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
921    
922    checkpoint62i (2010/07/21)
923    o pkg/flt:
924      - with OBCS: stop floats which enter the OB region
925    o model/src:
926      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
927        for implicit vertical advection.
928    o pkg/seaice:
929     - account for melting in seaice age evolution.
930     - remove double counting of seaice ridging effect on seaice age.
931    
932    checkpoint62h (2010/06/18)
933    o pkg/exch2:
934     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
935    o tools/genmake2
936      - remove "-pdefault" option: redundant with the use of "packages.conf";
937      - remove file pkg/pkg_default : set the default as a pkg group
938        ("default_pkg_list") defined in pkg/pkg_groups;
939      - fix for case pkg/pkg_depend is missing (was hanging before);
940      - add option "-pgroups" to specify a different pkg_groups than the default.
941    o verification/adjustment.cs-32x32x1:
942       add a "minimal" set-up test (code_min & input_min) which only compiles
943       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
944    o tools/genmake2
945      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
946      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
947    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
948      files are nearly the same anyway.
949      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
950       - redefinition of tau(i,i) (by a factor of ustar)
951       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
952       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
953       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
954       - replace
955         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
956         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
957         by
958         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
959         (changes results)
960       -> exf_bulkformulae v1.22,
961          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
962          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
963                    output.txt 1.63
964           offline_exf_seaice: output.seaicetd.txt 1.7
965           seaice_obcs: output.txt 1.10)
966      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
967       -> exf_bulkformulae v1.23,
968          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
969          and global_ocean.cs32x15.icedyn (only 11 matching digits)
970      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
971    o adjoint of exch-1:
972     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
973       (note: was already like this when using EXCH-2) and remove flow dir
974       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
975     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
976     - update pkg/exch2 diff list.
977    
978    checkpoint62g (2010/05/19)
979    o eesupp/src (exch-1):
980     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
981       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
982       (renamed to exch1_*rx_cube.F).
983     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
984       to call new exch1 S/R ; update Makefile and .cvsignore.
985     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
986       exch2_xy_rx later)
987      Note: after updating your code, need to run "make clean" in eesupp/src
988    o test experiment bottom_ctrl_5x5:
989       new output_adm.txt with fewer grdchk & less monitor output.
990    o model/src:
991      remove the call to ini_cori in initialise_varia.F (just keep the usual one
992       in initialise_fixed.F). More consistent with coriolis & horizontal grid
993       beeing treated in the same way (ini_grid is not called a 2nd time).
994    o pkg/exf:
995      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
996      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
997      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
998      - cosmetic changes to exf_bulkformulae.F to make it look more like
999        exf_bulk_largeyeager04.F
1000    o eesupp/src (exch-1):
1001      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1002      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1003        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1004        (even without using MPI).
1005      - Message mode: move RecvAck setting (indicator of buffer being ready)
1006        from send_put to recv_get S/R (was useless before, but not sure if
1007        it's much more useful now);
1008      - Switch the order of sync: MPI-proc 1rst and then threads;
1009      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1010      - fix AD code for communication mode ='get' (but not used).
1011    o model/src:
1012      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1013      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1014    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1015    o pkg/ctrl: require a specific set of control variables and exf-flags for
1016      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1017    o model/src:
1018     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1019       1rst forward sweep, to avoid over-writing output files during recomputations
1020       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1021     b) 2nd version:
1022      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1023      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1024         writePickupAtEnd) + seaice & ptracers output;
1025      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1026    o model/src:
1027      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1028    o pkg/exch2:
1029      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1030      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1031    o pkg/autodiff & exch2:
1032      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1033      (for now, only if ALLOW_EXCH2 is defined).
1034    o pkg/autodiff:
1035      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1036        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1037       + clean-up comments (_RS is not always real*4)
1038      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1039      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1040        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1041    o testreport (AD-tests):
1042      no longer link files from dir "../input" (1rst link files from
1043      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1044    
1045    checkpoint62f (2010/04/29)
1046    o model/src/the_main_loop.F:
1047      adjust store directives for seaice evp and multicategory according to
1048      pkg/ecco/the_main_loop.F
1049    o adjoint:
1050      global_sum_ad was incomplete (noted many times by many people ;)
1051      nice description by Jean U. as follows:
1052      * allreduce(var) in global_sum.F can be interpreted as
1053        reduce(sum) followed by broadcast of sum.
1054      * The adjoint of that is
1055        sum(adjoint) followed by broadcast(summed adjoint value)
1056        or in other words, allreduce(sum, adjoint vars)
1057      We were missing the sum(adjoint)!
1058      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1059      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1060      The fix should produce 16-digit accuracy between
1061      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1062      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1063      We'll probably change this yet again shortly
1064    o eesupp/src:
1065      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1066    o pkg/icefront
1067      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1068        specification of addmass array based on a 2D field, which is added
1069        at bottommost wet level at each horizontal location.
1070    o model/src:
1071     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1072     layout; (not always compatible with delX,delY setting; commented out for now).
1073    o pkg/exch2:
1074     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1075     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1076    
1077    checkpoint62e (2010/04/15)
1078    o pkg/obcs:
1079      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1080    o pkg/dic:
1081      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1082        (note: not presently tested in any forward verification exp.)
1083       update tutorial_global_oce_biogeo AD output file.
1084    o pkg/exf:
1085      - account for the variation of albedo as a function of zenith angle
1086        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1087    o build_options:
1088     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1089    o pkg/dic:
1090      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1091      - use binary pickup file for restart;
1092      - initialise atmos-CO2 box from dic_pCO2 parameter;
1093      - fix multi-threaded.
1094    o pkg/rbcs:
1095     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1096       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1097     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1098       and update output.txt
1099    o pkg/kpp:
1100     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1101     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1102       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1103       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1104     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1105       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1106    o pkg/offline:
1107      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1108      (bug was added in version 1.10 on 2007-08-23).
1109    o pkg/offline:
1110      - no need to specify periodicExternalForcing, etc ... to use offline pack
1111      - offline input files no longer just single prec --> parameter offlineLoadPrec
1112    o verification/lab_sea:
1113      change AD test to multi-tile setup and update all 4 AD output.
1114      NOTE: while cost function values remain very similar,
1115      gradients are very different, although gradient checks are self-consistent
1116      Should try to get to the bottom of this (cost function summation order?)
1117    o pkg/dic:
1118      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1119      a weakness of TAF that drops part of double precision in log10 derivative.
1120      <= changes removed since problem has been fixed in current TAF version 1.9.71
1121      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1122    o pkg/ecco:
1123      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1124      update all 4 lab_sea AD output.
1125    
1126    checkpoint62d (2010/03/22)
1127    o build_options:
1128      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1129    o remove unbalanced quote (single or double) in commented line of source code
1130      (may cause some warning with some preprocessor/makedepend versions).
1131    o pkg/seaice:
1132      fix seaice_model.F for adjoint (gael) and update AD results of experiments
1133       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1134    o testreport:
1135      add option '-runonly' (short: '-ro') to just do the run part (without make).
1136    o eesupp: remove JAM communication code (obsolete).
1137    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1138      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1139      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1140      (update also the output).
1141    
1142    checkpoint62c (2010/03/02)
1143    o tools/build_options :
1144       move (some) old optfiles from build_options/ to build_options/unsupported/
1145    o model/src and pkg/exf
1146       surface relaxation -- separating data and data.exf options
1147       The point is to ensure that we specify the surface relaxation
1148       either in data or in data.exf (but not half and half) and to
1149       avoid an accidental relaxation to 0 (which happened if a time
1150       scale was specified but the file name was left empty)
1151    o model/src model/inc and pkg/mom_common
1152       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1153       => addition to the viscosity field as computed by others schemes
1154    o tools/build_options:
1155      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1156        but keep the former optfile for few weeks for smooth transition
1157    o pkg/ecco
1158      - allow user defined cost function contributions
1159         CPP: ALLOW_USERCOST_CONTRIBUTION
1160         USAGE: compute contributions in cost_usercost_all.F
1161      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1162          the two options are complementary.
1163    o pkg/smooth
1164      - migration from contrib to the main repository
1165    
1166    checkpoint62b (2010/01/26)
1167    o pkg/monitor:
1168      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1169        (in case someone forgot to update customized pieces of code)
1170    o nonHydrostatic:
1171      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1172      - add a simple 2-D experiment (short_surf_wave) to test it.
1173    o pkg/icefront:
1174       adding the shell of, and the hooks to, a new package that
1175       will model melting and freezing of vertical glacier ice fronts
1176    o momentum:
1177      add diagnostics of momentum tendency from Hydrostatic pressure gradient
1178       (without surf.pressure term: would need a 2nd filling since implicit term).
1179    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1180      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1181      cannot deal with the former
1182    o cleaning:
1183      - remove all (except OpenAD) old TLM output from results_ad dirs.
1184      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1185      - comment out maskH definition (replaced by maskInC)
1186    o pkg/monitor:
1187      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1188        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1189    
1190    checkpoint62a (2010/01/15)
1191    o model/src:
1192      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1193    o pkg/diagnostics:
1194      - add optional level number diagnostics (i.e., level number to be define
1195        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
1196      - strictly check for valid parser-code(10) ;
1197      - check if adding diag to the list from the right place.
1198    o pkg/longstep:
1199      - change parameters and fix tracer conservation with rstar/nonlinear free surface
1200    o diagnostics:
1201     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
1202       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
1203    o pkg/diagnostics:
1204     - Add option for writing vertical integral (sum of selected levels) of an output
1205        field instead of writing output field levels. Activate this option on a per
1206        output-file basis, by setting the 2nd character of fileflag to 'I'.
1207     - Add field-specific information relative to level integral in 3rd postion
1208        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
1209        vertically (x level-thickness x hFac), "r"=same but without hFac.
1210    o do_the_model_io:
1211      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
1212        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
1213        writing pickups and stopping.
1214    o pkg/diagnostics (for now, only with mdsio):
1215      - write time information to meta file (and modify accordingly rdmds.m) :
1216        time-averaged diagnostics output: write starting and ending time of the
1217        time-averaging interval ; snap-shot diagnostics output remains unchanged;
1218    o pkg/timeave:
1219      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
1220        always Nr), now assumed to be equal to number of levels of averaged field;
1221        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
1222    o pkg/sbo:
1223      - fix ocean bottom pressure global-average & 2-D time-ave output (was
1224        neither initialised nor filled).
1225      - add starting iteration in suffix of global-average output file
1226        (to avoid over-writing the file after a restart)
1227      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
1228    o time-average:
1229      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
1230        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
1231         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
1232        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
1233      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
1234      - fix missing accumulation for pkg/opps.
1235      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
1236         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
1237      - fix initialisation of time-ave vars and do only full time-step increment
1238        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
1239    o pkg/layers:
1240      - use standard RW pkg S/R to write the output
1241        and remove local write_fld version (which had a problem).
1242      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
1243      - fix LAYERS_CALC argument list.
1244    o pkg/timeave:
1245      - store cumulative-time in a simple tiled array (drop the level index)
1246      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
1247    o pkg/ocn,aim_compon_interf
1248      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
1249    
1250    checkpoint62  (2009/12/23)
1251    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
1252        (was not previously tested in any other exp.)
1253    o pkg/monitor:
1254      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
1255        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
1256        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
1257      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
1258      - change del2 calculation.
1259      - use interior masks (instead of maskH, <- to be remove).
1260      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
1261    o mask & obcs:
1262      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
1263      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
1264        (called after packages_init_fixed)
1265    o pkg/obcs:
1266      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
1267        Fixes bug in obcs+exf with nSx*nSy.GT.1
1268      - fix multi-tile handling in obcs balance code
1269    o nonHydrostatic:
1270      - Implement AB-3 for non-hydrostatic vertical momentum ;
1271        (change ordering of var. stored in pickup file when using NH)
1272      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
1273      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
1274        (in prep. for new NH free surface form).
1275    o pkg/obcs:
1276      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
1277    o model/src:
1278      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
1279    
1280    checkpoint61z (2009/12/01)
1281    o nonHydrostatic:
1282      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
1283        a spurious source of energy in simple baroclinic adjusment test case.
1284      Update all non-hydrostatic exp output.
1285    o model/src (3-d solver):
1286      Change again 3-D solver free-surface RHS term when exactConserv=T:
1287        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
1288        (which was not the case with previous formulation).
1289      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
1290      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
1291    o nonHydrostatic:
1292      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
1293        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
1294      - change 3-D solver to work with r* (for now, only with linear free-surf.)
1295      - add few debug diagnostics (cg3d_x, residual)
1296    o model/src:
1297      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
1298        update output of exp. global_ocean.cs32x15.viscA4
1299    o update output of exp. global_ocean.cs32x15.icedyn after removing
1300      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
1301    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1302    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
1303      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
1304    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
1305      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
1306      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
1307      to test this code
1308    o pkg/cd_code:
1309      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
1310       C-grid momentum. D-grid velocity used to be stepped forward in time with
1311       Adams-Bashforth only on surface pressure term. Tests show that using AB on
1312       D-grid coriolis term improves stability (as expected from CD-scheme paper).
1313      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
1314      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
1315       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
1316       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
1317      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
1318           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
1319    o pkg/obcs:
1320     - fix bug in initialisation (broken since Oct 1rst modification)
1321       for useOBCSprescribe without useEXF.
1322    
1323    checkpoint61y (2009/11/15)
1324    o pkg/seaice
1325     - change (once again) the discretization for the evp solver: rather than
1326       squaring the averages of strain rates, average the squares to give
1327       a better approximation to VP behavior (in simple test); this breaks
1328       verification experiments that use EVP (lab_sea and lab_sea.hb87)
1329        --> update outputs
1330    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
1331      to improve vectorization of adjoint code on TARGET_NEC_SX
1332    o verification/vermix:
1333      - change vermix to a more "classical" 1d column with high vertical
1334        resolution, seasonal heat flux forcing and constant wind forcing
1335        --> update outputs
1336    o pkg/seaice
1337     - fix diagnostics of principal stress components for EVP
1338     - add optional diagnostics of non-linear convergence for LSOR solver
1339     - make maximum zeta a runtime parameter
1340    o model/src (3-d solver):
1341      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
1342       which consisted in removing the Surf. Non-Hydrostatic pressure from the
1343       whole column and adding it to Eta (inspired from Casualli, 1999):
1344       Only affects 3-D solver initial guess and only if using ExactConserv,
1345       but tests did show a degradation of solver convergence. For this reason,
1346       decide to disable this piece of code.
1347       to recover previous version, just set zeroPsNH = exactConserv (line 78).
1348      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
1349    o pkg/ggl90:
1350     - fix previous modif (unfortunatly has not been documented here).
1351    o pkg/seaice/autodiff:
1352     - add CPP flag to include clipping of zeta in EVP code;
1353       although clipping of zeta is not necessary for EVP and not recommended
1354       it was done by default, now clipping is disabled by default
1355     - modify computation and store zetaC/Z in seaice_evp for TAF
1356     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
1357     - change seaice_calc_viscosities/strainrates for better
1358       vectorization after AD by TAF
1359     - rearrange common blocks in SEAICE.h once again for easier dumps of
1360       adjoint output, adjust adcommon.h and g_common.h
1361     - change flux form of default advection scheme for better vectorization
1362       of adjoint code
1363     - modify lab_sea/input.lsr to test the flux form of default advection
1364       scheme
1365    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
1366      transition in checkpoint61r)
1367    
1368    checkpoint61x (2009/10/19)
1369    o adjoint: adding two new verification experiments
1370      * tutorial_global_biogeo: an online dic sensitivity experiment
1371        (work with G. Forget)
1372      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
1373        (an update of the Dutkiewicz et al., 2006 paper)
1374      Both use the same CO2FLUX cost function, but different controls
1375      Gradient checks look good, but some recomp. could still be traightened out
1376      Should add xx_dic control variable to test at some point
1377    o model/src:
1378      add run-time parameters to check and/or mask initial Temp & Salt
1379    o pkg/ptracers:
1380      apply zonal filter (if used) to all passive tracers
1381    
1382    checkpoint61w (2009/10/12)
1383    o adjoint:
1384      * update and finish work on adjoint of dic package (G. Forget)
1385      * start adjoint of offline package
1386      * bug fix for cube-sphere TLM code (active_file_g.F)
1387    o tutorial_global_oce_optim:
1388      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
1389      and add SIZE.h_mpi for MPI testing
1390    o pkg autodiff
1391     - fix bug in autodiff_restore
1392     - make genmake2 remove comments and empty lines from ad_input_code.f in
1393       order to reduce file size (new script file remove_comments_sed)
1394    o allows to specify vertical profile of vertical viscosity (viscArNr)
1395    o pkg autodiff
1396      autodiff_ini_model_io: comment out writing of grid information to netcdf
1397      files, because at this time the grid fields are a bunch of zeros
1398      (this is analogous to ini_mnc_vars.F)
1399    o pkg seaice/autodiff:
1400     left-over from removing the 3-time-level fields:
1401     - small rearrangement of common blocks (SEAICE.h)
1402     - fix field declaration in order to get meaningful output in
1403       adseaice.*.nc (adcommon.h)
1404    o pkg obcs:
1405     - go through NH code only if nonHydrostatic=T
1406     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
1407     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
1408       => Update output of experiment seaice_obcs
1409     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
1410     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
1411     - fix restart for useOBCSprescribe + useEXF
1412    o pkg ctrl
1413     - make obcs as control parameter work also with useSingleCPUio
1414     - replace a few sny and snx by Ny and Nx to be consistent with
1415       ctrl_set_globfld_x/yz.F
1416    o pkg seaice
1417     - re-introduce global field frWtrAtm for the case of
1418       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
1419     - catch the case of an empty filename in seaice_cost_init_fixed.F
1420    o pkg ecco:
1421     - small bug fixes in the_main_loop
1422      . fix order of monitor arguments
1423      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
1424      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
1425        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
1426     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
1427       imbalance diagnostics for wmean_h/sflux = 0
1428     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
1429     - catch the case of empty filenames in ecco_cost_init_fixed.F
1430       and ecco_readparms.F
1431     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
1432       to make this statement meaningfull in ecco_cost_weights.F
1433    o pkg zonal_filt:
1434      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
1435      - when using rStar, filter uVel*hFacW instead of uVel
1436       (tested without topography: fix a Pb of growing instability with NLFS)
1437    o pkg/aim/thsice:
1438     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
1439      (works as SST restoring)
1440    o pkg/thsice:
1441     -add specific parameter for salt restoring in slab mixed-layer
1442       (by default equal to the temperature restoring)
1443    
1444    checkpoint61v (2009/09/21)
1445    o pkg/kpp:
1446     -add double diffusive contributions as a hack, turned off by default
1447      for now, and the code can be excluded with a CPP-flag
1448      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
1449     -add a verification experiments to "vermix" to test this code
1450    o pkg/mom_common:
1451      Move computation of length scales to mom_init_fixed.F (avoid recomputation
1452      at each time-steps*levels).
1453    o pkg/layers:
1454      Created a new package for computing volume fluxes in temperature or
1455      [not yet implemented] density layers, e.g. for calculating residual
1456      overturning circulations.
1457    o pkg/diagnostics:
1458      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
1459    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
1460    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
1461      To avoid mixing type (RS/RL) of input/output array argument,
1462      replace single mixed-type array with a pair from each type (RS/RL).
1463    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
1464      is now implemented for all pkgs (previously only done for the main pickup)
1465    
1466    checkpoint61u (2009/08/25)
1467    o pkg/obcs:
1468      - change OB?eta from _RS to _RL and put them into a separate commen block
1469      - add code to read OB?eta from a file via obcs_prescribe_read: the code
1470        compiles and does not destroy any other experiments, the data is read
1471        properly, but the code is not tested in actual applications
1472    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
1473      create a meaningful unit attribute for the time coordinate variable
1474    o pkg/ebm: add plenty of missing "_d 0" ;
1475       update results of experiment global_ocean_ebm (fwd + adjoint tests)
1476      Notes: several pieces of code only works for (very) specific set up
1477       (domain size, lat range, etc ...); should be documented & stop if one
1478       of those assumptions is not meet.
1479    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
1480       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
1481          and offline_exf_seaice (seaicetd + adjoint).
1482    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
1483       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
1484        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
1485    o few changes to pass when compiling with strick checking of arguments
1486       across S/R (allow to find few bugs in S/R calls).
1487    o pkg/seaice:
1488     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
1489       2d-fields, for slightly better performance
1490    
1491    checkpoint61t (2009/07/22)
1492    o pkg/seaice:
1493     - remove unused variables in seaice_evp
1494     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
1495    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
1496       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
1497       each processor opens a different file (a fix from Matt).
1498    o cg2d:
1499       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
1500       this reduces number of EXCH calls by 2 when using exch2.
1501       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
1502       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
1503    o pkg/thsice:
1504       add code for Near Infra-Red albedo (from Jeff)
1505       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
1506    o ini_model_io:
1507       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
1508       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
1509       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
1510    
1511    checkpoint61s (2009/06/30)
1512    o pkg/exch2 (exch2_rxN_cube*):
1513       remove last BARRIER (no need to synchronise after getting data from shared
1514       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
1515    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
1516      and generate new output (for the 2 tests) using default rotationPeriod.
1517    o pkg/exch2:
1518      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
1519        (was already the case with AUTODIFF_EXCH2 defined)
1520      - add bj in exch2 arrays and S/R.
1521      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
1522        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
1523    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
1524      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
1525        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
1526      - verification experiment natl_box.longstep
1527    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
1528      allow different versions of ifort (8 or 9) and different versions
1529       of mpi (mpich or mpich2) to be used with the same optfile.
1530      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
1531       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
1532    o pkg/seaice:
1533      fix previous modif (3-level field removed) for old-pickup reading
1534    
1535    checkpoint61r (2009/06/25)
1536    o pkg/seaice:
1537     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
1538      1. introduce fields for time step (N-1)
1539      2. do not use levels 2 and 3 anymore (but keep them)
1540      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
1541         includes changes to pkg/thsice/thsice_get_velocity.F,
1542         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
1543         pkg/obcs/obcs_apply_uvice.F.
1544     - completely remove code for leap-frog time stepping for second order
1545       advection
1546     - adjusted adjoint accordingly;
1547       gradient checks have improved by an order of magnitude!
1548    
1549    checkpoint61q (2009/06/22)
1550    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
1551     - the boundary conditions along open boundaries are unclear, because the
1552       associated masks are set to zero and are thus treated as closed when
1553       applying the slip-boundary conditions.
1554     - move initialisation of grid variables from seaice_init_varia to _fixed
1555    o adding doc/diags_changes.txt
1556    o model/src:
1557      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
1558       to avoid "_diags" naming if no relation to pkg/diagnostics.
1559      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
1560       file and only call PLOT_FIELD_XYZ if debugMode=T.
1561      remove few PLOT_FIELD_XY calls outside initialisation.
1562      remove few unnecessary BARRIER.
1563    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
1564      of salt_plume package in Southern Ocean
1565    o pkg/thsice:
1566     - fix hOceMxL in overlap (needed for sea-ice advection);
1567       update output of experiment global_ocean.cs32x15.icedyn.
1568    o pkg/seaice:
1569     - make the (placeholder-)tracer IceAge a little more meaningful
1570      by avoiding ridging of age due to convergent ice flow
1571     - add diagnostics for surface temperature, atmospheric and oceanic
1572       heat flux, and atmospheric and oceanic ice growth
1573    
1574    checkpoint61p (2009/06/10)
1575    o eesupp (global_max & global_sum):
1576     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
1577     - remove starting & endding barrier (no longer needed)
1578    o pkg/mdsio, writelocal:
1579       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
1580       (remove the STOP): uses shared buffer IO to store data from all threads
1581       and then let master-thread write nThreads tiles.
1582    o pkg/mdsio (read/write field):
1583     - tiled IO done in 1 piece (all levels at a time);
1584     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
1585     - multi-threaded: allow to read/write local (non-shared) array
1586       (was already working with singleCpuIO ; now works also without);
1587       => no longer needs barrier call after reading a file (added inside
1588       mds_read/write field).
1589     - move barrier calls outside gather/scatter_2d to mds_read/write_field
1590    o pkg/obcs/exf
1591      - exf_getffieldrec.F: add a few ". _d 0" and
1592                            add code to catch the case fldperiod = 0.  
1593      - obcs_precribe_read.F: change if statements so that they match
1594                              the variable type (_RL)
1595      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
1596        exf_iprec) as part of namelist EXF_NML_01
1597    o pkg/mdsio:
1598      - read/write tiled (local) files: read/write 1-level tile chunk at a time
1599        (instead of segment of length sNx); expected to speed up tiled IO.
1600    o pkg/exch2:
1601      - take buffer copy from/to array out of S/R exch2_send/recv into new
1602        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
1603        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
1604      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
1605      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
1606        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
1607        including Topology header file (and common blocks).
1608      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
1609        remove 2nd exch call in exch2_s3d_rx (no longer needed).
1610      - document S/R arg. list (+ update some comments)
1611    o pkg/seaice:
1612      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
1613        temperature and humidity over sea ice based on climatological values.
1614      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
1615        of LSR (this change is expected to change the results slightly because now
1616        it uses slightly difference moduli from the second last LSR solution, but
1617        that is more consistent with the stress computations; this part of the code
1618        is not tested in the verification experiments)
1619      - fix diagnostics for flux of ice in case of B-grid
1620      - turn strain rates eij and press into global fields within global
1621        common block in SEAICE.h for more straighforward diagnostics
1622      - fix diagnostics for principal stress components, press, zeta, eta
1623        to give something meaning full
1624    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
1625      new output (all 4 tests) using default rotationPeriod.
1626    o pkg KPP:
1627      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
1628      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
1629        and normal grid from 1 to Nr)
1630    o Fix computations of L4rdt in mom_calc_visc.F
1631    o eesupp:
1632      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
1633      should be called before a "stop" if we know that all process are going
1634      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
1635    
1636    checkpoint61o (2009/05/26)
1637    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
1638    o model/src/ini_curvilinear_grid.F:
1639       compute angleSin/CosC when they are not read from a file
1640    o pkg/seaice:
1641       add pseudo time stepping for LSOR
1642    o pkg/exch2:
1643       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
1644    o pkg/seaice:
1645       Adding separate sea ice albedo, drag coefficients, and HO in Southern
1646       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
1647    o SingleCpuIO:
1648       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
1649    o pkg/seaice:
1650       put exchanged variable in (local) common block for MPI+Multi-Threads
1651       to work (necessary with exch1, and for now with exch2 too).
1652    o verification: to get more experiments tested with mpi, mth and mpi+mth,
1653      change tiling of:
1654       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
1655       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
1656      update output of exp:
1657       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
1658       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
1659      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
1660                       (note: output.txt generated on faulks using only 1 tile)
1661    o eesupp & mdsio (SingleCpuIO):
1662     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
1663       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
1664       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
1665     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
1666     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
1667       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
1668    o pkg/exch2:
1669     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
1670       read parameter file "data.exch2" if it exists; otherwise try default regular
1671       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
1672     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
1673       with new code (not to be used, just as a backup solution).
1674     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
1675       in utils/exch2/input.
1676    
1677    checkpoint61n (2009/05/12)
1678    o eesupp & mdsio (SingleCpuIO):
1679      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
1680        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
1681        receive real*4 array (instead of real*8) to read/write 32.bit files.
1682        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
1683         and remove new mapping S/R)
1684    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
1685      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
1686        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
1687        when using exch2. Add S/R to map global io-buffer to global model array.
1688      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
1689    
1690    checkpoint61m (2009/04/29)
1691    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
1692      and add 3 other S/R for other types (R4,R8,RS).
1693      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
1694    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
1695     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
1696     - reduce number of macro definitions (keep only those which are used);
1697       can always call directly the corrresponding S/R if needed.
1698     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
1699       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
1700     Fixed wrong type of arg in:
1701       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
1702       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
1703     To fix: global_sum of var in common block is wrong (multi-threaded) in:
1704       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
1705     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
1706    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
1707      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
1708    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
1709    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
1710      edges are closed (zero depth); might happen with "blank tiles";
1711      for now, disabled if using OBCS.
1712    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
1713      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
1714    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
1715      to reduce length of 1.D array print in STDOUT.
1716    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
1717      + use 48 tiles (16x8): this will allow to test "blank tiles".
1718    o start to test MPI + multi-threaded (change testreport to skip tests
1719      where number of tiles do not match).
1720    o genmake2: add option "-omp" to turn on Open-MP ;
1721      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
1722    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
1723      and keep the original tile numbering. Note: compatible with old
1724      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
1725    
1726    checkpoint61l (2009/04/07)
1727    o Overlaps had been forgotten in calculating ijk keys : fixed
1728    o fix cyrus makedepend for gcc 4.4
1729    o experiment fizhi-cs-aqualev20:
1730      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
1731      and generate new output. Note: new output is much closer to the old
1732      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
1733      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
1734    o pkg/fizhi:
1735     - change to avoid indices going deliberately over array-bounds
1736     - remove unnecessary MPI stuff
1737     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
1738     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
1739       does not go over array-bounds and therefore returns reliable output.
1740     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
1741       this S/R has 4 output arguments, which are used inside "get_alarm";
1742       when it is called with the same variable "ndum" in place of several
1743       output arguments, this produces weird side effect inside "get_alarm"
1744      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
1745       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
1746       address) and produces error.
1747    o tools/gemake2: (March 27-29 2009)
1748      with option "-mpi": link *_mpi files from "MODS" dir (this is what
1749      testreport does).
1750    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
1751    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
1752       update lab_sea.lsr & lab_sea.salt_plume results
1753    o pkg/seaice:
1754      Major overhaul of the LSOR solver: change discretization from original
1755      finite differences to finite volume. The old routine is still in the
1756      file seaice_lsr.F and can be turned on with the CPP-flag
1757      SEAICE_OLD_AND_BAD_DISCRETIZATION
1758      Along with this change, the discretization of the strain rates is changed.
1759      The same flag turns on the old discretization in seaice_calc_strainrates.F
1760      All verification experiments with seaice are affected (except for
1761      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
1762      results by setting the above flag.
1763      Further changes involve changes in defaults:
1764      - ALLOW_FLOODING is defined and turned on by default
1765      - SEAICEadvSnow = .true. is now the default
1766      - SEAICEadvSalt = .true. is now the default
1767      - SEAICEadvAge  = .true. is now the default
1768      - SEAICE_clipVelocities  = .false. is now the default
1769                                         (as per J. Zhang's recommendation)
1770      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
1771        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
1772      - seaice_growth: replace computation of UG by a simple copy from wspeed
1773    
1774    checkpoint61k (2009/03/18)
1775    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
1776      seaice_lsr: fixed a few metric terms,
1777                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
1778                  add more debugging diagnostics
1779      seaice_evp: removed superfluous many metric terms of FV discretization
1780                  of stress divergence
1781                  affects lab_sea, lab_sea.hb87
1782      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
1783                  of stress divergence for non-evp solver
1784                  (this part is not tested anywhere)
1785      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
1786                  they were effectively only half slip
1787                  affects lab_sea.hb87
1788      updated all relevant verification experiments (except lab_sea//output_adm.txt
1789        which was left over, but fails at level 7 & 6)
1790    
1791    checkpoint61j (2009/03/17)
1792    o pkg/seaice: turn a few hard wired parameters into run time parameters
1793    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
1794      time in seconds as promised by the usints in seaice_monitor and exf_monitor
1795    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
1796      that are not cubed-sphere grids
1797    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
1798    o pkg/ctrl:
1799      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
1800    o non-hydrostatic (calc_gw.F):
1801      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
1802      update output of exp. global_ocean.cs32x15.viscA4
1803    o remove backward compatibility for thetaMin,phiMin
1804      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
1805    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
1806      interpolated wind field not only for curvilineargrid=.true., but also
1807      for a rotated grid (rotateGrid=.true.)
1808    o pkg/exf: add capability to bypass interpolation for runoff
1809      by setting yet another CPP-flag
1810    o eesupp/src, B-grid exchange:
1811      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
1812    o autodiff
1813      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
1814      allows to switch to single-prec common blocks;
1815      corresponding switch occurs in tamc.h, integer isbyte
1816      TAF store directivs "byte" and "kind" seem equivalent;
1817      Most tamc.h have been updated correspondingly.
1818    
1819    checkpoint61i (2009/02/13)
1820    o autodiff:
1821      fix autodiff_sore/_restore indices for obcs
1822      (spotted by I. Hoteit, M. Mazloff)
1823    o pkg/autodiff, pkg/ctrl:
1824      Add flag to reduce all tapelev I/O to single-prec.
1825      In data.ctrl set
1826        doSinglePrecTapelev = .TRUE.
1827    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
1828      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
1829    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
1830      real fresh water flux (not yet)
1831    o pkg/mdsio & rw:
1832     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
1833     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
1834    o pkg/flt:
1835     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
1836       init_fixed & ini_varia.
1837     - clean-up & simplify linear interpolation S/R:
1838       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
1839     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
1840     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
1841     - add vert. coordinate & horiz. indices to output files.
1842     - change vertical position in initial condition, from index to depth [m].
1843     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
1844       (easier to get to a curvilinear grid) ; delX,delY no longer used.
1845    o pkg/ggl90: a few modifications:
1846     - fix bottom boundary condition, and interpolation of KappaE
1847       near top and bottom
1848     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
1849     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
1850     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
1851    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
1852      (maintain temporary backward compatibility, until next checkpoint)
1853    
1854    checkpoint61h (2009/01/27)
1855    o pkg/diagnostics with "periodic averaging diagnostics":
1856      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
1857    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
1858    o pkg/obcs: fix loop ranges for balancing code
1859    o pkg/flt:
1860     - improve criteria for finding which tile owns a float.
1861     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
1862    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
1863      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
1864      with ocean biogeo)
1865    o pkg/flt:
1866     - do some cleaning and fix the restart ;
1867     - add output.txt in flt_example/results to get this pkg tested.
1868    o genmake2: add an EXTENDED_SRC option and flag.
1869       for now, cannot be turned on on command line (only through genmake_local)
1870    o pkg/mdsio: read/write vector:
1871     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
1872     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
1873       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
1874     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
1875      (drop to 4 digits matching for grad). But this test does not look very
1876      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
1877    
1878    checkpoint61g (2008/12/29)
1879    o pkg/flt:
1880      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
1881       + make OPTIONS file more standard.
1882      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
1883      - fix _BYTESWAPIO CPP-Flag
1884      - standard reading of file-parameter "data.flt"
1885      - fix argument list of S/R FLT_RESTART
1886      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
1887    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
1888    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
1889      a still unfixed compiler/optimization bug
1890    
1891    checkpoint61f (2008/11/21)
1892    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
1893      update results of global_ocean.cs32x15.icedyn test.
1894    o move getcon.F from model/src to pkg/fizhi.
1895    o pkg/exf: add parameter for extrapolation of temp up to the surface
1896       and option to prevent negative evap (in bulk_largeyeager04 only).
1897    o Prather Advection scheme: fix tracer conservation for divergent flow
1898      (e.g., when using NonLin Free-Surface).
1899    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
1900    o gmredi (Visbeck-variable-K):
1901     - add more parameters to Visbeck-variable-K.
1902     - use a 5 points average for dSigmaR in Visbeck-K calculation
1903       (more "homogenous": same stencil and same weights as in dSigmaH)
1904     - update output of ideal_2D_oce experiment.
1905    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
1906      (#undef REAL4_IS_SLOW)
1907     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
1908       coordinate variable
1909     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
1910       (surface forcing fields), removes some of the functionality
1911     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
1912     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
1913       probably not all: copy _RS surface flux fields to RL field before
1914       calling DIAGNOSTICS_FILL
1915     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
1916       real*4 (CALL EXCH_*_RS) versions.
1917     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
1918       (generate new output).
1919    
1920    checkpoint61e (2008/10/23)
1921    o gmredi (Visbeck-variable-K):
1922      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
1923      - change computation of Visbeck-K where Slope > Smax :        
1924        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
1925        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
1926    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
1927      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
1928    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
1929    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
1930      does not become too large (to avoid precision problems in implicit-diffusion
1931      solver); update ideal_2D_oce output.
1932    o pkg ggl90:
1933      - in ggl90_cal.F: compute only one set of visc/diff, used to
1934        step forward TKE/T/S/momentum
1935      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
1936        have Prandlt =1)
1937    o gmredi (fm07):
1938      - add lower limit on Transition layer thickness + lower limit on 1/lambda
1939      - allow to set few more params from data.gmredi
1940    o pkg ggl90:
1941          - add missing sqrt(2) factor in computation of mixing length
1942            scale in ggl90_calc.F
1943            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
1944    
1945    checkpoint61d (2008/09/25)
1946    o adjoint modifs
1947      - adapt to new field rhoInSitu
1948      - allow to revert from StoreDynVars2D, StoreDynVars3D
1949        to individual fields
1950        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
1951    o store 3-D (in-situ) density in commom block (DYNVARS.h)
1952     - save 1 rho computation.
1953     - no longer modify T & S inland when using down_slope pkg.
1954    o gad_som : allow to switch to SOM advection for T & S without corresponding
1955      pickup files (using new S/R: MDS_CHECK4FILE).
1956    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
1957      (for useSingleCpuIO to work in multi-threaded)
1958    o pkg/shelfice:
1959     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
1960       with SHELFICEtopoFile in data.shelfice
1961     - move code for reading ice shelf topography and modifying hFacC into separate
1962       subroutines of the shelfice package
1963     - separate initialisation of "fixed" and "variable" variables
1964     - kTopC is not (yet) replaced by kSurfC, although this is possible
1965    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
1966    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
1967      and rename:
1968      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
1969      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
1970    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
1971    
1972    checkpoint61c (2008/08/30)
1973    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
1974      to add mass source/sink of fluid in the interior (3-D generalisation
1975      of oceanic real-fresh water flux).
1976    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
1977    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
1978    o new pkg: down_slope
1979      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
1980      - presently, modify T & S inland (dwnslp_calc_rho.F).
1981        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
1982      - implementation for ocean in P-coords not tested.
1983      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
1984    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
1985      (to facilitate conversion of oceanic pkg to p-coordinate).
1986    o change FIND_RHO to FIND_RHO_2D :
1987      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
1988    o new pkg: cheapaml
1989    
1990    checkpoint61b (2008/08/05)
1991    o exch2:
1992      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
1993      - no longer depend on the order sequence (N,S,E,W).
1994      - 3rd exchange no longer needed (tested with 24 tiles).
1995      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
1996      - exch_UV_A-grid readily available (but not yet tested).
1997      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
1998      (both are no longer needed) in exch_uv: no effect in forward run; but
1999       get truncation error differences with adjoint exch.
2000    o exch2:
2001     - change index-bounds storage (moved from target to local tile,
2002       more intuitive this way) ; rename/remove some variables.
2003     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
2004    
2005    checkpoint61a (2008/07/29)
2006    o exch2/matlab-topology-generator:
2007      fix bug in index bounds for N-S internal exchange (hard to tell if this
2008      had any effect on the solution).
2009    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
2010      is exceeded
2011    o testreport: modify syntax of awk, so that it works also with
2012      awk, and not only with nawk and gawk
2013    
2014    checkpoint61 (2008/06/24)
2015    o autodiff
2016      Change default for TAF usage by removing argument '-nonew_arg'
2017      This changes TAF subroutine argument list (ordering of active var.)
2018      Omission of this flag leads to incompatibility w.r.t. TAMC
2019      To restore TAMC-compatibility, need following modifs:
2020      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
2021      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
2022      Tested TAF version is 1.9.22
2023      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
2024    
2025    checkpoint60 (2008/06/19)
2026    --->>> This is the last checkpoint for which generating the adjoint
2027    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
2028    --->>> by default.
2029    --->>> Future checkpoints will ommit this flag by default.
2030    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
2031    o pkg/grdchk: Add gradient check to etan0 perturbations.
2032    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
2033    o pkg/autodiff: more flexibility in zeroadj.
2034      model/src: modifying do_oceanic_phys.F accordingly.
2035    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
2036    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
2037      special setup of gmredi for which the adjoint is stable
2038      enough for parameter optimization.
2039    o bridging the gap between eddy stress and GM.
2040      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
2041          along with a change in CPP option (now ALLOW_EDDYPSI).
2042      -> when using GM w/ GM_AdvForm:
2043          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
2044          is applied either in the tracer Eq. or in momentum Eq.
2045          depending on data.gmredi (intro. GM_InMomAsStress).
2046      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
2047      The key modifications are in model/src/taueddy_external_forcing.F
2048      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
2049    
2050    checkpoint59r (2008/05/29)
2051    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
2052      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
2053      fix option to read coriolis(@ cell-corner) from files with CS-grid.
2054    o pkg/mnc: add some attributes to standard 1D-coordinate variables
2055    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
2056      mass points, when using mnc for output
2057      - add runtime parameter (missing_value, missing_value_int) to override
2058        default (which is the value of getcon('UNDEF'))
2059    o pkg/mnc: prepare mnc for the actual use of missing values with the
2060      diagnostics package: small fix in mnc_cw_readwrite.template and more
2061      initialisation of never used fields
2062      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
2063      versions
2064    o pkg/thsice/thsice_ini_vars.F added default initial values so that
2065      thermodynamics sea ice solver does not blow up when some initial fields
2066      are missing.
2067    o move from external_forcing_surf.F to ini_forcing.F
2068      the p-coord. hack consisting in using pLoad to set phi0surf ;
2069      update output of tutorial_global_oce_in_p (affected @ truncation level).
2070    o Freshen up a bit hs94.1x64x5, notably:
2071      remove rotationPeriod and tRef=5*0. (adjoint only), and add
2072      exactConserv=.TRUE.
2073    o pkg/generic_advdiff:
2074      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
2075      applies to files where Temperature & Salinity 2nd Order moments are used.
2076    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
2077      this uses a dynamically allocated internal state data structure
2078      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
2079      and requires a fortran 90 compiler
2080    
2081    checkpoint59q (2008/05/06)
2082    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
2083       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
2084    o Refresh tutorial_global_oce_biogeo, notably:
2085      - change bathymetry (put back seamounts in ACC, use hFacs)
2086      - change EOS (POLY3 --> JMD95Z)
2087      - use Bryan-Lewis vertical diffusivity
2088      - use multidimensional advection
2089      - remove old virtual virtual in dic pkg, now done through ptracer pkg
2090      - change a couple of parameters in dic pkg
2091    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
2092    o pkg/obcs: change default to OBCSfixTopo = .true.,
2093      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
2094      - replace "debugMode" with "debugLevel .GE. debLevB"
2095    o implementation of TAF directives for gchem,cfc,dic
2096    o remove "exp5" (replaced by tutorial_deep_convection).
2097    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
2098      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
2099      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
2100      --> changes results in exp4, seaice_obcs
2101    o tutorial_deep_convection :
2102      update the set-up and increase resolution and domain size ; start
2103      from pseudo initial conditions = output at t=120mn in order to see
2104      something happening when running testreport.
2105    o pkg/seaice: add os7mp as an advection scheme
2106                  add check for advection schemes
2107                  add a flag for restoring T and S underneath sea ice
2108    o pkg/my82: add netcdf-support and diagnostics
2109    o thsice pkg:
2110      - Now hsMax limits snow height by turning it into ice following
2111        flooding scheme (and now conserving energy)
2112      - Slight rewriting of the formula in thsice_calc_thick.F
2113      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
2114      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
2115    
2116    checkpoint59p (2008/04/10)
2117    o gchem / dic / cfc :
2118      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
2119      - add new parameter files: "data.dic" & "data.cfc" ;
2120      - various re-arrangement in initialisation & header file ;
2121      - fix tutorial_global_oce_biogeo for multi-threaded test.
2122    o pkg/dic: test for "pickup_dic" file when restarting ;
2123      if no pickup-file, can restart with a re-initialised pH (same as it did
2124      before) providing pickupStrictlyMatch is set to False.
2125    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
2126      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
2127    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
2128      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
2129    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
2130     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
2131       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
2132    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
2133       scheme to use for vorticty-term ;
2134     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
2135       (with default selectVortScheme, return to original discretisation)
2136     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
2137    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
2138    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
2139      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
2140      also fix diagnostics VISCAHW & VISCA4W.
2141    
2142    checkpoint59o (2008/03/07)
2143    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
2144    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
2145      move a few statemens out the main loop into separate loops
2146    o pkg/shelfice:
2147      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
2148        (kg/m^2/s), does not break tests, because in verification/isomip,
2149        rhoConstFresh=rhoConst (by accident)
2150      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
2151      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
2152        new file model/src/seawater.F, so that they are available for all pkgs.
2153      - convert potential temperature into in-situ temperature. This changes the
2154        isomip tests => update tests
2155    o add a flag writePickupAtEnd (default=true) to be able to suppress
2156      writing a pickup at the last timestep
2157    o tools/mpack-1.6 :
2158      - disable automake (not working) and autoconf (not needed).
2159      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
2160        also cleaner with much less compilation warnings.
2161    o pkg/profiles:
2162      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
2163      (for "less than 32 characters name" compiler requirement)
2164    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
2165      conditions that have a different sampling frequency than S/T/U/V obcs
2166    o pkg/diagnostics (stats-diags):
2167      - fix global Min/Max in case 1 processor get only empty tiles
2168    o genmake2: replace (4 times)
2169         make genmake_tc_1.o >> genmake_warnings 2>&1
2170      with
2171         COMM="$CC $CFLAGS -c genmake_tc_1.c"
2172         echo $COMM >> genmake_warnings
2173         $COMM >> genmake_warnings 2>&1
2174      to make genmake2 always see the value of CC as specified in the optfile.
2175    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
2176      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
2177      - modify verification advect_cs test to test SOM-advection on CS-grid.
2178    o pkg/ctrl:
2179      - Rewrite of ctrl_map_ini_ecco.F,
2180        introducing a generic routine (ctrl_map_ini_gen.F).
2181      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
2182    
2183    checkpoint59n (2008/02/09)
2184    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
2185      number in dedicate array "hdiag":
2186      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
2187        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
2188      - many small changes (integer format) for large number of diagnostics
2189      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
2190        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
2191    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
2192      usingSphericalGrid, this allows to define the rotated grid coordinates
2193      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
2194      geographical coordinates according to the inverse of the rotation defined
2195      by the Euler angles, so that Coriolis parameter and online-interpolation by
2196      exf works with the geographical coordinates on XC/YC/XG/YG.
2197      Naturally, this feature does not work with all packages, so some
2198      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
2199      profiles), because there the coordinates are assumed to be regular
2200      spherical grid coordinates.
2201    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
2202      - introduce isopycnal diffusion coefficient control.
2203    o tools/adjoint_options:
2204      - additional control vector components.
2205    o pkg/mnc: have mnc create marginally meaning full coordinate variables
2206      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
2207    o pkg/mypackage:
2208      - add example of read/write pickup for state-var ;
2209      - add entry points to the main code for state-vars diags & write-pickup.
2210    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
2211      transitions for useExfYearlyFields
2212      - add new subroutine that determines the file to read from for
2213        use*YearlyFields = .TRUE. and .FALSE.
2214      - add a verification experiment to global_with_exf that tests
2215        useExfYearlyFields with USE_EXF_INTERPOLATION defined
2216    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
2217      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
2218      subroutines (which could be generated from a template, because they are
2219      almost identical), for now they are included in obcs_prescribe_read.F for
2220      simplicity
2221    o pkg/exf:
2222      - add a little more diagnostic to exf_interp_read (in analogy to
2223        mds_read_field, can be turned off with debugLevel < debugLevA=1)
2224      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
2225        ugly but fast by unrolling short inner loops, inserting a unroll=8
2226        directive in routine lagran, and splitting a loop and making do while the
2227        outermost loop (the latter requires the intoduction of index arrays)
2228    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
2229    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
2230      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
2231    o verification/seaice_obcs: updated for restart test and latest options
2232    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
2233      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
2234      for now this is only available for the C-grid code and also within
2235      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
2236    
2237    checkpoint59m (2008/01/14)
2238    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
2239      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
2240    o gad_som : fix flux output (& diagnostics) to have same units as other  
2241      advection scheme fluxes (was previously multiplied by deltaT).  
2242    o added verification/seaice_obcs both to test seaice open boundaries
2243      and to provide an example matlab scrpt for generating them
2244    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
2245    o pkg/salt_plume: clean up salt_plume_frac.F to
2246      remove redundancy in PlumeMethod 1 and 4
2247    o pkg/kpp: added saltplume diagnostics
2248    o pkg/obcs and pkg/seaice:
2249      - do not set uice and vice to zero when OB*icefile are unspecified
2250      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
2251      - moved seaice tracer obcs after call to seaice_growth
2252    o pkg/salt_plume: added various options for salt plume depth
2253      criterion and for vertical distribution of the salt
2254    
2255    checkpoint59l (2007/12/18)
2256    o pkg/ptracers: new version of ptracers pickup:
2257      read meta file and write only fields which are needed to restart.
2258      ( same logic as main pickup file ; also using pickupStrictlyMatch )
2259    o pkg/seaice:
2260      - add timescale for melting due to warm mixed layer as a means of
2261        setting SEAICE_availHeatFrac more conveniently
2262      - add a CPP-flag/runtime parameter check for flooding algorithm
2263      - reformulated availHeat in seaice_growth.F to be independent of AREA
2264    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
2265      unit changes
2266    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
2267    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
2268      SX vector computer.
2269    o pkg/seaice:
2270      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
2271        seaice forcing fields can now be read only through pkg/exf
2272      - removed some unused halos
2273    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
2274    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
2275      or U/VICE from U/VWIND before computing U/VSTRESS
2276    
2277    checkpoint59k (2007/11/30)
2278    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
2279      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
2280    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
2281      all experiments pass when compile with un-initialised var. checking option.
2282    o added pkg/salt_plume
2283    o script to test restart (for now, in MITgcm_contrib/jmc_script)
2284    o pkg/seaice: new read/write pickup version.
2285      read meta file and write only fields which are needed to restart.
2286      ( same logic as main pickup file ; also using pickupStrictlyMatch )
2287    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
2288    o lab_sea.hb87: modify the domain & update output.hb87.txt :
2289      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
2290      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
2291      process. Fixed here by closing the domain at the Northern boundary.
2292    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
2293    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
2294      a set of consecutive levels in/from a 3-D array.
2295    o pkg/ptracers:
2296      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
2297      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
2298    
2299    checkpoint59j (2007/11/09)
2300    o in pkgs: dic, obcs, offline, rbcs:
2301      standard way to compute coeff. for time interpolation between 2 time reccords
2302      which retains full precision (& make results less dependent on compiler).
2303      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
2304    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
2305      packages instead of reading ice cover and wind speed separately
2306    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
2307     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
2308      to allow to compile customized code before the update)
2309    o cleaning-up:
2310      - fix CPP instruction syntax in pkg/obcs
2311      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
2312        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
2313      - fix some threads issue in IO parts.
2314    o pkg/dic:
2315      - add tons of "_d 0" (--> much better testreports !)
2316       and then update outputs of tutorial_global_oce_biogeo
2317    o pkg/mom_fluxform:
2318      add a special version of momentum advection intended to conserve momentum
2319      next to a bathymetry step or a coastline edge. (default = off = #undef)
2320    o new read/write pickup version:
2321      - for now, only implemented for main (mdsio) pickup file.
2322      - write out only what is needed to restart; merge pickup_nh , pickup_ph
2323        and main pickup together.
2324      - read meta file; read only what is needed to restart; stop if a field
2325        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
2326        if it make sense (even if the restart is not perfect).
2327      - if no meta file, assume that pickup to read corresponds exactly to
2328        a pickup that would currently be written.
2329      - read pickup written in the old format (until checkpoint59i) if it
2330        recognizes an old meta file (no field-list).
2331      - add a meta file in exp. which starts from a pickup: 2 cases:
2332        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
2333         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
2334        b) a meta file describing the content of the associated pickup file
2335         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
2336    o pkg/mdsio & pkg/rw:
2337      - new routine to read a meta file ; new set of routine to read
2338        Multiple-fields file (with meta file).
2339    o added open boundary conditions capability for seaice
2340        HSNOW, HSALT, UICE, and VICE
2341    
2342    checkpoint59i (2007/10/21)
2343    o adjoint:
2344      * fix multiDimAdvection adjoint
2345        (partial recomputation problem by TAF for fVerT(:,:,kDown)
2346        and comlev1 size definition (maxpass vs. max. number of tracers)
2347      * verification/global_ocean.90x45x15 adjoint now tests
2348        NLFS and multiDimAdvection using DST3 (=30)
2349      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
2350    o pkg/kpp: add "_d 0" to real constant (if missing);
2351      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
2352      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
2353    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
2354      for internal parameters related to restart process (formerly from PARAMS.h)
2355      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
2356    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
2357      as argument. (only atm2d & obcs write_pickup have not yet been updated)
2358    o pkg/monitor:
2359      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
2360      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
2361      - account for deep Atmosphere factor and density factor (anelastic)
2362    o added open boundary conditions capability for seaice HEFF and AREA
2363    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
2364      thermodynamics
2365      - requires a little reorganization, which affects the testreport results
2366        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
2367        so that now the conservative form is tested
2368      - add a few comments
2369    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
2370    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
2371    o add new diagnostics to seaice: advective, diffusive fluxes (only for
2372      multidim-advection, for scheme 2 they are not filled) and transports,
2373      thermodynamic growth rates
2374    o change units of EmPmR (inside the code, + within coupling interface)
2375      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
2376      Affects results @ truncation level (cg2d match) and update output of
2377       experiments: lab_sea(6), global_ocean.90x40x15(10),
2378      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
2379      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
2380      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
2381      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
2382    
2383    checkpoint59h (2007/09/29)
2384    o pkg/exf:
2385      - improve vectorization by moving if-statement out of loops in
2386        exf_mapfields, exf_radiation
2387      - exf_bulkformulae.F: introduce 2D fields and vectorize code
2388    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
2389    o testreport:
2390      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
2391        monitor & update offline_exf_seaice exp. output.
2392      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
2393    o pkg/seaice:
2394      - bug fix in the evp solver: boundary conditions were affected be
2395        masking of zMax/zMin (changes results)
2396      - minor bug fix in boundary conditions in seaice_calc_strainrates
2397        (changes results for no_slip)
2398      - seaice_lsr.F: make interpolation of eta dependent on boundaries
2399      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
2400      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
2401        stress formulation and no-slip boundary conditions
2402    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
2403      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
2404    o pkg/seaice: a first HSALT time stepping equation has been checked in
2405    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
2406      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
2407      without requiring DO-IF statements
2408    o pkg/thsice:
2409      use continuous power-law function for partition of energy between lateral
2410      melting/freezing and thinning/thickening ; old code using step function
2411      still available with #undef THSICE_FRACEN_POWERLAW
2412      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
2413    o testreport: change AD testing : check against results/output_adm.txt
2414      using same scripts as for forward test.
2415    
2416    checkpoint59g (2007/09/17)
2417    o adjoint testing: in preparation for changing testreport:
2418      - output format: cost and grad written on separated lines
2419      - ad output results in directory "results" (instead of "results_ad")
2420    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
2421    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
2422    o pkg/ecco: allow user defined cost function contributions
2423    o testreport:
2424      Allow to choose (per experiment) the list of tested output variables
2425       and the main variable (used to issue a pass/FAIL ) ;
2426      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
2427      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
2428      Also modify printing of summary:
2429       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
2430       b) echo the list of tested variables in the individual summary.txt of
2431          each experiment.
2432    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
2433      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
2434      (but still depend on the tile decompostion of the domain).
2435    o pkg/seaice: change a discretization detail to make the B-grid code
2436      "more symmetric". This change is likely to remove all "ridges/leads" that
2437      where quasi-aligned with the grid in B-grid solutions. It may also be
2438      the solution to the stress coupling issues with the B-grid.
2439    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
2440      remove .cvsignore from input dir. (since testreport no longer run here).
2441    o pkg/thsice:
2442     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
2443     - fix reshaping of sea-ice just after advection:
2444       melt all the ice only if ice-volume is too small.
2445     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
2446       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
2447     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
2448    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
2449      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
2450    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
2451      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
2452      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
2453      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
2454      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
2455      -> update output.txt
2456    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
2457     this affects truncation error: -> update output.txt of exp:
2458      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
2459      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
2460    
2461    checkpoint59f (2007/08/21)
2462    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
2463    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
2464      a bounded range (in forward mode)
2465    o pkg/ecco, ctrl, autodiff and mom_common:
2466     internal parameter controls, completements of implementations
2467    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
2468    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
2469      (not seem any difference in testing results).
2470    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
2471       at face corners.
2472    o pkg/generic_advdiff:
2473     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
2474      loop range indices for computing vertical advection tendency
2475      and do the calculation in the interior only (no overlap) ;
2476      for now, only implemented for SOM advection (to save CPU time).
2477     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
2478    o exch2 adjoint
2479      First set of changes:
2480      - add exch2 hand-written adjoint templates
2481      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
2482        This will require cleanup in pkg/autodiff/*.F
2483        (changed routines currently kept separate in verif. code/)
2484      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
2485        that used to hide exch2 or cubed-sphere specific code
2486        (commented via 'cph-exch2')
2487    o pkg/seaice
2488      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
2489    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
2490       output of global_ocean.cs32x15.thsice .
2491    
2492    checkpoint59e (2007/07/26)
2493    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
2494      for B-grid vector (not yet tested) and C-grid vector (<- only used
2495      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
2496    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
2497      (#ifdef ALLOW_SALT_PLUME)
2498    o gather_2d/scatter_2d: removed halo regions
2499    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
2500      scheme and the corresponding test case (under front_relax dir). For now,
2501      only available with Skew-flux form and not yet tested in realistic set-up.
2502      adjoint: store directives updated, but gradient checks deteriorated,
2503      so maybe GM/Redi adjoint is now broken.
2504    o seaice adjoint
2505      * add AREA, HEFF, HSNOW as control variable
2506        (should not change lab_sea results)
2507      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
2508    o pkg/seaice:
2509      * added computation of saltFlux in seaice_growth;
2510        For time being, sea ice salinity is assumed constant
2511        contribution of snow flooding to freshening of sea ice is neglected.
2512        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
2513        defaults to 0.0 in order to maintain backward compatibility.
2514        Typical values for SEAICE_salinity are 4 to 10 g/kg.
2515      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
2516      * added SEAICE_availHeatFrac, which specifies fraction of surface level
2517        heat content used to melt or grow ice
2518      * commented out cap of HICE: it helps keep ice thinner
2519      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
2520      * applied OBCS T/S mask to HEFFM sea ice mask
2521    
2522    checkpoint59d (2007/06/21)
2523    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
2524     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
2525     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
2526    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
2527     and change default value of parameter "GM_Small_Number";
2528     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
2529       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
2530       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
2531    o pkg/ecco: cost function when applying pkg/smooth to controls
2532    o pkg/ctrl: add forcingPrecond run time parameter
2533    o pkg/seaice:
2534     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
2535     - fix bug in metric terms of u-equation in LSR solver (implicit part),
2536       changes verification/lab_sea
2537     - rearrange implicit part of u-equation in LSR solver to make it easier to
2538       read, understand, and debug. This causes changes at the truncation level.
2539     - fix (serious) bug in the boundary conditions (sign error in the implicit
2540       part) of the LSR solver. Changes all LSR results.
2541     - fixed problem with HSNOW initialization to avoid thick snow when AREA
2542       is initilized with small values - does not change lab_sea results.
2543     - added HsnowFile initialization capability
2544    o pkg/smooth: addition to model/src and pkg/ctrl so allow
2545     initialization of pkg/smooth and application to control vector
2546    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
2547    o dependencies: pkg/profiles requires pkg/cal
2548    o pkg/profiles:
2549     - added option ALLOW_PROFILES_GENERICGRID
2550         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
2551         that interpolation information (grid points and coefficients) is provided
2552         within the netcdf input files.
2553         -> sample matlab scripts can be found in MITgcm_contrib/gael
2554         that allow you to prepare netcdf input files.
2555     - also modified: cleaner include statements, cleaner error print statements,
2556       cleaner stops when error, and more tests of the netcdf input files consistency.
2557    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
2558    o pkg/seaice:
2559     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
2560       requires a new routine: seaice_diagnostics_fill.F
2561     - make sure that seaice does not move if not forced (pressure replacement
2562       method, Hibler and Ip, 1995), changes results
2563     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
2564     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
2565       It is turned off by default (=-1.), because it changes the results.
2566     - make it possible to read AREA from a file, too.
2567    
2568    checkpoint59c (2007/06/04)
2569    o add S/R and diagnostics for oceanic mixed-layer depth
2570    o move GMRedi call after all vertical mixing schemes (including KPP)
2571    o pkg/thsice:
2572     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
2573      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
2574    o pkg/obcs:
2575     - bug fix for balance code
2576    o pkg/seaice:
2577      - allow values of SEAICE_elasticParm > 1
2578      - add new parameter SEAICE_evpTauRelax as an alternative
2579        to SEAICE_elasticParm
2580      - make lsr boundary conditions free slip (by default), changes result
2581      - add code for no slip boundary conditions for lsr
2582      - set minimum of zeta to zero (and not 4e8) (changes results)
2583      - add a cap on AREA after advecting AREA if seaice_growth is not called
2584    o change calculation of Visbeck K:
2585      - no longer depend on tapering scheme; instead, compute slope (limited
2586        by GM_maxSlope). this is equivalent to what was comuted before with
2587        clipping or linear tappering.
2588      - fix vertical averaging (wrong by 1/2 level)
2589      - leave the old version (but will not be maintained) within
2590        #ifdef OLD_VISBECK_CALC / #endif
2591      - update output of exp. ideal_2D_oce
2592    o change error catch in calc_r_star to improve vectorization
2593    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
2594      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
2595    o adjoint:
2596      Re-organized adjoint checkpointing according to Matt Mazloff
2597      (but with modifs/completions/cleanups)
2598      Storing is now bundled into large arrays to optimized I/O
2599      (and second step in cleanup of the_main_loop)
2600    
2601    checkpoint59b (2007/05/16)
2602    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
2603      - export/import (between ocean & coupler) fields needed for ocean DIC.
2604    o pkg/seaice:
2605      - get rid of three more exchanges seaice_calc_viscosities (required
2606        different loop boundaries in seaice_lsr and seaice_ocean_stress)
2607      - bug fix in seaice_ocean_stress (update of lab_sea required)
2608      - reduce loop boundaries to necessary minimum also in seaice_evp
2609      - go back to the old way of computing deltaC/Z as the adjoint likes that
2610        better
2611    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
2612      passive tracer to an Age Tracer) + update output.txt
2613    o pkg/exf:
2614      - implement A-grid / C-grid selection for wind-stress input files.
2615      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
2616      for now, in exf_bulk_largeyeager04.F only :
2617      - change implementation for case where windspeed + 2. components wind-stress
2618        are read-in. AND use rhoConstFresh to convert evap.
2619    o pkg/seaice:
2620      - use correct EXCH_UV for wind-forcing (on A-grid).
2621      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
2622        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
2623    o pkg/exf:
2624      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
2625      EXF_INTERPOLATION:
2626      - merge global_with_exf/code version of exf_interp_read.F
2627        to the main code ;
2628      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
2629        reading the file ; Important: This options needs to be defined to recover
2630        previous code.
2631        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
2632      - no longer loose real*8 precision along the way when using exf_iprec=64.
2633    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
2634      - change discretisation of evp-solver in order to avoid another exchange
2635        (changes lab_sea) and clean up a little
2636      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
2637        help the adjoint (this also changes the results slightly)
2638      - add a few "_d 0" where they had been missing in seaice_evp.F
2639      - cleaning up: remove unused seaice_calc_rhs.F
2640    o pkg/exf: some cleaning-up:
2641      - change various "constants" into runtime parameters
2642      - cleaned-up Large&Yeager04 routine which should eventually
2643        replace exf_bulkformulae.F (changed names of S/R and CPP)
2644        and merged various ALLOW_ATM_WIND options
2645     only used with thsice pkg (in thsice_get_exf.F):
2646      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
2647        which are used when useStabilityFct_overIce=TRUE (= the default)
2648      - change default values of ice & snow emissivity and scale downward LW
2649        by ice & snow emissivity.
2650    o pkg/thsice:
2651     fix few little problems, in thsice_calc_thickn.F:
2652      - growth vertically (and not laterally) if iceFrac == iceMaskMax
2653      - melt only laterally if hIce < hThinIce (as the comments say)
2654      and in thsice_extend.F:
2655      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
2656      - start to form ice as soon as the minimum ice-volume is reachable.
2657     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
2658      and cpl_aim+ocn
2659    o pkg/kpp
2660     - move computation of surface related input fields to KPP into a new
2661       subroutine kpp_forcing_surf.F
2662     - remove wrong (within bi,bj loops) EXCH calls.
2663     - little cleaning (add argument myThid in last position, cvs header ...)
2664     - for now, fix conservation problem by exchanging KPPviscAz (may not
2665       be the best fix)
2666    o pkg/seaice
2667     - check for inconsistent evp parameter/cpp-flag combination
2668     - remove leftover errIO flat for obsolete name list error handling
2669    o OpenAD
2670     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
2671    
2672    checkpoint59a (2007/05/01)
2673    o pkg/seaice: some parameter clarifications and a little bit of clean up
2674    o pkg/thsice: rename run-time parameters:
2675       himin       -> hIceMin
2676       himin0      -> hThinIce
2677       hihig       -> hThickIce
2678       i0          -> i0swFrac
2679       transCoef   -> bMeltCoef
2680       frac_energy -> fracMelting
2681      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
2682       with default values (for now) that do not change the results.
2683      remove old version of thsice vars advection in pkg/seaice.
2684    o in FFIELDS.h:
2685      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
2686      - make pLoad & sIceLoad always available (but still only used if
2687         ATMOSPHERIC_LOADING is #define).
2688    o pkg/kpp: replaced _KPP_RL with _RL
2689    o bug fixes for vertical diffusivity computations when both KPP and
2690        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
2691        are no longer updating the vertical diffusivity array
2692        (passed as argument) but are (re-) setting those arrays.
2693    o pkg/seaice: fix bug in evp solver, while doing that
2694      - change (improve?) discretization of stress computations for both
2695        cgrid-lsr and evp solver
2696      - add a new routine to compute strain rates
2697      - the above changes lab_sea results
2698      - add no slip conditions for evp solver (off by default), lsr-version
2699        may follow
2700      - fix exchange for shear at Z-points (does not change lab_sea)
2701      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
2702        (to force the user to pick a time step since there is not "safe" way
2703        of choosing it)
2704      - add principal stress diagnostics
2705      - rearrange fields for evp a little to avoid having to call a: too many
2706        exchanges and b: exchanges for stress trensor components which we do
2707        not have.
2708      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
2709        of evp, complete rewrite for lsr case (latter is does not yet work
2710        in all cases)
2711    o pkg/kpp: add code to have mixing in shelf ice caverns
2712      - add myThid to all kpp routines (long overdue)
2713    
2714    checkpoint59 (2007/04/19)
2715    o pkg/exf:
2716      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
2717        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
2718      - move exf header files from lower_case.h to UPPER_CASE.h ;
2719        add missing cvs Header & Name
2720      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
2721      - add namelist param. selectStressGridPosition, exf_monFreq
2722      - retire many _CLIM routines, and remove data.exf_clim
2723        + params moved to data.exf
2724        + climsst, climsss now handled by exf_set_gen, i.e.
2725          climss?period=0 refers to constant field,
2726          climss?period=-12 to monthly forcing
2727      - split up namelists in data.exf
2728    o pkg/seaice:
2729      - remove seaice_exch and seaice_exch_uv
2730      - remove superfluous exchange of theta
2731      - add myThid to seaice_budget_ocean/ice
2732      - add new interface for atmospheric wind forcing (C-grid only)
2733        + new routine
2734        + two new field (taux, tauy for stress over ice)
2735        + removed one global field (DAIRN) for C-grid case only
2736    o pkg/thsise
2737      - 2nd set of modifs for thsice adjoint in conjunction with exf
2738    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
2739    
2740    checkpoint58y_post (2007/04/15)
2741    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
2742      vertical diffusivity, similar to that in MOM4; turned on using
2743      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
2744      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
2745    o Added capability for 3D specification of background vertical diffusion
2746      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
2747      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
2748      "data" file that contains the 3D vertical diffusivity coefficients.
2749    o ice dynamics (pkg/seaice) with thsice thermodynamics:
2750      - add code within pkg thsice to advect & diffuse sea-ice fields
2751      similar to (and will replace) what has been added in  seaice_advdiff.F,
2752      but: - conserving Mass, Heat & Salt.
2753           - better when using non-linear advection scheme (not yet fully tested)
2754           - can also be used in atmospheric set-up (for now, only the diffusion).
2755    
2756    checkpoint58x_post (2007/04/04)
2757    o IO option for global-file compact format:
2758      - add options when generating topology (utils/exch2/matlab-topology-generator)
2759      - add I/O capability (pkg/mdsio).
2760      - adapt utils/matlab/rdmds.m to read this format.
2761      for now long-line format not yet supported by pkg/mdsio (& exch2).
2762    o shelfice: add a few diagnostics
2763    
2764    checkpoint58w_post (2007/03/13)
2765    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
2766      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
2767      (and replace horiVertRatio in NH code).
2768      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
2769                         and tutorial_plume_on_slope (sensitive to truncation)
2770    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
2771      directly to drive seaice model (C-grid only)
2772    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
2773     - reintroduce computation of wind from stress,
2774     - compute tau (in exf_bulkformulae.F) from windstress averaged to
2775       mass points to avoid tau = 0
2776     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
2777    o rdmnc.m: make it work with "global" files created with gluemnc
2778    o rdmnc.m : some improvements in dealing with singleton dimension
2779      (tested on all testreport mnc output files).
2780    o genmake2: disable pkg/profiles if netcdf test fails.
2781    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
2782    o move call to cal_readparms up to make calendar parameters/variable available
2783      to all packages
2784    
2785    checkpoint58v_post (2007/02/08)
2786    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
2787      useDynP_inEos_Zc tested.
2788    o pkg/exf: changes to properly interpolate/mask/scale initial fields
2789    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
2790      and portions thereof.  See read_cs.txt for description and examples.
2791    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
2792      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
2793      following the great-circle arc between those 2 points.
2794    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
2795      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
2796    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
2797     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
2798     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
2799     - still needs work (not working with some options ; efficiency to improve)
2800       and serious testing.
2801     - use this scheme for temperature & salinity in 2 advection test exp.:
2802       advect_xy & advect_xz, respectively.
2803    
2804    checkpoint58u_post (2007/01/12)
2805    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
2806    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
2807    o testreport: add option "-skipdir" to skip some test.
2808    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
2809      momentum calculation.
2810    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
2811    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
2812      remove checkpoint.F and the_correction_step.F (no longer used);
2813      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
2814    o add option (linFSConserveTr) to correct for tracer source/sink due to
2815      Linear Free surface
2816    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
2817    o pkg/thsice: fix reading mnc-pickups
2818    
2819    checkpoint58t_post (2006/12/30)
2820    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
2821    o pkg/mdsio:
2822     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
2823       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
2824       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
2825     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
2826     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
2827       either MDS_READ_FIELD or MDS_WRITE_FIELD )
2828     - new S/R (to replace MDSWRITEMETA), which allows to write more
2829       informations (variable names, time ...) to meta files.
2830     - modify rdmds.m to give back the meta file content.
2831    o pkg/diagnostics: change vertical interpolation to be safer, and more
2832       flexible (define p-levels to interpolate to in data.diagnostics);
2833      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
2834       diagnostic pointer.
2835    o pkg/seaice: more cleaning up of seaice_growth, added many comments
2836    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
2837    o fix multi-category seaice:
2838     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
2839       SEAICE_MULTICATEGORY
2840     - fix short wave heat flux
2841    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
2842       and allow to use EVP solver. Change forward lab_sea: test both EVP
2843       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
2844    o Initial check-in of lab_sea adjoint
2845      (very similar to natl_box_adjoint/code_seaice)
2846      * used C-grid and EVP solver
2847      * used KPP, GM/Redi
2848      * uses inAdExact=.TRUE.
2849      * gradient checks fail for both ADM and TLM
2850        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
2851        f.d. gradients actually seem more problematic than ADM, TLM gradients;
2852        issue is related to forward mismatch between g77 an ifort
2853    o pkg/seaice: overhaul of thermodynamics
2854     - growth.F and groatb.F are replaced by new routine seaice_growth.F
2855     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
2856     - move a few global fields out of SEAICE.h into seaice_growth.F and
2857       make them 2D (FICE/QNETO/ ...)
2858     - remove FO (it is the same as QNETO)
2859     - introduce a few local fields to avoid modifying external fields such
2860       as atemp, etc.
2861    
2862    checkpoint58s_post (2006/12/11)
2863    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
2864      changed exf_set_gen.F so that
2865        genperiod=0 means input file is one time-constant field and
2866        genperiod=-12 means input file contains 12 monthly means
2867    o CG2D: use pre-computed solver main-diagonal (stored in common block);
2868      this affects truncation error ; generate new output file for exp. which
2869      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
2870        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
2871        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
2872        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
2873        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
2874        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
2875    o start implementation of deep-atmosphere and anelastic formulation
2876    o verification: remove 2nd copy of input files and use script "prepare_run"
2877      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
2878    o mom_common/vecinv/fluxform: fix a few initialisation isssues
2879    o profiles: fix for multithreaded case
2880    
2881    o diagnostics: rename few diags:
2882      s/'PRESSURE'/'RCENTER '/g
2883      s/'TICE    '/'oceFreez'/g
2884      s/'TAUX    '/'oceTAUX '/g
2885      s/'TAUY    '/'oceTAUY '/g
2886      s/'SWFLUX  '/'oceQsw  '/g
2887      s/DIFx/DFxE/g
2888      s/DIFy/DFyE/g
2889      and add few ocean-forcing diagnostics:
2890      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
2891    o modifications to pkg/seaice/growth.F and budget.F, which change results of
2892      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
2893      as actual snow thickness.  It now refers everywhere to effective snow
2894      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
2895    
2896    checkpoint58r_post (2006/11/17)
2897    o modifications to pkg/seaice/growth.F, which change results of
2898      lab_sea experiment: fixes pertain to melting snow over open water, to
2899      masking EVAP under sea ice, and to using the correct AREA variable for
2900      computations of EVAP, PRECIP, HSNOW, and GHEFF
2901    o add ability to read bathy, salt, and theta using MNC (off by def)
2902    o add flooding algorithm and advection of HSNOW for pkg/seaice;
2903      both are turned off by default and do no change any results
2904    o seaice advection with pkg/thsice: a step toward the use of non-linear
2905      advection scheme, but #ifdef or commented out for now (requires more EXCH).
2906    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
2907      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
2908      in natl_box (affects results @ truncation level: update output.txt)
2909    o multi-threading and IO:
2910      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
2911      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
2912        (needed to work with SingleCpuIO): tested in all verif. exp.
2913    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
2914      affects the results (but none of the verification test uses this scheme).
2915    o Adding some pkg/diagnostics capability to pkg/seaice
2916      (will certainly be subject to changes)
2917    o ctrl: adding new control variables:
2918      lwflux, lwdown, evap, snowprecip, apressure, runoff
2919    
2920    checkpoint58q_post (2006/10/20)
2921    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
2922      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
2923      high_res_cube configuration by 4% on Columbia.
2924    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
2925      add (in global_with_exf/code) a version of EXF_INTERP_READ without
2926      dynamical allocation (seems to work in multi-threaded).
2927    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
2928      single CPU io) so that TAF does not have to see EESUPPORT.h
2929    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
2930    
2931    checkpoint58p_post (2006/09/08)
2932    o obcs: stop if obcs is used with useCDscheme = .true.
2933    o shelfice:
2934     - fix a sign error so that no slip at shelfice interface works
2935     - remove stop for combination non-hydrostatic code and shelfice. That does
2936       not mean, that the results are correct, but at least they are numerically
2937       stable
2938    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
2939    o added adjoint exch routined for all exch*3d* routines
2940      and updated flow directives
2941    
2942    checkpoint58o_post (2006/08/28)
2943    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
2944      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
2945    o change controling S/R for writing pickup file (new S/R do_write_pickup)
2946      and clean-up reading/writing of pickup files.
2947    o fix local version of read/write pickup (NH part) in rotating_tank/code
2948    o simplify EXCH interface:
2949     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
2950     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
2951    o added the regrid package
2952    o shelfice:
2953     - add a simple boundary layer scheme to reduce noise
2954     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
2955    
2956    checkpoint58n_post (2006/08/14)
2957    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
2958       local variable (not in common block).
2959    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
2960      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
2961      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
2962        to work with SingleCpuIO.
2963    o add "_d 0" to real constant of pkg/cfc subroutines ;
2964       update exp. cfc_exemple & tutorial_cfc_offline output files.
2965    o multi-threading and IO:
2966      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
2967        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
2968      - barrier before and after reading.
2969      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
2970      - avoid using MDS_WRITELOCAL for LAND pkg output.
2971      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
2972        common-block variables ; Allows multi-threading with master-thread IO.
2973    o change default MAX_NO_THREADS from 32 to 4 ;
2974      and stop cleanly when MAX_NO_THREADS is too small.
2975    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
2976    
2977    checkpoint58m_post (2006/07/17)
2978    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
2979       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
2980    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
2981       keep global_ocean.90x40x15 (for AD testing) with former secondary test
2982       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
2983    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
2984        add MITgcm_tutorials (= code + all the tutorials)
2985    o ecco, option to compute cost for total ssh (mean+anom)
2986    o consistent with addition of ptracer and ssh in pkg/profiles
2987    o profiles: adding ptracer and ssh
2988    o testreport: change multi-test output-file name
2989      (from output.txt.{name} to output.{name}.txt)
2990    o profiles: now ok for mutli-tiles case
2991    o seaice: add 4 parameters for different advection schemes for area,
2992      (effective) seaice thickness, enthalphy, and snow height. Their default
2993      is the standard parameter SEAICEadvScheme
2994    o calc_gw:
2995     - add cosFacU in zonal viscous flux (harmonic.visc.).
2996     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
2997       of tutorial_plume_on_slope.
2998    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
2999    o calc_gw: true flux-form, account for horizontal grid spacing.
3000      update rotating_tank results, but not plume_on_slope (affected at
3001      truncation level, 11 digits).
3002    
3003    checkpoint58l_post (2006/07/12)
3004    o calc_gw:
3005     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
3006     - remove side-drag for now (need to fix it); update plume_on_slope results.
3007     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
3008    o commit code to make SST/SSS weights spatially variable
3009      (based on either variable in-situ or variable initial T/S weights)
3010    o pkg/ecco:
3011      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
3012        now based on horizontally varying weights wthetaLev, wsaltLev
3013      * cost_averagesflags now returns year indices in addition to day, month
3014      * sflux balance is performed on annual basis
3015        (sflxumm, sfluxmm2, bal_sfluxmm)
3016      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
3017        including separate counting and multipliers
3018    o pkg/rbcs
3019      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
3020    
3021    checkpoint58k_post (2006/07/06)
3022    o testreport:
3023     - always build in dir. "build" (if not there, mkdir build instead of building
3024       & running in input)
3025     - run in dir run (if it exists), in build otherwise.
3026     - call prepare_run (if input/prepare_run exists)
3027     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
3028    o pkg/exf modifications to interpolation and rotation routines for more
3029       reasonable treatment of North Pole singularity: for tracers North Pole
3030       value is set to northernmost zonal-mean value, for zonal velocity it is
3031       set to zero, and for meridional velocity it is set to northernmost value.
3032    o pkg/exf/exf_check_range.F
3033     - add tile index to diagnostics and move stop statement to the very
3034       end of the routine.
3035    o pkg/diagnostics: (diagnostics_main_init.F)
3036      define title of isomorphic variables according to the current config.
3037    o pkg/thsice with pkg/seaice dynamics:
3038    - fix domain of computation (interior only, required for exf) and do exchanges
3039    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
3040    o towards a standard way of dealing with multi-threading in MONITOR
3041      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
3042    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
3043       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
3044    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
3045    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
3046    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
3047       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
3048    o tracer advection:
3049     - clean-up and simplify calc_common_factors.F
3050     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
3051       advection subroutine (but still not used within DST advection S/R)
3052    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
3053    
3054    checkpoint58j_post (2006/06/15)
3055    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
3056      from file (collects calls previously in FORWARD_STEP)
3057    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
3058    o adjoint store dir. adjusted accordingly
3059    o genmake2
3060      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
3061    
3062    checkpoint58i_post (2006/06/14)
3063    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
3064      on wind stress (SEAICEstressFactor defaults to 1.)
3065    o Total number of Timers is finite (<=40): comment out 2 non-essential one
3066      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
3067    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
3068      on CS-grid: no longer loosing mass.
3069    o exf & curvilinear-grid: no longer modify longitude xC & xG.
3070    o pkg/ggl90: fix sloppy output and fix a bug
3071    o pkg/seaice: added SEAICEuseEVPpickup parameter
3072      - Set to false in order to start EVP solver with
3073        non-EVP pickup files when using SEAICEuseEVP
3074      - fix sign error in diffusion in seaice_calc_rhs
3075    
3076    checkpoint58h_post (2006/06/07)
3077    * Modifications for bottom topography control
3078      o replace hFacC by _hFacC at various places
3079      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
3080      o add non-self-adjoint cg2d_nsa
3081      o update autodiff support routines
3082      o re-initialise hfac after ctrl_depth_ini
3083      o works for 5x5 box, doesnt work for global_ocean.90x40x15
3084    * Adding verification for 5x5 box (4-layer) bottom topography control
3085    
3086    checkpoint58g_post (2006/06/07)
3087    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
3088       used for mean seasonal cycle, mean diurnal cycle); add an example
3089       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
3090    o pkg/ggl90:
3091      - add parameter (minimum surface kinetic energy)
3092      - fix bug (avoiding division by zero)
3093    o couple pkg/thsice to pkg/seaice:
3094      - modify advection in seaice to accomodate new scalar fields to be advected
3095      - only muliDimAdection scheme work with seaice/thsice
3096      - mapping of thsice-variables to seaice-variables, back and forth
3097      - does not break the verification experiments, but does not give the
3098        desired results either
3099    o pkg/seaice
3100      - make (default) second order advection a bit less confusing?
3101    
3102    checkpoint58f_post (2006/06/05)
3103    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
3104      to pkg/seaice):
3105      - new routines thsice_map_exf and thsice_get_exf provide the interface
3106      - add an additional formal parameter to thsice_solve4temp
3107    o pkg/exf:
3108      - add new fields wspeed, snowprecip (to be able to couple to thsice)
3109      - correct Stefan-Boltzmann constant
3110      - new parameter for longwave surface emittance
3111      - separate some stuff from exf_bulkformulae into new routines  
3112        exf_radiation, exf_wind
3113      - add new parameters and constants: longwave emissivity for ocean, ice
3114        and snow, evaporation parameters over ice
3115      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
3116        either wind from stress or stress from wind
3117    o pkg/thSIce:
3118    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
3119    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
3120       and THSICE_CALC_THICKN
3121    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
3122    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
3123      to make debugging easier.
3124    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
3125    o pkg/bulk_force:
3126      - clean-up comments and parameters ;
3127      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
3128    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
3129      generate new output for test-experiment: aim.5l_cs.thSI
3130    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
3131      testreport accordingly
3132    
3133    checkpoint58e_post (2006/05/17)
3134    o SEAICE_CGRID adjoint done
3135    o R_STAR adjoint implemented.
3136      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
3137      * need to sort out init. of h0facc, etc.
3138    o Make pkg/profile fully independent of ecco,cost, etc. stuff
3139      to be able to use it in pure forward.
3140    
3141    checkpoint58d_post (2006/04/21)
3142    o upgrade simple test-experiment to tutorial example:
3143     step.1: duplicate the experiment and (step.2) will remove the old copy.
3144      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
3145      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
3146      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
3147      tutorial_global_oce_biogeo    <- copy of dic_example
3148      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
3149      tutorial_plume_on_slope       <- copy of plume_on_slope
3150      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
3151      tutorial_global_oce_optim     <- empty for now (David ?)
3152      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
3153     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
3154    o correct a sign problem in cost_scat.F
3155    o obcs and ptracers: fix boundary conditions for advections schemes
3156      with larger stencil
3157    o thsice adjoint: start
3158    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
3159      completeness
3160    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
3161      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
3162    o ptracers adjoint:
3163      * avoid extensive recomputatations
3164      * fix missing re-init. of gptr (missed by TAF)
3165    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
3166      me to turn off the excessive output to STDOUT that this package produces
3167    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
3168      and add those terms in Vector-Invariant formulation.
3169    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
3170      if the control period (xx_hfluxperiod etc) is 0
3171    o in profiles pkg, clean routines and fix details
3172    o in ecco pkg, reading ssh data:
3173      fix problem in case the model does not start at iter0=0
3174    o fix mnc-pickup/restart for ptracers
3175    o new package prifiles:
3176      code to compute profile-based cost by Gael Forget
3177      (modifs in ecco, ctrl, autodiff)
3178    o Benign bug fix in initialization (spotted by M. Mazloff) of
3179      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
3180    
3181    checkpoint58c_post (2006/03/23)
3182    o adjoint: finish NLFS adjoint and provide reference output in
3183      verification/global_ocean.90x40x15/results_ad_nlfs
3184    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
3185      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
3186      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
3187      with SEAICE_CGRID defined.
3188    o move calendarDumps from "data" to "data.cal" and clean-up the code
3189      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
3190    o add useEXF & useCAL flags (for now, set in hard-coded way)
3191    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
3192      (were missing in NH mode, and wrong in quasihydrostatic mode).
3193      waiting for Chris updated version of calc_gw to add those CALLs.
3194    o fix bug in quasihydrostatic S/R ;
3195      add a test for this option: global_ocean.90x40x15.qshyd
3196    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
3197      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
3198    o add on/off flag useOffLine for package OFFLINE
3199    o seaice:
3200      - modify advection so that it works also on the C-grid
3201      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
3202        problem in multi-tile runs with C-grid
3203      - add flags for clipping ice velocities and/or masking solver forcing
3204      - fix drag (ocean on ice) formulation and a bug that caused noise in the
3205        C-grid solver
3206      - added a few comments to seaice_diffusion.F
3207      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
3208        are now exclusive)
3209      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
3210        required re-ordering the code a little:
3211       + make DAIRN global variable (defined in SEAICE)
3212       + move computation of the viscosities eta and zeta into a new separate
3213         routine (because I need to recompute them in seaice_ocean_stress.F)
3214    
3215    checkpoint58b_post (2006/03/13)
3216    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
3217      update output.txt of exp. aim.5l_cs.thSI
3218    o various mnc cleanups and improvements:
3219      + shrink lookup tables by factor of ~4
3220      + better error reporting when running out of lookup space
3221      + able to handle longer path/file names (up to 500 chars)
3222    o adjoint:
3223      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
3224      - TBD: "hidden" mom_vecinv recomp. in dynamics
3225    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
3226     (allow to differentiate between forcing components using new integer flags:
3227      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
3228     and add new flag to put Dissipation tendency out of Adams-Bashforth.
3229    o ecco
3230      - enable trend removal from SSH anomaly obs.
3231    o adjoint
3232      - a fix for PmEpR when #undef EXACT_CONSERV
3233      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
3234      - try to fix "hidden" recomp. in forward_step for NLFS
3235        (NLFS seems broken sometimes after I checked it in)
3236    o seaice:
3237     - add c-grid version of the dynamic solver:
3238       + three new routines that are the c-grid substitute lsr, dynsolver
3239         and ostres
3240       + put a few fields that were local to dynsolver into global common
3241         blocks, so that I can move the computation of stresses etc into
3242         seaice_lsr (saves coding but may break the adjoint).
3243     - replace more hardwired parameters by runtime parameters
3244     - add ice masks that mask the rhs of the implicit solvers where there
3245       is no ice (commented out in seaice_dynsolver, because i am not sure
3246       if this works properly), eventually this should replace the clipping
3247       of ice velocities in seaice_dynsolver to +/-40cm/s.
3248    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
3249      include it only where its needed
3250    o move balancing of fluxes before the call of external_forcing_surf
3251    o seaice:
3252      - correct units of turning angles (now they are really in degrees)
3253      - move computation of GWATX/Y out of main routine into dynsolver
3254      - initialize GWATX/Y in seaice_init
3255    o Apply mask on Fresh-Water flux (needed for SSH forcing).
3256      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
3257    o seaice: add runtime flags for turning angles (default to zero)
3258    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
3259      and trend from exf forcing and ctrl control adjustments
3260    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
3261      (since checkpoint57x_post)
3262    o change the default rotation period to 86164.s = the Earth rotation
3263    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
3264      and based on a reference stratification. Tested within hs94.cs-32x32x5.
3265    o seaice advection: add code for choosing between the default (2nd order
3266      central differences) and multiDim advection schemes provided by
3267      pkg/generic_advdiff
3268    o seaice:
3269      - removed all references to SEAICE_GRID.h fields from
3270        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
3271        (cubed-sphere configuration will change a little)
3272      - grid computations in seaice_init are obsolete now.
3273      - cleaned up code a little so that is easier to read (hopefully).
3274      - added new (better?) discretizations of default advection and diffusion
3275        (turn on with SEAICEuseFluxForm)
3276      - replace 1 in 3d global fields by kSurface in growth.F
3277      
3278    checkpoint58a_post (2006/02/13)
3279    o seaice:
3280      - bug fix in advect.F
3281    o shelfice:
3282      - separate shelfice load anomaly from pload (breaks with time
3283        dependent forcing), => introduce constant field shelficeLoadAnomaly.
3284        Its default is 0., but it may be computed more cleverly from (unknown)
3285        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
3286        done offline. A good approximation of the pressure load anomaly is
3287        necessary to avoid large initial adjustment processes underneath
3288        deep-reaching shelfice.
3289      - small fix in ISOMIP shelfice_thermodynamics
3290      - add more sophisticated thermodynamics of Hellmer (1989), this is
3291        now the default
3292      - give a few constants more intuitive names
3293    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
3294      if bulk formulae are used in long integration (especially EmPmR). Turn
3295      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
3296      if balancePrintMean, the imbalance that is substracted is printed to
3297      STDOUT.
3298    o fix bug (typo) in obcs_apply_eta.F
3299    o add a new package shelfice which enables us to model the circulation
3300      underneath shelf-ice with draughts of hundreds of meters.
3301     - works
3302     - to do: + include improved thermodynamics
3303              + check whether kSurfC (from model/inc/SURFACE.h) can be used
3304                instead of new field kTopC
3305              + can we use topoFile, Ro_surf and existing code in ini_depth.F
3306                instead of new field R_shelfIce and new code in ini_depth.F
3307                and ini_mask_etc.F?
3308              + adjust vertical mixing schemes?
3309    o seaice pkg:
3310     - add a cpp-flag to include a simple formula for a salinity dependent
3311       freezing point of sea water at the surface
3312     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
3313       meridional stresses are now different (and hopefully correct)
3314    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
3315       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
3316       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
3317    o pkg/diagnostics: add options and parameters for regional-statistics
3318       diagnostics ; define regions by reading a region-mask from a file
3319       (might add other options later)
3320    o pkg/bulk_force:
3321     - add option and parameters to use AIM surface-flux formulae.
3322     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
3323       others forcing fields (defined in PARM05, parameter file "data") are loaded
3324       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
3325     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
3326     - use the right EXCH call for uwind,vwind (to work on CS-grid).
3327     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
3328       and parameters (note: calcWindStress replaces .NOT.readwindstress).
3329     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
3330    
3331    checkpoint58 (2006/01/12)
3332    o add "--embed-source" option to genmake2 which, when the supporting
3333      tools can be compiled (as determined by genmake2) will turn on the
3334      embed_files package which then embeds the entire MITgcm source code
3335      (*.[fFhc] + Makefile) used for the build within the executable
3336      - requested by CNH but off by default
3337      - adds a paltry <9MB to the mitgcmuv executable in most cases
3338      - only writes the output when useEMBEDSRC in eedata is true
3339    o clean up 3-dim. relaxation codes:
3340      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
3341      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
3342      * Thanks to Tom Haine for testing!
3343    
3344    checkpoint57z_post (2005/12/31)
3345    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
3346      affects output (@ truncation level) of exp. plume_on_slope ; updated.
3347    o fix the pickup behavior for obcs in combination with ptracers
3348    o fix a bug in ptracers_external_fields_load
3349    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
3350      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
3351    o transfered surface NH pressure to eta field (if exactConserv).
3352    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
3353         and update lab_sea output.txt file.
3354    o completing 3-dim. relaxation code: additional term
3355         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
3356      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
3357      * At compile time, in "EXF_OPTIONS.h" set
3358          #define  ALLOW_CLIMTEMP_RELAXATION
3359          #define  ALLOW_CLIMSALT_RELAXATION
3360      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
3361          tauThetaClimRelax3Dim = 15552000.0,
3362          tauSaltClimRelax3Dim  = 15552000.0,
3363      * 3 cases:
3364          1) Use a constant-in-time 3-dim. field
3365          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
3366          3) Real-time relax. to time-evolving prescribed field
3367    o Adding Laplacian-type smoothness constraint on
3368      initial and boundary (forcing) controls (ic, bc)
3369      * enable at compile-time via
3370        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
3371      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
3372      * Absolute scale somewhat unclear so far
3373      * no area weighting was included since no other cost term does so far
3374    
3375    checkpoint57y_post (2005/12/08)
3376    First step for a NLFS adjoint
3377    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
3378    o new init. routines for calc_r_star, calc_surf_dr
3379    o still need to deal with ini_masks_etc
3380    o testreport seemed happy
3381    checkpoint57y_pre (2005/12/08)
3382    
3383    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
3384    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
3385    o add new offset feature to offline pkg (plus minor cleanup)
3386    o cfc fixes for final year of integration
3387    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
3388      be in GCHEM_OPTIONS).
3389    
3390    checkpoint57x_post (2005/12/04)
3391    o fix testreport Pb in multiple test experiment.
3392    o cleanup our namelist syntax in verification:
3393      - make it more F95 standards compliant (some work still needed)
3394      - allows the vast majority of our tests to work with gfortran
3395    o Non-Hydrostatic:
3396     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
3397     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
3398    o Allow to apply AB on T,S rather than on AB(gT,gS):
3399     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
3400     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
3401       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
3402     - need a "clever" read_pickup to restart from the other AB formulation
3403    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
3404    o remove some unused variables (reduces number of compiler warnings)
3405    o adjoint
3406      * Disable useVariableViscosity for adjoint for time being
3407        (there are a number of extensive recomputations)
3408      * Initialize certain variables needed for adjoint
3409    
3410    checkpoint57w_post (2005/11/03)
3411    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
3412                 fix the singleCpuIO RS version of MDSWRITEFIELD
3413       and add a WARNING if using globalFiles=T with multi-processors.
3414    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
3415      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
3416    o tracer advection scheme:
3417      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
3418       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
3419       was not very convenient).
3420      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
3421       (further tests needed for the implicit DST & Flux-Limiter schemes).
3422    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
3423      and sRef for convenience, handy, when you want to initialize
3424      ptracers in a large domain with a constant non-zero value. Also,
3425      untangle ptracers_init.F a little.
3426    
3427    checkpoint57v_post (2005/10/13)
3428    o change dome exp. to use variable viscosity in side-drag terms.
3429    o remove all the files from the cfc_offline test since they are now
3430      incorporated into tutorial_cfc_offline which has been producing
3431      identical results for a few days of testing
3432    o add new parameter: sideDragFactor to enable half-slip-side BC
3433      and change side-drag S/R to use viscosity from mom_calc_visc
3434      (can switch back by setting sideDragFactor=0.); affects results at
3435      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
3436       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
3437    o vorticity & strain are now computed without masking, to account for
3438      no-slip-side BC in variable viscosity calculation ; mask is applied
3439      anyway later on, before computing advection/coriolis terms.
3440    o modify exp4 to test new obcs support for reading from external files
3441      and for passive tracers
3442    o fix behavior of ptracers_monitor when monitor output is written to a
3443      netcdf-file; still not independent of monitor.F (writes in the same
3444      file).
3445    o change default value of tRef (put a uniform, meaningful value for ocean
3446      & atmos) and initialize sRef (was missing, as Martin mentioned).
3447    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
3448      to be proportional to enstrophy dissipation length.  Thus,
3449       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
3450      This is now consistent with Smagorinsky and with the manual.
3451    
3452    checkpoint57u_post
3453    o OBCS and PTRACERS: add open boundary support for passive tracers
3454      - either use homogenous (pseudo) v.Neumann conditions or prescribe
3455        OB-values from file; this is not different from the way theta and salinity
3456        are treated
3457      - however, Orlanski-radiation conditions are not supported, and the model
3458        will stop if you use pTracers and Orlanski at the same time.
3459      - beefed up the rountine obcs_external_fields_load: now only those open
3460        boundary values are overwritten with values from files for which there
3461        are really files, otherwise the OB-fields remain untouched. This makes
3462        it possible to use different OBs at different ends of the domain (as
3463        with EXF)
3464    o reduce number of exch calls in shap_filt (s2).
3465    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
3466      truncation level) 4/5 MLAdjust test results (11&12 digits match).
3467    
3468    checkpoint57t_post (2005/10/03)
3469    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
3470    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
3471      same truncation, independent of the face number: affects affects several
3472      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
3473    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
3474      note that biharmonic viscosity + no-slip was not tested in any experiment.
3475    o fix bug in non-linear free-surf side-drag ; generate new output for
3476      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
3477    o make mnc honor the writeBinaryPrec flag for most kinds of output
3478    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
3479    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
3480      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
3481    o add brackets in multi-terms sum to get same truncation, independent of
3482      the face number (manage to get exactly same value of gU,gV at the cs-edge)
3483      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
3484    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
3485      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
3486      a maximum grid-scale Reynolds number.  Also, changes all length calculations
3487      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
3488      Suggested values of viscosity parameters found in mom_calc_visc.
3489      Many new viscosity diagnostics available.
3490    
3491    checkpoint57s_post (2005/09/20)
3492    o Add clearing-house for viscosity calculations, mom_calc_visc and
3493      correct numerous bugs in LeithD and Smagorinsky discretizations.  
3494      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
3495      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
3496      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
3497      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
3498      The Strain-Tension form is now called with useStrainTensonVisc=.true.
3499      ViscAhStrain and viscAhTension are now retired.
3500    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
3501    o In response to JMC's bug report, genmake2 now ignores any soft-links
3502      that it finds in the *current* directory when searching for files.
3503      Soft-links found in any other source directories will still work as
3504      they did before.
3505    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
3506      a C routine to unlimit the stack size
3507    o mnc-ify pkg/aim snapshot vars
3508    o mnc-ify pkg/land as requested by Daniel
3509    o various changes to mnc including:
3510      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
3511      - output can now be grouped so that all files within a group
3512          change the ITER portion of their names in lock-step together
3513      - can now read ("global") PER-FACE (in addition to PER-TILE) files
3514          and works with both EXCH1 and EXCH2 (but needs more testing)
3515      - writing works for all verification test cases w/ g77 on Linux
3516    
3517    checkpoint57r_post (2005/09/07)
3518    o make MNC variable initialization happen earlier
3519    o add diagnostics for (almost) each term of the momentum Eq.
3520    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
3521    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
3522    o remove MINIMAL_TAVE_OUTPUT option ;
3523      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
3524    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
3525      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
3526    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
3527    o add time-dependent SST, SSS control
3528    o cost terms in ecco/ modularized (new cost_generic.F)
3529    o cost_averages routines are modularized (new cost_averagesgeneric.F)
3530    o new infrastructure for seaice model vs. obs misfits in seaice/
3531      * driver from the_main_loop.F is seaice_cost_driver.F
3532      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
3533      * gradient check in Exp. 6a of natl_box_adjoint/
3534    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
3535      (see README file)
3536    
3537    checkpoint57q_post (2005/08/19)
3538    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
3539    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
3540      - bug was reported by Jean-Michel and Ian Fenty
3541    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
3542      update exp. cpl_aim+ocn output.
3543    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
3544      Needed for high-res. runs with large global files
3545      to be able to limit tapelev size
3546    o Changed some tests for adjoint:
3547      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
3548      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
3549      * global_ocean.90x40x15/ back to default 3-level checkpointing
3550    o Modifications to enable scripted COMMON to MODULE conversion
3551      * verification/OpenAD/code/ has necessary scripts and description;
3552      * converts, compiles and runs successfully;
3553    
3554    checkpoint57p_post (2005/08/01)
3555    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
3556    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
3557      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
3558    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
3559    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
3560      (was already the case for dissipation with mom_vecinv,
3561       and also the case for grad.PhiHyd when staggered-timeStep)
3562      This will allow to put dissipation out-off the AB time-stepping.
3563     Unfortunately, affects truncation error. Update output of exp. that "fails"
3564      (cg2d matching number) and leave the others for later: front_relax(10),
3565      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
3566      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
3567    
3568    checkpoint57o_post (2005/07/30)
3569    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
3570      (2) its ready to be documented during the 20050801 DocFest
3571    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
3572      for ideal_2D_oce and lab_sea on linux_ia32_g77
3573    o set to #undef CTRL_SET_OLD_MAXCVARS_30
3574      in global1x1_tot/code_seaice_adj to access indices 32, 33
3575      (worth another tag)
3576    
3577    checkpoint57n_post (2005/07/29)
3578    o adding precip control xx_precip 32
3579    o adding swflux control xx_swflux 33
3580    o Replacing 10 forcing penalty cost routines by 1 generic.
3581    o Implementing partitioning in time-mean and variable adjustment
3582      for atmos. state.
3583    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
3584    o in natl_box_adjoint:
3585      * updated exp 1 to 10
3586        (but does not have time-mean vs. variable split results yet)
3587    o updated global1x1/*_seaice_adj/
3588      to incorporate latest changes
3589    o enable useSingleCpuIO for mdsio vector routines
3590      (applies in particular to tapelev I/O)
3591    o removed inefficient K-loop in all active_file*control*.F
3592    
3593    checkpoint57m_post (2005/07/28)
3594    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
3595      and advect_cs (use EXCH-2 and standard cs-32 grid files).
3596    o pkg/exch2: filling of face-corner halo regions is optional
3597      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
3598    
3599    checkpoint57l_post (2005/07/14)
3600     tag before updating tutorials (pre-release-2)
3601    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
3602       for output and interpolation of input fields onto model grid)
3603    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
3604       Affects results of exp. rotating_tank ; update output.txt.
3605    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
3606          and taking the square quantity and/or using a fraction-weight field.
3607    o fix aim_diagnostics_init.F mate numbers.
3608    o add mnc output capability to diagnostics/diagstat and update
3609      our cvsignore files for the ACSII output generated
3610    
3611    checkpoint57k_post (2005/07/02)
3612    o lab_sea now uses diagnostics package and provides a suite of
3613      new EXF diagnostics output.
3614    
3615    checkpoint57j_post (2005/06/30)
3616    o exf
3617      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
3618        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
3619        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
3620      * extended diagnostics output
3621        - now includes all EXF variables
3622        - hs, hl moved to common block
3623        - separate S/R for diagnostics, called after ctrl vector is added
3624        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
3625        - EXFqnet contains true Qnet (i.e. includes qsw)
3626      * updated verif. lab_sea, global_with_exf
3627      * Rearranging hflux (exf_mapfields -> exf_getforcing)
3628        to ensure that diagnostics sees a true EXFqnet
3629    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
3630    o diagnostics pkg: change pointers so that 1 diagnostic can be used
3631      several times with different frequencies.
3632    o mnc-ify the thsice package as requested by Daniel Enderton
3633      - the monitor--MNC output needs work
3634      - many attributes need to be added (most are currently blank)
3635    o mnc-ify theaim_v23 package as requested by Daniel Enderton
3636      - many attributes need to be added (most are currently blank)
3637    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
3638    o add Sadourny like discretization to the 4th.O vorticity advection scheme
3639    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
3640      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
3641         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
3642    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
3643     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
3644    
3645    checkpoint57i_post (2005/06/19)
3646    o Diagnostics package was changed: diagnostic allocation is now deactivated
3647      by setting an empty file name in the namelist (used to be by setting 0 frequency)
3648    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
3649      add 1rst Order upwind vertical Shear.
3650    o add a quick fix for A/B checkpointing in OFFLINE mode
3651    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
3652      end-run around the C/Fortran linking horror in eesup/src/timers.F
3653    o added pkg/runclock: allows user to terminate run based on wall clock
3654    o added non-hydrostatic scaling parameter: nh_am2
3655    o pkg/my82: futile attempt to make results compiler-independent by adding
3656      some "_d 0", etc. no effect.
3657    o for mnc output, fill the 'T' coordinate var with myTime and create a
3658      separate 'iter' variable for iteration count
3659    o pkg/diagnostics:
3660      add new capability: output of Global/Regional & per-level statistics ;
3661      tested against monitor output (including land & thSIce) on various exp.
3662    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
3663    
3664    checkpoint57h_done (2005/05/19)
3665      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
3666      data.diagnostics, data.gchem, data.ptracers) is done.
3667    
3668    o pkg/diagnostics: prepare for Global/Regional statistics.
3669      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
3670    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
3671      and rename it: DIFFERENT_MULTIPLE
3672    
3673    checkpoint57h_post (2005/05/14)
3674    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
3675    o pkg/diagnostics: change output frequency, now in seconds (instead
3676      of Nb of iterations). This requires to change data.diagnostics.
3677    checkpoint57h_pre (2005/05/12)
3678    
3679    o in mnc, let the user create the output dir if both mnc_outdir_date
3680      and mnc_outdir_num are false
3681    o add fflags() to pkg/diagnostics which allows one to specify, on a
3682      per-file basis, the file precision [default behavior is unchanged]
3683    o added diagnostics to pkg/kpp, including computation of mixed layer
3684      depth based on a temperature/density criterion
3685    o updated verification/natl_box to test the new pkg/kpp diagnostics
3686    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
3687    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
3688    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
3689      not mnc -- this mistake was found by JMC and is now corrected
3690    
3691    checkpoint57g_post (2005/04/15)
3692    o add Adams-Bashforth 3rd Order time stepping:
3693      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
3694      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
3695    checkpoint57g_pre (2005/04/15)
3696    
3697    o make lambda[Theta,Salt]ClimRelax spatially varying
3698      (default remains spatially uniform constant based on tau)
3699    o added new control variables
3700      * init. uVel, vVel, etanN
3701      * lambda[Theta,Salt]ClimRelax
3702    o separate masks used for ctrl_pack/unpack 'from write_grid' output
3703      (suggested by G. Forget)
3704    
3705    checkpoint57f_post (2005/04/06)
3706    o add parameter "baseTime" = model base time = time at iteration zero
3707      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
3708      account for baseTime shift
3709    o move Coriolis arrays from PARAMS.h to GRID.h
3710    checkpoint57f_pre (2005/04/06)
3711    
3712    o mnc-ifying the seaice package
3713    o introduced an alternative length scale calculation for use in the limiting
3714      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
3715    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
3716    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
3717      as well as grad(vort3).  Made it compatible with both approximate form
3718      for the cubed sphere and full form of these gradients.  Added flag
3719      useFullLeith to select between approximate and full form.  
3720    o add "d0" in getcon.F to reduce differences between compilers/platforms
3721      update output.txt of exp. fizhi-gridalt-hs
3722    o change port_rand funtion to allow to set the seed.
3723    o fix obscure MNC bug involving conversion between reals and integers
3724      - it caused no problems with certain (eg. gcc, ifc) compilers but the
3725        new version is now more standards-compliant
3726    o adjoint-related modifications
3727      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
3728      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
3729      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
3730    
3731    checkpoint57e_post (2005/02/28)
3732    o Adding eddy stress controls a la Ferreira et al.
3733    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
3734    
3735    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
3736      update output.txt of exp. fizhi-gridalt-hs
3737    o add more "Z" dimensions and associated coordinate vars to MNC
3738    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
3739    o parameter calendarDumps: when set, approximate months (30-31 days) and years
3740      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
3741      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
3742      months and years.  Requires pkg/cal.
3743    o diagnostics: add pickup functionality
3744      - off by default for backwards compatibility
3745      - current version only uses MDSIO -- MNC will be added
3746    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
3747    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
3748    
3749    checkpoint57d_post (2005/02/11)
3750    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
3751    o modify verification/ideal_2D_oce so that it tests the creation of mnc
3752      output from the diagnostics package
3753    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
3754    o make genmake2 more portable by using ".$FS" instead of ".f" for more
3755      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
3756    o add coordinate variables to the MNC output from the diagnostics package
3757    o change MNC-flags default value: true when useMNC=TRUE
3758    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
3759      the ability (off by default) to read the grid information using MNC
3760    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
3761    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
3762    o do snap-shot diagnostics at the middle of the time-interval (instead of
3763      at the end).
3764    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
3765      new test for AIM with thSIce + slab-ocean
3766    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
3767    o move state variable diagnostics to the beginning of the time step ;
3768      (note: still needs some work specially for snap-shot diagnostics)
3769      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
3770    
3771    checkpoint57c_post (2005/01/27)
3772    o Change testing option (-ieee) to get closer agreement between g77 & ifort
3773    o generate new output.txt files on faulks with g77 & the new -ieee option
3774    checkpoint57c_pre (2005/01/27)
3775    
3776    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
3777      update output.txt of exp. global_ocean.90x40x15
3778    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
3779      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
3780    o add saltFlux(+File) forcing capability with periodicExternalForcing
3781    o allow to use pkg diagnostics for GM-Redi & ThSIce output
3782    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
3783    o improvements for the MNC output from DIAGNOSTICS:
3784      - correct handling of the unlimitied dimension
3785      - all dims now have associated coordinate variables
3786      - variables located at U, V, and Corner ("Z") points are now written
3787        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
3788        *all* data points are output
3789    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
3790    o added pkg/seaice/seaice_monitor.F
3791    o mdsio_readfield.F can now read files visible only to master MPI process.
3792    o pkg/seaice: some test code for ice-modified ocean stress
3793    o exf_getffields interpolation defaults to bilinear for all scalar forcing
3794      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
3795      spurious negative numbers for precipitation and humidity.  Will cause
3796      some small numerical differences for integrations using pkg/exf/exf_interp.F.
3797    o pkg/ctrl/
3798      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
3799        May be enabled via doPackDiag
3800      *  introduce z-scaling of
3801         + gradient (doZscalePack) and
3802         + control (doZscaleUnpack)
3803    o pkg/mdsio/
3804      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
3805      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
3806    
3807    checkpoint57b_post (2004/12/20)
3808    o simplify options in diagnostics_fill arguments (remove weird combinations)
3809    o fix MNC coordinate variables so that they now contain per-face index
3810      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
3811      general, EXCH2 grids are only aligned to a "local" coordinate system
3812    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
3813    o Implement instantaneous output within pkg diagnostics:
3814      setting a negative frequency in data.diagnostics produces
3815     "snap-shot" output (as opposed to time-average if freq > 0)
3816    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
3817      NOTE: change ptracer diagnostics name: use 2 characters to work with
3818            more than 9 tracers. Add also diagnostics of advect & diffus flux.
3819    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
3820      becomes the coordinate variable for the 'T' dimension
3821    o add CF-style coordinate variables to MNC
3822      - just a first cut:  numbers are meaningless on the cubesphere and
3823        missing along the T axis but otherwise it works!
3824    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
3825    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
3826    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
3827      this is based directly on what the model compute, so that the content of
3828      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
3829    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
3830    o clean up build options files for SunOS, in particular
3831      - remove -traditional from xmakedepend
3832      - change -xarch=v9 to -xarch=native for f77
3833      - restore use of make (not gmake)
3834      - add CC=gcc if using g77
3835    o changes per discussion of AM, JMC, & EH3 today:
3836      - move redundant "grid" variables out of "state" -- in preparation of
3837        creating proper CF-style coordinate variables and in recognition
3838        that any/all grid variables can be easily copied (eg. w/NCO) from
3839        the grid files into any of the other NetCDF files
3840      - *always* output grid variables with MDSIO (this will eventually be
3841        changed)
3842      - output MNC grid file if useMNC is true
3843    o every instance of _END_MASTER() has been found and replaced with
3844      _END_MASTER( myThid ) in order to satisfy certain picky Sun
3845      preprocessors
3846    o re-arrange diagnostics pkg initialisation:
3847     - allow each package to extend the available diagnostics list
3848     - add some checking and fix small problems (multi-threaded, ...)
3849     - new S/R diagnostics_fill (replace fill_diagnostics):
3850       look through the short list of active diag. (instead of the long list)
3851       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
3852    
3853    checkpoint57a_post (2004/12/10)
3854    o this set of changes restores TAMC compatibility
3855      tested for global_ocean.90x40x15 adjoint on trough
3856      (what a pain)
3857    
3858    checkpoint57a_pre (2004/12/10)
3859    o some modifs in tools/build_options for sunos
3860    o call ctrl_pack for ctrl at end for optimcycle=0
3861    
3862    checkpoint57 (2004/12/09)
3863    o add horizontal bi-harmonic viscosity for vertical velocity
3864      - new parameter viscA4W (defaults to viscA4)
3865      - affects only non-hydrostatic code
3866      - to be done: no-slip lateral boundary conditions
3867    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
3868    o implement Implicit Vertical advection for pTracers
3869    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
3870      (implemented also for implicit vertical diffusion & advection)
3871    o OBCS: extend application of tracer open boundary conditions
3872      to a strip beyond the boundary of width Olx/Oly
3873    o add call monitor to TAF set of required calls (flow directives)
3874      and include in natl_box_adjoint
3875    o untangle a few ifdefs related to cost, ctrl, autodiff
3876      untangel a few ALLOW_ECCO_OPTIMIZATION
3877    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
3878      (theta2, salt2 in ecco_cost_weights)
3879    
3880    checkpoint56c_post (2004/12/03)
3881    o OBCS as control variables
3882      - update ctrl_ad_diff.list, obcs_ad_diff.list
3883      - remove balance of obcs controls from default
3884      - fix index bug nobcs in ctrl_init
3885      - fix dummy fields filen in ctrl_pack
3886      - add dummy weights for obcs
3887    o lsopt: comment out fort.94 output
3888    o optim:
3889      - remove unnecessary header files
3890      - adjusted namelists
3891      - add xerbla.F to Makefile
3892    o exf:
3893      - multiple modifications of exf_check_range
3894      - unit change in exf_init_runoff from [m/year] to [m/s]
3895    o mdsio:
3896      - i/o-vector change debugLevel from debLevA to debLevB
3897    
3898    checkpoint56b_post (2004/12/01)
3899    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
3900      is called from DO_THE_MODEL_IO
3901      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
3902      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
3903      - clean up PTRACERS_WRITE_TIMEAVE a little
3904    o add another verification experiment that tests both the cfc-pkg and
3905      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
3906      reactive tendencies treated inline with regular timestepping
3907    o testreport previously did a lousy job of comparing small numbers, so
3908      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
3909      implemented in the little c-progam tmp_cmpnum.c which is embedded in
3910      testreport.
3911    o ptracers_monitor: bug fix for MPI
3912    
3913    checkpoint56a_post (2004/11/28)
3914    o GCHEM: finish reorganizating the package
3915      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
3916        (introduces another 3D-array for each passive tracer, but only if
3917        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
3918        gchemTendency is not needed because the timestep is done separately)
3919      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
3920      - GCHEM is now---more or less cleanly---separate from PTRACERS
3921      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
3922        so clear to me how that should be done in a general way.
3923    o CFC: improve formatting of output in CFC_ATMOS
3924    o PTRACERS:
3925      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
3926        that ALL experiments with ptracers enable can be checked. This makes
3927        GCHEM_MONITOR obsolete.
3928      - include a runtime parameter PTRACERS_monitorFreq that defaults to
3929        monitorFreq
3930      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
3931    o add PTRACERS (PTR0[1-5]) to testreport output
3932    o exf_check_range:
3933      * default changed to .TRUE.
3934      * will check values for niter0 if debLevA, every timestep if debLevB
3935      * STOP in exf_check_range if 'out of range'
3936      * range chosen generous to allow for potential extema
3937      TBD: a version with stricter range
3938           permitted range would be runtime parameters
3939    o GMredi:
3940      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
3941      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
3942      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
3943    o GCHEM:
3944      - move call to GCHEM_FORCING_SEP, so that it is now called before
3945        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
3946      - introduced a useGCHEM runtime flag and applied it everywhere.
3947      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
3948        this flag is now only visible within GCHEM-pkg routines.
3949      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
3950        be replaced by a 3D array that is computed before thermodynamics; for
3951        this, the tracer ID iTracer had to be included into the parameter list
3952        of ptracers_forcing
3953      - set up forward_step to call gchem_forcing, that will replace
3954        gchem_forcing_int in ptracers_forcing
3955      - cleaning up
3956    o small cleaning of exch2: remove files that are also in eesupp/src
3957    
3958    checkpoint56 (2004/11/17)
3959    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
3960    o mnc: cleanup "full" files--fixes out-of-memory problem
3961    o ECCO-GODAE
3962      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
3963      * fully merged and updated from SIO code
3964        windstress sign change affects
3965        - exf_inscal_[u/v]stress
3966        - sign of xx_tau[u/v] adjustments
3967        - signs in cost_scat
3968      * ctrl_get_gen: avoid update of tau[u/v] for first few days
3969      * natl_box_adjoint updated and compressed
3970      * 2-level checkpoint switch added
3971        (tested in EXP. 1 of natl_box_adjoint)
3972      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
3973    o SVD
3974      * first complete, non-hacked version for SVD calculations
3975      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
3976        performed via direct access files admtlm_vector.it????
3977        (via ctrl_[un]pack)
3978      * optimcycle is used for ARPACK iteration counter
3979        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
3980      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
3981        and add linear transforms where necessary
3982      * controls are initial/final SST, SSS (can be extended; need to check
3983        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
3984    o mdsio: filename info to both stderr, stdout
3985    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
3986      from sign change
3987    
3988    checkpoint55j_post (2004/11/10)
3989    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
3990      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3991    o add consistent build directories and .cvsignore files to verification
3992    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
3993    o make all subroutines 30 or less characters in length for certain older
3994      compilers to work (a thorough search only turns up two routines in
3995      pkg/ptracers)
3996    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
3997      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
3998    
3999    checkpoint55i_post (2004/10/28)
4000    o change arrays for total vertical diffusivity (2.D if explicit,
4001      3.D if implicit) ; each ptracer uses its own background value.
4002    o added mnc/NetCDF output capability to ocn_compon_interf
4003      - added bits to verification/cpl_aim+ocn so that it can run on
4004        ITRDA and other clusters without the mpirun "-wd" option
4005    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
4006      configuration
4007    o give MNC the ability to create additional files rather than
4008      exceeding a specified file size limit "MNC_MAX_FILESIZE"
4009      - the default is just less than 2GB which is a practical limit
4010        on many systems
4011    o Compute the non-local term using either KPP vertical diffusivity (=default)
4012       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
4013    
4014    checkpoint55h_post (2004/10/20)
4015    o add verification test "vermix"
4016    o remove all the *_ioinc flags and replace with the single global
4017      outputTypesInclusive flag
4018    o allow to set a vertical profile of vertical diffusivity for T & S
4019    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
4020    o useMNC moved from data.mnc to data.pkg
4021    
4022    checkpoint55g_post (2004/10/14)
4023    o Renaming carbon AD experiments to comply with testreport conventions
4024    o Updating adjoint of Held-Suarez hs94.1x64x5
4025    o Fixing directives for non-ECCO forward_step, after ECCO directives
4026      have been fixed to avoid recomp. of do_oceanic_phys
4027      Works well for global_ocean.90x40x15,
4028      but recomp. issue remains for carbon
4029    o Updating adjoint output for natl_box_adjoint after
4030      pkg/ecco has been modified (see taga c55d_post)
4031    
4032    checkpoint55f_post (2004/10/13)
4033    o rename to timeave_init_fixed
4034    
4035    checkpoint55e_post (2004/10/13)
4036    o some delicate re-shuffle of store directives to avoid one
4037      extra call of do_oceanic_physics
4038      affects ecco_the_main_loop.F, do_oceanic_physics.F
4039      checkpoint_lev1_directives.h
4040    o NB: this may break global_ocean adjoint temporarily,
4041      but it is clear how to fix it. Will do later, need this now.
4042    
4043    checkpoint55d_post (2004/10/11)
4044    o ECCO specific cost function terms (up-to-date with 1x1 runs)
4045    o ecco_cost_weights is modified to 1x1 runs
4046    o modifs to allow observations to be read in as
4047      single file or yearly files
4048    o enable to read exf forcing fields as either
4049      single file or yearly files (flag useExfYearlyFields)
4050    checkpoint55d_pre (2004/10/08)
4051    
4052    o switch between 2-level and 3-level checkpointing
4053    o add ability of MNC to write local and "partial" (eg. 2D slices where
4054      the full 3D field is never actually stored) arrays to NetCDF files
4055      with the correct (that is, the complete multi-dimensional) set of
4056      array indicies
4057      - used in mom_vecinv() to write the diagFreq output
4058      - tested (demonstrated) in verification/aim.5l_cs
4059    o further mnc-ification
4060      - add verification/lab_sea to the list with mnc setups
4061      - fix undefined mnc v-names in cd_code
4062      - add kpp to mnc output (both snapshot and timeave)
4063    o non-hydrostatic code
4064      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
4065        in calc_gw.F
4066      - defaults to viscAh
4067      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
4068        friction or Leith) in non-hydrostatic mode, as long as there is
4069        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
4070    o pkg/cost
4071      extend simple cost functions to treat time mean quantities
4072      (T,U,V) via cost_accumulate_state from cost_tile
4073    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
4074        be 2 times larger than the minimum size the advection scheme requires.
4075        now get a perfect conservation of salt in advect_cs test-exp (updated)
4076    o GGL90 (Gaspar's TKE mixed layer)
4077      - add horizontal diffusion of TKE, requires exchanges in
4078        do_fields_blocking_exchanges, horizontal diffusivity is zero by
4079        default. In OPA there is no horizontal diffusion of TKE but the
4080        mixing coefficients are computed from a horizontal average of TKE of
4081        6 points or so. I think that diffusion has a little more physical
4082        justification.
4083      - clean up ggl90_calc in the hope of reducing memory usage (this hope
4084        was in vain)
4085      - mask tke-variable in ggl90_init
4086    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
4087    o fix biharmonic diffusion on CS-grid.
4088    o more obcs stuff
4089      - added obcs_external_fields_load as an alternative to the EXF-pkg option
4090        for reading boundary values. This routine is called from
4091        obcs_prescribe_read
4092      - updated obcs_check
4093      - changed sponge layer relaxation parameter units for days to seconds
4094      - turned off sponge layer by default
4095      - changed argument list of OBCS_CALC to myTime+deltaTclock
4096      - fixed about 35 bugs in obcs_external_fields_load
4097    
4098    checkpoint55c_post (2004/09/23)
4099    o obcs stuff
4100      - new runtime flags useOBCSprescribe, useOBCSbalance
4101      - re-arranged obcs_calc
4102      - moved exf_getobcs to obcs_prescibe_read
4103        obcs_prescibe_read is called after ORLANSKI stuff
4104        and independent of it (executable can contain all).
4105      - updated obcs_check
4106      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
4107        These may be necessary only if tangential velocities are
4108        prescribed at OB, not sure, needs testing.
4109    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
4110      which simplifies the calls and passes the ifc check-bounds test
4111    
4112    checkpoint55b_post (2004/09/22)
4113    o add a 2D scalar, Z location, exchange_2 routine.
4114    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
4115      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
4116      affects advect_cs results (for the wrong reason): update output.txt
4117    o use a more standard discretization for biharmonic viscosity ;
4118     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
4119      affects results of dome set-up: update output.txt
4120    o fix gad_advection.F (CubedSphere part), back to version 1.23
4121    o fix bug in mom_vi_del2uv.F (CubedSphere part).
4122    
4123    checkpoint55a_post (2004/09/20)
4124    o merged code to
4125      * prescribe/read time-dependent open boundaries
4126        (works in conjunction with exf, cal)
4127      * sponge layer code for open boundaries
4128      * each boundary N/S/E/W now has its own CPP option
4129        (healthy for the adjoint)
4130    
4131    checkpoint55 (2004/09/17)
4132    o up-to-date adjoint of previous breaks
4133      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
4134      - global_ocean_ebm: adjoint still needs fix (TLM ok)
4135      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
4136      - carbon: * remove tr1-related adjoint verification
4137                * add ptracer as control variable
4138    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
4139      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
4140    
4141    checkpoint54f_post (2004/09/16)
4142    o in verification/carbin/ remove experiment related to
4143      ALLOW_PASSIVE_TRACER (array tr1 etc)
4144      code_ad/ input_ad/ results_ad
4145    
4146    o add two new packages
4147      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
4148        + subject to optimization (memory)
4149      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
4150        + subject to reordering (many GOTOs in the original code)
4151        + so far opps is called for every (i,j) point, and then operates in
4152          the vertical; one may want to reorder the scheme in order operate in
4153          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
4154          fields)
4155    o overhaul of IO so that we now have flags for MDSIO and/or MNC
4156      - all verification tests compile and run with linux_ia32_g77
4157      - defaults are compatible with current input files--nothing
4158        should change if you were not previously using MNC
4159      - MNC output has been added in numerous places (eg. timeave)
4160        but there are still a few writes not yet do-able with MNC
4161        (this is in progress)
4162      - flags now allow for either/or/both use of MDSIO and MNC and
4163        documentation will soon follow
4164      - numerous small formatting cleanups for ProTeX
4165    o add version info (via BUILD_INFO.h) to MNC and stdout
4166    
4167    checkpoint54e_post (2004/09/02)
4168    o add two new packages
4169      - pp81 (Packanowski and Philander, 1981), Richardson number and
4170        stratification dependent mixing
4171      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
4172      - these scheme operate in a similar manner as KPP (without ghat, of
4173        course), however there is only one diffusivity that is used for both
4174        temperature and salinity (and passive tracers)
4175    o add offline package
4176    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
4177      provided by Stephanie Dutkiewicz
4178    o genmake2: add ability to search for C compilers and cleanup test output
4179      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
4180    
4181    checkpoint54d_post (2004/07/27)
4182    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
4183    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
4184      leading to additional shift by 5 days each year of integration
4185       (i.e. leading to considerable offset over the years)
4186    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
4187    o start with no AB and no initial filtering (staggerTimeStep):
4188      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
4189    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
4190      (external loading & cpl import/export stay in forward_step.F)
4191    o update coupling interface to work with new staggerTimeStep
4192    o change MDSIO ptracers_pickup.
4193    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
4194    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
4195    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
4196    
4197    checkpoint54c_post (2004/07/18)
4198    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
4199      this affects (truncation error) output.txt of test-exp:
4200       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
4201    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
4202    o change Qnet to always be the net heat flux, (+upward).
4203      affects (truncation error) output of natl_box exp.: updated
4204    o define the max number of passive tracers in PTRACERS_SIZE.h
4205    o start to test mnc routinely in exp0
4206    o add sea-ice loading (sIceLoad) as a new forcing field.
4207    
4208    checkpoint54b_post (2004/07/08)
4209    o add testreport "-j JOBS" option for parallel builds (tested and pretty
4210       impressive on Altix and Opteron systems)
4211    o diagnostics can now write NetCDF files through the mnc package
4212    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
4213    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
4214    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
4215      affects (truncation error) output of lab_sea & natl_box exp.: updated
4216    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
4217    
4218    checkpoint54a_post (2004/07/06)
4219    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
4220    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
4221    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
4222    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
4223      + internal_wave (shift in writing cg2d_ini_res)
4224    checkpoint54a_pre (2004/07/05)
4225    
4226    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
4227      - modified verification/lab_sea and natl_box_adjoint accordingly
4228    
4229    checkpoint54 (2004/07/02)
4230    checkpoint53g_post (2004/07/02)
4231    o prepare splitting of thermodynamics: store convect.counter in common block
4232    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
4233      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
4234    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
4235    o new parameter "nShapS": allow to treat differently S from T (nShapT)
4236    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
4237    o restore adjointability
4238    
4239    checkpoint53f_post (2004/06/25)
4240    o modifications that affect AIM experiment results (update output.txt):
4241      - no advection of S at top interface Nr (pkg/generic_advdiff)
4242      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
4243    o AIM pkg:
4244      - include stability function into surf.Flux derivative relative to Tsurf
4245      - calculate clear-sky radiation & surface temp. change (for diagnostics)
4246    
4247    checkpoint53e_post
4248    o merged cylindrical coord configuration
4249    o added rotating_tank experiment
4250    checkpoint53e_pre
4251    
4252    checkpoint53d_post (2004/06/14)
4253    o faulks upgraded: re-generate output.txt that have changed:
4254       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
4255    o Added Bryan and Lewis, 1979, vertical diffusivity profile
4256    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
4257    o added Sadourny discretization of Coriolis
4258      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
4259      - re-enabled use of omega3 (useAbsVorticity)
4260    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
4261      vector-invariant equations
4262      - note: does *NOT* yet use same variable visc. for no-slip BC's.
4263    o recoded the lateral boundary conditions for non-hydrostatic w, this time
4264      hopefully without new bugs
4265      - still to do: biharmonic friction for non-hydrostatic w
4266    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
4267    o regenerated output for global_ocean_ebm (using -ieee)
4268    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
4269      of mom_common/
4270      - simple re-arrangement of instructions within computing loop
4271    checkpoint53d_pre (2004/05/21)
4272    
4273    checkpoint53c_post (2004/05/21)
4274    o new version of coupler for AIM+thSIce and Ocean models
4275     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
4276     - land: change Evaporation of snow
4277     - aim with thSIce: fix bug in snow-precip.
4278    o changes to calc_gw.F
4279     - bug fix for w^2 term near the bottom boundary
4280     - (hopefully) improve the lateral slip boundary condtions for use with
4281        partial/looped cells
4282      - because the bug fix changes two verification experiments anyway (exp5
4283        and plume on slope), change the lateral boundary condition from half slip
4284        to the value of no_slip_sides
4285    o ebm package wasnt quite up to the parallel task. Fixed that.
4286    o Adjoint of EBM package + verification
4287      * TLM OK
4288      * ADM not sufficient accuracy yet (needs further testing)
4289    
4290    checkpoint53b_post (2004/05/14)
4291    o Commiting new energy balance model to repository
4292      * package is pkg/ebm
4293      * verif. is verification/global_ocean_ebm
4294      * references are in ebm_driver.F
4295    C      * X. Wang, P. Stone and J. Marotzke, 1999:
4296    C        Global thermohaline circulation. Part I:
4297    C        Sensitivity to atmospheric moisture transport.
4298    C        J. Climate 12(1), 71-82
4299    C      * X. Wang, P. Stone and J. Marotzke, 1999:
4300    C        Global thermohaline circulation. Part II:
4301    C        Sensitivity with interactive transport.
4302    C        J. Climate 12(1), 83-91
4303    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
4304    C        Destabilization of the thermohaline circulation
4305    C        by atmospheric eddy transports.
4306    C        J. Climate 7(12), 1870-1882
4307    o Will need long integration testing.
4308    checkpoint53b_pre (2004/05/14)
4309    
4310    o created pkg/mom_common in preparation for variable viscosity code
4311    o renamed and split ini_mnc_io
4312    o pkg/land: only liquid water can diffuse or run-off
4313    o AIM using land: soil wetness availability account for snow
4314    o added printMapIncludesZeros to EEPARMS namelist
4315    
4316    checkpoint53a_post (2004/05/11)
4317    o restore TAMC compatiility for exf_constants.h
4318      (no usage of _d in .h)
4319    o Additional storing in KPP in an attempt to fix
4320      TAMC problem with adjoint of KPP code.
4321      (no success...)
4322      Identical code works fine with TAF.
4323    o Fixed verification/natl_box_adjoint experiments.
4324      Initial conditions for Experiments 4 and 5 are now
4325      set to "SEAICE_initialHEFF=0", which is more reasonable,
4326      and hence gives results closer to that of Experiment 2.
4327      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
4328    
4329    checkpoint53 (2004/05/06)
4330    o stable checkpoint with up to date adjoint
4331      TLM tests only run for 1st grdchk at the moment. Its unclear if
4332      this is a code problem or a problem with resetting code for g_
4333      variables that is being autogenerated wrong.
4334      Otherwise:
4335       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
4336       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
4337         are both still in chaos following their security messes.
4338    
4339    checkpoint52n_post (2004/05/06)
4340    o various build (mostly genmake2) changes including:
4341      - ability to build/run more easily within Cygwin and MacOS X
4342      - more complicated Makefiles with a stronger dependence on Gnu Make
4343    o pkg/seaice modifications
4344      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
4345        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
4346        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
4347      - changed proxy for geostrophic velocity and updated
4348        verification/lab_sea/results/* accordingly
4349      - removed ADI dynamic solver from pkg/seaice
4350      - replaced all occurrences of 1/CSTICE or 1/CSUICE
4351        they caused a segmentation fault under certain circumstances
4352      - removed unused field WATR
4353    o bug fix in exf-package:
4354      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
4355         now reflect that.
4356    o small fixes in the cal-package:
4357      - set reference date to first of January for the 'model'-calendar
4358      - failing of cal_CheckDate in cal_FullDate now actually results in a
4359        warning
4360    o small modifications in exf-package to increase flexibility:
4361      - change climtempfreeze from a constant to a runtime parameter that
4362        is specified in data.exf_clim (default = -1.9)
4363      - introduce runtime parameter windstressmax (default = 2.0) that is
4364        specified in data.exf
4365    o fix in pkg/thsice:
4366      - update Evap (Tsf changes) to be consistent with Latent heat flux
4367      - maintain snow precipitation unchanged (even if Tsf >=0).
4368     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
4369    
4370    checkpoint52m_post (2004/04/18)
4371    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
4372      this does not change any of the results, because myIter=0 in swfrac always
4373      lead to jwtype=2 (the default anyway), but the call makes little sense
4374      as a default
4375    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
4376    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
4377      atmospheric model (AIM) to use it ; add a "slab ocean" component.
4378    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
4379    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
4380    o extending useSingleCpuIO option to work with new exch2 I/O format
4381      - old-style, missing-tile I/O is still accessible by defining CPP
4382        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
4383    o monitor package can write to NetCDF files and/or STDOUT
4384    o fix re-definition bug in MNC_GRID_INIT_ALL()
4385    o doc/api_reference added
4386      - a framework for building an API Reference Manual using all
4387        the "protex" comments embedded in the code
4388      - see pkg/generic_advdiff, pkg/mnc for examples
4389    o MNC:
4390      - make myThid the last argument for all subroutines
4391      - new default for the grid files: NO halos
4392      - add useMNC and other run-time flags
4393      - separate per-file-group handling of the unlimited dimension
4394      - early initialization of MNC w/ flags read at the eeboot stage
4395        and lookup tables set in initialize_fixed
4396      - write all MNC output to a freshly-created directory
4397    o thermodynamics sea-ice (thsice) is now tested with testreport.
4398    o test exp. advect_cs: use the standard cs32 grid ; update output.
4399    o Added functionality to grdchk:
4400      pick global i,j,k position (or nearest wet) where to perform check.
4401    
4402    checkpoint52l_post (2004/03/11)
4403    o new land formulation:
4404      a) use ground enthalpy as prognostic variable to ensure exact
4405         energy conservation.
4406      b) account for water temperature and for latent heat of freezing
4407         in all processes (rain, run-off, ground storage)
4408      c) compute surface and ground temperature implicitly.
4409    o aim_v23 modification for new land model:
4410      a) Treat separately land / ocean / sea-ice surface fluxes
4411         to allow implicit computation of land & sea-ice surface temp.
4412      b) add snow precipitation.
4413    checkpoint52l_pre (2004/03/11)
4414    
4415    o fix problem (when 1 tile is empty) in min/max monitor.
4416    o fix bug in timeAve (u,vZetatave in common block)
4417    o no restoring terms under ice for pkg/seaice
4418    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
4419    o bug fix for pkg/seaice pickups
4420    o change MNC call locations and add coordinate attributes
4421    o mask vorticity at the corner ; affects global_ocean.cs output
4422    o fix ini_curvilinear_grid ; test CS experiments with mpi
4423    o aim.5l_cs: modify sea-ice fraction input file ; update output
4424    o exf: Adding simple range check routine for exf fields after read
4425    
4426    checkpoint52k_post (2004/02/23)
4427    o removed top-level directory "diags"
4428      - we migrated these functions to pkg/timeave a long time ago
4429    o fixed bug introduced in pkg/monitor
4430    o accuracy ctrlprec = 32 insuffient for gradient checks using
4431      averaged fields (I/O via cost_averages)
4432      -> use ctrl.h in active_file*.F to control I/O precision.
4433    o paramter list of CALL ADTHE_MAIN_LOOP
4434    o added initial do_the_model_io to ecco
4435    o set all ...Freq to zero after cost_final
4436      taveFreq, dumpFreq, pChkptFreq
4437    o MAIN and ECCO differentiability restored
4438    
4439    checkpoint52j_post (2004/02/18)
4440    o fix nchklev in tamc.h for global_ocean...
4441    o Bringing flow and store directives up-to-date
4442    o Really weird thing!
4443      call do_the_model_io from the_main_loop with parameters
4444      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
4445      TAF places a faulty re-call of initialise_varia
4446      after cost_final call which should not be there!
4447    checkpoint52j_pre (2004/02/03)
4448    
4449    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
4450      error messages
4451    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
4452    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
4453      debug output
4454    o modfied mdsio_writefield.F to handle non-global files under exch2
4455    o update AIM Cubed-Sphere exp (aim.5l_cs):
4456      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
4457    o update AIM Equatorial Channel exp:
4458      use standard aim_v23 pkg and change the SST fields to be more realistic.
4459    o globalFile now works with exch2
4460    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
4461      mon_vort3.F to make exch2 friendly with >1 tile per cube face
4462    o limit timeave output for hi-res integrations
4463    
4464    checkpoint52i_post (2004/01/21)
4465    o removed CPP_EEOPTIONS.h from verification/*/code
4466    o updated the tiling for global_ocean_pressure
4467    checkpoint52i_pre (2004/01/20)
4468    
4469    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
4470      the old pkg/aim).
4471    
4472    checkpoint52h_pre (2004/01/20)
4473    o shortened offending lines in exch2_send_rx?.template
4474    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
4475    o genmake2: add build & execute test for NetCDF code
4476    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
4477      old grid files, moved CPP_EEMACROS.h to pkg/exch2
4478    o added useSingleCPUIO flag to monitor.F and mon_out.F
4479    o added temporary hack for sea-ice dynamics on the cube:
4480      metric terms are ignored and it is assumed that
4481      there is no sea-ice on cube faces 1, 2, 4, and 5.
4482    
4483    checkpoint52f_post (2004/01/09)
4484    o added exch2 cube routines to pkg/exch2
4485    o modified hs94.cs-32x32x5 to use it
4486    o added new grid files to hs94.cs-32x32x5
4487    checkpoint52f_pre (2004/01/07)
4488    
4489    checkpoint52e_post (2004/01/07)
4490    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
4491      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
4492    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
4493      to work with implicit vertical advection and AB ;
4494    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
4495    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
4496     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
4497    checkpoint52e_pre (2004/01/02)
4498    
4499    o fix bug in impldiff when Nr=1 or Nr=2.
4500    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
4501    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
4502    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
4503      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
4504    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
4505    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
4506    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
4507    
4508    checkpoint52d_post (2003/12/16)
4509    o re-tiled many expts to allow comparison in multi-processor mode
4510      - updated output accordingly
4511      - changed hs94.128x64x5 to use intial T from file rather than use the
4512        random number generator
4513    o add infrastructure in model routines for fizhi and gridalt packages
4514    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
4515    o changes to permit hi-res, cubed-sphere, configuration
4516      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
4517      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
4518      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
4519        of surface winds for the cube
4520      (A verification experiment, based on global_ocean.cs32x15, but with
4521       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
4522       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
4523       complete with example surface forcing files and matlab scripts to look
4524       at the output and compare it with that of global_ocean.cs32x15.)
4525    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
4526       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
4527       to conform to the common rule.
4528    o check-in the first version of the coupler + interfaces for multi-components
4529       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
4530       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
4531       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
4532       - ocean and atmos. share the same horizontal grid (no interpolation).
4533       - exchanges between component and coupler is done in forward_step
4534    o new verification experiment, cpl_aim+ocn:
4535       coupled ocean - AIM atmosphere on cs32 grid.
4536    
4537    checkpoint52d_pre (2003/12/06)
4538    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
4539    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
4540    
4541    checkpoint52c_post (2003/11/25)
4542    o Fixing OPTIONS files for use of exf:
4543      - ALLOW_ECCO not needed
4544      - ECCO_CPPOPTIONS.h should not be included from
4545        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
4546        as has been the case in the past
4547      - All cal/exf related options are currently set in
4548        single header file. Should remain so until we
4549        agree on a consistent new policy.
4550    o Removed all CPP options for cal package.
4551      cal has no more CPP options.
4552    o modified STOREs in GAD_ADVECTION
4553    o corrected key comp. for passkey
4554    
4555    checkpoint52b_post (2003/11/23)
4556    o new version: "thsice" of thermodynamic sea-ice pkg:
4557     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
4558     - modify fluxes but do not change theta directly;
4559     - light cleaning of bulk_force pkg (still needed with thsice).
4560     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
4561       + output_thsice.txt to test thsice & bulk_force pkgs.
4562    o put back grid & coriolis monitor output.
4563    checkpoint52b_pre (2003/11/23)
4564    
4565    o call "do_the_model_io" at the beginning (=> dump initial state)
4566    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
4567    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
4568      (need info on NUMBER_OF_PTRACERS)
4569    o missing PTRACERS headers in some routines
4570    o default tamc.h in pkg/autodiff supposed to crash
4571      to ensure proper customization
4572    
4573    checkpoint52a_post (2003/11/17)
4574    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
4575      - moved surfaceTendencyTice from pkg/seaice to main code
4576      - subroutine FREEZE_SURFACE now limits only surface temperature
4577        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
4578        => new output.txt for global_ocean.cs32x15 & global_with_exf
4579      - keep the old version of FREEZE for backward compatibility;
4580        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
4581      - corresponding modifs for TAF directives
4582    o added surface flux output variables to TIMEAVE_STATVARS
4583    o time-averaged output for pkg/ptracers
4584    o fix problem with ECCO-related divided adjoint
4585      snapshot file was missing some ad-variables,
4586      but no warning issued by TAF
4587    
4588    checkpoint52a_pre (2003/11/12)
4589    o some bug fixes for #undef REAL4_IS_SLOW
4590    
4591    checkpoint52 = ecco_c52_e35
4592    o after testing adjoints of checkpoint51u_post
4593    
4594    checkpoint51u_post (2003/11/06)
4595    o this is the post-merge tag of the ecco-branch
4596      (needs another clean checkout and re-testing)
4597    o various natl_box_adjoint configs and results
4598      but no input fields
4599    o obcs adjoint not yet merged!
4600    o adding ECCO global 1x1 and 2x2 degree configs
4601    o updated/extended some store directives for seaice
4602    o pkg/ecco now containes ecco-specific part of cost function
4603    o top level routines the_main_loop, forward_step
4604      supersede those in model/src/
4605      previous input data.cost now in data.ecco
4606      (new namelist ecco_cost_nml)
4607    o in ctrl/ cleaned some cross-dependencies and updated CPP options
4608    
4609    checkpoint51t_post (2003/11/04)
4610    o this is the pre-merge tag of the ecco-branch
4611    
4612    checkpoint51s_post (2003/11/04)
4613    o cleanup: removed various obsolete #define-s
4614    o pkg/grdchk
4615      - renamed 'ph-grd 3' to 'grad-res'
4616      - merged from ecco-branch
4617        (remaining bug fixes for obcs gradient checks)
4618      - additional high-precision output for testreport
4619        (grep for 'precision_grdchk_result')
4620    
4621    checkpoint51r_post (2003/11/03)
4622    o cleaned up or removed CPP_OPTIONS.h files
4623    o updated results for some of the tests to reflect the new
4624      optfiles (-ieee: -O0 instead of -O3)
4625    
4626    checkpoint51q_post (2003/10/30)
4627    o cd_code:
4628      - moved cd_scheme.F -> cd_code_scheme.F
4629      - separate read_checkpoint from cd_code_ini_vars.F
4630      - separated cd_code part from write_checkpoint
4631      - updated AD_SOURCE, generated .flow
4632      - added CD_CODE_VARS.h to the_main_loop
4633      - Moving cd_code specific store dir.s to pkg/cd_code
4634    o ctrl package totally restructured
4635      - pack/unpack now optional and decoupled from
4636        xx_/adxx_ I/O
4637      - ctrl_pack/unpack cleaned
4638        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
4639      - confined inclusion of AD_CONFIG.h to where necessary.
4640    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
4641    
4642    checkpoint51p_post (2003/10/30)
4643    o create initial cd_code package
4644      - WARNING: the initialization of fields within packages
4645        is broken because INI_FIELDS (where READ_CHECKPOINT is
4646        called) is called *before* PACKAGES_INIT_VARIABLES.
4647        This seems to be backwards since
4648        1) its important to initially zero the entire field including
4649           the "halo" region
4650        2) zeroing needs to be done *before* reading pickup info
4651           and the pickup call might or might not happen in any
4652           particular run
4653      - this needs an overhaul for R2
4654    o cleanup verification/*/code/GMREDI_OPTIONS.h
4655    o cleanup testreport
4656    
4657    checkpoint51o_post (2003/10/27)
4658    o bringing AD-related verif's up to date with genmake2
4659      - carbon/
4660      - global_ocean.90x40x15/
4661      - hs.94.1x64x5/
4662      - (front_relax/ )
4663    o (more) consistent directory structure for AD-related verif.'s
4664    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
4665    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
4666    o bug fix in find_alpha.F for MDJWF:
4667      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
4668        change rho -> rho-rhoConst
4669      - replace call find_rho to find_rhonum
4670    o initialisation of rFlx extended to full array (required by TAF)
4671      and shifted to thermodynamics
4672    o removed PTRACERS.h in ptracers routine
4673    o added surfacetendencyPtr to S/R parameter list pracers_forcing
4674    o Correcting initialisations for fVerU, fVerV.
4675    o helping TAF to recognize dependency on kUp for
4676      fVerU, fVerV
4677    o Replacing delZ by delR in pkg/ctrl/
4678    checkpoint51o_pre (2003/10/24)
4679    
4680    o undid all of cp51 pending some cleanups and discussion
4681    o added the [#include "AD_CONFIG.h"] statement to all files that need
4682       it for adjoint/tl #defines
4683     o re-worked the build logic in genmake2 to support AD_CONFIG.h
4684     o removed tools/genmake since it no longer works
4685    
4686    checkpoint51n_post (2003/10/23)
4687    o modifications to make FREEZE flux visible to pkg/kpp
4688      - moved surfaceTendencyTice from pkg/seaice to main code
4689      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
4690      - subroutine FREEZE now limits only surface temperature
4691        (this means new output.txt for global_ocean.90x40x15,
4692         global_ocean.cs32x15, and global_with_exf)
4693    o added surface flux output variables to TIMEAVE_STATVARS
4694    
4695    checkpoint51n_pre (2003/10/23)
4696    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
4697    o added [#include "AD_CONFIG.h"] to all files that use the following
4698      defines:
4699      - ALLOW_ADJOINT_RUN
4700      - ALLOW_TANGENTLINEAR_RUN
4701      - ALLOW_ECCO_OPTIMIZATION
4702    
4703    checkpoint51m_post (2003/10/21)
4704    o incorporating changes to get TAMC/TAF working in genmake2
4705      - added new TAMC/TAF targets to the Makefile
4706      - various cleanups related to package handling
4707      - these changes should have no impact on the forward model
4708    
4709    checkpoint51l_post (2003/10/20)
4710    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
4711     - faster algorithm for cal_addtime.F
4712     - higher precision arithmetic, where needed
4713     - pkg/exf *startdate variables changed from calendar date to
4714       model integration time
4715    
4716    checkpoint51l_pre (2003/10/17)
4717    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
4718    o enable to apply restoring on S & T only in a latitude band.
4719    o update output (external_forcing_surf modif. change truncation errors)
4720       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
4721    
4722    checkpoint51k_post (2003/10/16)
4723    o change default to: useNHMTerms=.FALSE.
4724     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
4725       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
4726     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
4727        exp1, ideal_2D_oce
4728     - change data file of oceanic exp (leave the results unchanged for now)
4729       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
4730    o set gravitySign automatically according to the vertical coordinate used
4731      (and change sign: back to "logical" value: +1 when R increases downward)
4732    o added an include barrier to the default CPP_OPTIONS.h and
4733      removed the #include "PACKAGES_CONFIG.h" from it
4734    o fix a bug in mom_fluxform (from chk51j_post)
4735    
4736    checkpoint51j_post (2003/10/10)
4737    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
4738    o adjusted some flow directives (dynamics, thermodynamics)
4739    o added cubed-sphere case to test cost function
4740    o heckpoint_lev?_directives.h now include
4741      pkg-specific directives, whenever those are enabled.
4742    o Moving pkg-specific flow directives to corresponding pkg
4743      Moving pkg-specific differentiation list to corresponding pkg
4744      Moving pkg-specific checkpoint-lev storing to corresponding pkg
4745      ---> conventions are
4746           - pkg_ad.flow
4747           - pkg_ad_diff.list
4748           - pkg_ad_check_lev?_dir.h
4749    
4750    checkpoint51i_post (2003/10/09)
4751    o merge of the branch-genmake2
4752      - knowingly breaks the older genmake
4753      - automatic generation of all ALLOW_${PKG_NAME} defines
4754      - new testreport supersedes older testscript
4755    o large number of package inclusion and header cleanups
4756    checkpoint51i_pre (2003/10/08)
4757    
4758    o new output for adjoin of global ocean vector invariant
4759    o fix for checkpoint of thermodynamic seaice and bulk_force
4760    o Steph gchem various cleanups
4761    
4762    checkpoint 51h_pre
4763    o fixed some single quotes
4764    o modify gchem pkg to be more versatile
4765    o modifications to clean up dic pkg
4766    o add pkg/cfc
4767    
4768    checkpoint51g_post (2003/10/02)
4769    o provide links for ARPACK and ADM*TLM
4770    o start removing verification/vero/
4771    o update AD-related stuff
4772      (in particular some IF-statements in model/src/ routines)
4773    o adding to verification/global_ocean.90x40x15/ adjoint of
4774      vector invariant setup
4775    
4776    checkpoint51f_post (2003/10/02)
4777    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
4778    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
4779      of tracer Green's fucntions for ocean inversion project.
4780    
4781    checkpoint51f_pre (2003/08/07)
4782    o Added on-the-fly spatial interpolation capability
4783        "USE_EXF_INTERPOLATION" to pkg/exf.
4784      - This is a temporary Cartesian-grid hack until
4785        the super-duper ESMF coupler becomes available.
4786      - See verification/global_with_exf/README for usage example.
4787      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
4788        flags and modified pkg/seaice accordingly.
4789    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
4790        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
4791        non-local transport term.
4792    
4793    checkpoint51e_post (2003/08/03)
4794    o pkg/mom_vecinv:
4795      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
4796      - add time-ave diagnostic of vorticity advection.
4797    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
4798    o atmospheric geopotential: - include water vapor effect;
4799                                - use p^kappa in p* scaling.
4800    o land pkg: read initial state from files.
4801    o AIM : add stratospheric drag in the upper level
4802    
4803    checkpoint51d_post (2003/07/18)
4804    o change function ILNBLNK (=> last non-blank char.) to return zero
4805      (instead of the string length) when the string. char is empty
4806    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
4807    o modif's to restore TAMC compatibility
4808      - avoid "_d" constructs in PARAMETER declarations
4809      - avoid interrupting lines by comment lines
4810    o Use cluster local disks for purely local I/O
4811      vs. globally visible disks needed for ctrl stuff
4812      (merged from ecco-branch)
4813      - new active_file_loc... and mdsio_..._loc routines
4814      - affected packages: autodiff, ctrl, grdchk, mdsio
4815    
4816    checkpoint51c_post (2003/07/08)
4817    o introducing integer flag debugLevel
4818      - debLevZero: suppress all output
4819      - debLevA: standard
4820      - debLevB: equivalent to current debugMode=.TRUE.
4821    o introducing pathname variable mdsioLocalDir for mdsio
4822      that can be specified at runtime
4823      (relevant for cluster I/O to local disk)
4824    `
4825    >>>checkpoint51b_post
4826    adjoint of ptracers
4827    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
4828    o extended state in checkpoint_lev?, etc.
4829    o alternative ctrl/cost with tr1 or ptracer
4830    o new comlev1_bibj_ptracers
4831    o new ptracers.flow
4832    o made ptracers_forcing same as external_forcing_s
4833    o added verification for adjoint with ptracers
4834      - adm. grdchk fail so far
4835      - tlm. grdchk OK
4836      - checked tapelev/comlev recomputations: OK
4837    <<<checkpoint51b_pre
4838    
4839    checkpoint51a_post (2003/06/25)
4840    o added code for biogeochemistry package
4841      - new pkgs: dic, gchem
4842      - new subroutine in ptracers
4843    o modify code for biogeo packages
4844      - in model/src and pkg/ptracers
4845    
4846    checkpoint51 (2003/06/24)
4847    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
4848      - autodiff, ctrl, exf, grdchk, seaice
4849      kept separate packages
4850      - cost, ecco, obcs
4851    o updating verification/internal_wave, verification/lab_sea
4852      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
4853    
4854    checkpoint50i_post (2003/06/23)
4855    o Preparing next differentiable checkpoint and sync
4856      of MAIN vs. ecco-branch
4857      - 1st step: this one is differentiable
4858      - 2nd step: next(! not this) checkpoint will have updated packages
4859                  from ecco-branch)
4860    
4861    checkpoint50h_post (2003/06/20)
4862    o new package "land": provide surface BC for AIM.
4863    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
4864    o AIM: use true log-P extrapolation for near surface temp (= as in
4865        F.Molteni paper) ; update aim.5l_cs output.
4866    o New variable in PARM03 for more flexible pickups
4867    o somewhat cleaned package initialisation sequence for
4868      ctrl/ cost/ ecco/ in packages_... routines
4869    
4870    checkpoint50g_post (2003/05/23)
4871    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
4872      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
4873      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
4874        made the default because of faster convergence than ADI
4875    
4876    checkpoint50f_post (2003/05/23)
4877    o exf totally restructured
4878      - replaced all exf_set_ routines by one generic exf_set_gen.F
4879        and made sure it's still differentiable
4880      - split exf_getffields.F into new exf_bulkformulae.F
4881      - exf_inscal_/exf_outscal_ suffixes consistent with field names
4882      - updated adjoint/makefile and relevant verif. accordingly
4883    
4884    checkpoint50f_pre (2003/05/23)
4885     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
4886          + change Evap over land. (update aim.5l_cs output)
4887     o added missing .cvsignores and made uniform across expts
4888     o changed configuration of tidal_basin_2d expt
4889     o added pkg/debug functions for tracing code in fatal crashes
4890     o tidied pkg/monitor to use MONITOR_OPTIONS.h
4891     o new fn in pkg/monitor to stop model if solution grows too big
4892     o removed lots of single quotes from comments
4893    
4894    checkpoint50e_post (2003/05/14)
4895    o make KPP work with PTRACERS
4896     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
4897       nearly a copy of kpp_transport_s
4898     - there is no analogue to SurfaceTendencyS, so I have to use
4899       gPtr(of the surface layer) instead
4900    o add a new platform SunFire+mpi (SunFire 15000) to genmake
4901    checkpoint50e_pre (2003/05/13)
4902    
4903    checkpoint50d_post (2003/05/13)
4904    o change kpp output from multiple-record state files to single-record state
4905      files analogous to write_state.F
4906    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
4907      analogous to the cg2d-related output.
4908    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
4909      so that writing to internal file fn (with length 512) fails.
4910    checkpoint50d_pre (2003/05/12)
4911    
4912    checkpoint50c_post (2003/05/12)
4913    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
4914    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
4915    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
4916    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
4917    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
4918    
4919    checkpoint50c_pre (2003/04/30)
4920    Merging from release1_p13:
4921    o bug fix for pkg/seaice dynamic solver
4922    o Added SEAICE_initialHEFF to pkg/seaice
4923    
4924    checkpoint50b_post (2003/04/17)
4925    o store u*,v* in gU,V instead of in guNm1,gvNm1
4926    o in order to put the momForcing out of the Adams-Bashforth:
4927      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
4928      to timestep.F
4929    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
4930    o re-generate output for highly sensitive test-exp:
4931       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
4932    
4933    checkpoint50b_pre (2003/04/17)
4934    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
4935    o corrected CPP option mismatch in exf_Bulk... functions for case
4936      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
4937    
4938    checkpoint50a_post (2003/03/21)
4939    o Bug fix for merging between c50 and KPP.
4940      ikey was passed from thermodynamics to kpp_calc via
4941      common block rather than being recomputed in kpp_calc,
4942      in contradiction with new key itdkey.
4943      New key ikppkey created, and tamc.h headers updated.
4944    
4945    checkpoint50 (2003/03/08)
4946    - 2nd step of merge with ecco-branch:
4947      merge changes in ecco-branch back into main trunk
4948    - bug fix in find_alpha
4949    - more storing in gmredi_calc_tensor.F, kpp_routines.F
4950    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
4951    - merged some sliced AD support routines
4952    
4953    checkpoint49 (2003/03/06)
4954    merged from ecco-branch:
4955    o exf:
4956      - Enable initialisation of forcing fields to constant
4957        (runtime) values.
4958      - in exf_getffields.F
4959        Reduce i-/j-loop to interior domain, discarding overlaps.
4960        That also fixes wrong TAF-key computations for key_1, key_2
4961        with bulf formulae.
4962      - exf_init.F modify #ifdef for exf_init_evap
4963      - exf_getffieldrec.F, ctrl_getrec.F
4964        The following INT-usages are not safe:
4965          fldsecs  = int(fldsecs/fldperiod)*fldperiod
4966          fldcount = int(fldsecs/fldperiod) + 1
4967        and were modified.
4968    o autodiff: checkpoint_lev...
4969      - updated storing for bulk formulae (some arrays were missing)
4970      - added state for seaice package
4971      - synchronized with main branch
4972    o DIVA:
4973      Modif.s in
4974      - the_main_loop.F
4975      - the_model_main.F
4976      and added cost_final_restore.F cost_final_store.F
4977      o With these changes, it is possible to fully separate
4978        the first forward run to compute the cost function (mdthe_main_loop)
4979        and adjoint runs over individual DIVA intervals (adthe_main_loop)
4980        into separate model executions.
4981        This enables better tuning of DIVA to given queue sizes.
4982      o Loss of cost function value in consecutive DIVA runs is
4983        fixed by storing to 'costfinal' file.
4984      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
4985        beginning/end of adjoint integration is accounted for.
4986      The current changes apply to TAF-1.4.26.
4987      TAF has one remaining bug, requiring one manual change
4988      (see MITgcm manual).
4989    o cal: synchronized between MAIN and ecco-branch
4990    
4991    checkpoint48i_post (2003/03/05)
4992    o Changes to restore differentiability of code w.r.t. previous tag
4993      (mostly adding new routines to make list and replacing
4994      pressure by totPhiHyd).
4995    o Updated and merged grdchk package
4996      - has both ADM and TLM checks
4997      - works for single- and multi-proc.
4998      - output cleaned
4999      - worked successfully for parallel DIVA
5000    o genmake:
5001      - Adding -platform=SP4
5002      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
5003    o Modif. for DIVA:
5004      ctrl_unpack should not be called in intermediate DIVA interval.
5005      (similar thing would apply for active files such as
5006      tbar, sbar, psbar, which should not be reinitialised;
5007      only relevant for ecco-branch)
5008    
5009    checkpoint48h_post (2003/02/28)
5010    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
5011    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
5012    o Added SEAICE_initialHEFF to pkg/seaice
5013    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
5014    
5015    checkpoint48g_post (2003/02/18)
5016    --- EOS:
5017    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
5018      store total Potential in totPhyHyd for diagnostics & EOS.
5019    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
5020    --- Pressure/geopotential gradient:
5021    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
5022    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
5023      ( changes results of global_ocean_pressure )
5024    o NLFS + z-coord.: add eta*Rho' contribution.
5025    o accurate phiHyd when using interface-W at the middle between 2 centers
5026     ( changes results of ideal_2D_oce )
5027    o includes r* 2nd term in potential gradient.
5028    
5029    checkpoint48f_post (2003/02/18)
5030    Merging from release1_p12:
5031    o Modifications for using pkg/exf with pkg/seaice
5032      - improved description of the various forcing configurations
5033      - added basic radiation bulk formulae to pkg/exf
5034      - units/sign fix for evap computation in exf_getffields.F
5035      - updated verification/global_with_exf/results/output.txt
5036    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
5037      (SBO) core products, including oceanic mass, center-of-mass,
5038      angular, and bottom pressure (see pkg/sbo/README.sbo).
5039    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
5040      to avoid negative values in shallow regions.
5041      - updated verification/natl_box/results/output.txt
5042      - updated verification/lab_sea/results/output.txt
5043    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
5044    o Added useSingleCpuIO option (see PARAMS.h).
5045    o Updated useSingleCpuIO option in mdsio_writefield.F to
5046      work with multi-field files, e.g., for single-file pickup.
5047    o pkg/seaice:
5048      - bug fix in growth.F: QNET for no shortwave case
5049      - added HeffFile for specifying initial sea-ice thickness
5050      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
5051    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
5052      kpp_transport_t.F, forward_step.F, and the_main_loop.F
5053    o pkg/seaice:
5054      - adjoint-friendly modifications
5055      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
5056    
5057    checkpoint48e_post (2003/02/12)
5058    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
5059    o dynamics: change definition of computational domain & adapt mom_fluxform
5060      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
5061    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
5062        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
5063        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
5064        global_ocean.90x40x15 global_with_exf global_ocean_pressure
5065        inverted_barometer solid-body.cs-32x32x1
5066      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
5067    
5068    checkpoint48d_post (2003/02/09)
5069    o in preparation for r*:
5070     a) use pre-computed gradient of hydrostatic potential:
5071        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
5072     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
5073        => affects results of glob_oce_pressure (different truncation error)  
5074      update output.txt of ideal_2D_oce & global_ocean_pressure
5075    
5076    checkpoint48d_pre (2003/02/08)
5077    o in preparation for r*:
5078      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
5079      pass the 2 comp. of the grad. as arguments to momentum S/R.
5080      but for the moment, only used if it does not change the results.
5081    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
5082    
5083    checkpoint48c_post (2003/02/06)
5084    Modifications in treatment of initial flux forcing controls
5085    to avoid extra storing of flux fields.
5086    
5087    checkpoint48c_pre (2003/01/21)
5088    o Added tidal_basin_2d experiment (currently 1D!)
5089    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
5090    
5091    checkpoint48b_post (2003/01/27)
5092    o r* coordinate added in #ifdef NONLIN_FRSURF block.
5093     (modification to pressure gradient not yet implemented)
5094    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
5095      (for U & V) that are used for vertical advection of momentum.
5096    
5097    checkpoint48a_post (2003/01/24)
5098    o In preparation for r*, use temp. array to compute vertical transport
5099       in flux-form momentum pkg. => change results of few test-exp.
5100      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
5101                        lab_sea, natl_box & plume_on_slope
5102    
5103    checkpoint48 (2003/01/23)
5104    o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
5105    
5106    checkpoint47j_post (2003/01/21)
5107    o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
5108    o moved adexch from forward_step to addummy_in_stepping
5109    o added exch in ctrl_map_...
5110    o aveFreq.=0. at end of cost_final to avoid overwrite in
5111      reverse checkpointing loop
5112    o Yet more changes in gmredi:
5113      * adgmredi_calc_tensor
5114        avoiding all recomputation of gmredi_slope_limit
5115      * adgmredi_x/y/rtransport
5116        added flag for excessive storing to avoid recomp. of
5117        u/v/rtans, dTdx/y/z
5118        -> this is not really necessary and very memory-consuming
5119      * adgmredi_slope_psi:
5120        consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
5121      * gmredi_slope_limit
5122        re-activated full calculation of taperfct for case 'ac02'
5123    o updating verification/ adjoints of carbon, global_ocean.90x40x15
5124    
5125    checkpoint47i_post (2003/01/13)
5126    o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
5127    o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
5128      default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
5129    o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
5130    o gmredi: fix few bugs.
5131    
5132    checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
5133    This will be a good checkpoint to plug into the ecco-branch.
5134    o few modif.'s to get latest version adjointed
5135      (mainly kick out code in ini_linear_phisurf)
5136    o modif's to run adjoint with exactConserv
5137    o case GM_BOLUS_ADVEC should be cleaned
5138      S/R gmredi_slope_psi should be cleaned
5139    o verification/carbon now has exactConserv=.TRUE.
5140    
5141    checkpoint47g_post (2003/01/10)
5142    o time-average AIM output: becomes independent from statvars time-average
5143      (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
5144    o After TAF bug fix:
5145      Tested adjoint of gmredi package.
5146      Tests were done with checkpoint47 rather than with latest
5147      checkpoint47f_post since the latter is broken for the adjoint
5148      verification/carbon/ contains both ADM and TLM gradient checks.
5149    Here they are, before they get changed/lost/stolen.
5150    Mostly modif.'s to fix numerical sensitivities.
5151    Gradient checks OK for
5152    - GM_taper_scheme:
5153      * clipping
5154      * ac02
5155      * linear
5156      * glw91
5157      * dm95
5158      * ldd97
5159    - GMREDI_OPTIONS:
5160      * GM_VISBECK_VARIABLE_K
5161      * GM_NON_UNITY_DIAGONAL
5162      * GM_EXTRA_DIAGONAL
5163      * GM_BOLUS_ADVEC
5164    in conjunction with data.gmredi parameters to be checked in
5165    in a few minutes under verification/carbon/code/
5166    
5167    checkpoint47f_post (2002/12/28)
5168    Merging from release1_p10:
5169    o modifications for using pkg/exf with pkg/seaice
5170      - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
5171        and SEAICE_EXTERNAL_FLUXES
5172      - pkg/exf CPP options EXF_READ_EVAP and
5173        EXF_NO_BULK_COMPUTATIONS
5174      - usage examples are Experiments 8 and 9 in
5175        verification/lab_sea/README
5176      - verification/lab_sea default experiment now uses
5177        pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
5178    
5179    checkpoint47e_post (2002/12/27)
5180    o created a tag prior to creating a branch
5181    
5182    checkpoint47d_post (2002/12/16)
5183    o fixed bug in the oceanic pressure coordinates code: vertical viscosity
5184      at the bottom boundary had an erroneous half slip boundary condition
5185    o added bottom drag and no slip boundary condition capabilities to
5186      oceanic pressure coordinates code
5187    o added new verification experiment global_ocean_pressure, this experiment is
5188      also described in the tutorial section of the manual
5189    checkpoint47d_pre (2002/12/16)
5190    
5191    checkpoint47c_post (2002/12/16)
5192    o Added a verification experiment for a global cubed-sphere ocean run
5193      -  verification/global_ocean.cubed32x32x30
5194      -  uses pkg/therm_seaice and pkg/bulk_forcing
5195    
5196    o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
5197    o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
5198      when using P-coordinate; only implemented for atmospheric config.
5199    o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
5200      NOTES: requires option NONLIN_FRSURF to be "#define".
5201    o update advect_xz/results/output.txt (left from checkpoint44g_post)
5202    
5203    checkpoint47b_post (2002/12/05)
5204    Merging from release1_p9:
5205    o pkg/seaice
5206      - removed GOTO's and added taf directives
5207      - double precision constants to reduce the g77 (Linux)
5208        to F77 (SGI) differences reported in release1_p8
5209    o tools/genmake
5210      - added SGI options
5211    o verification/testscript
5212      - updated to that of checkpoint47a_post
5213    o verification/global_ocean.90x40x15/input/eedata
5214      - modified for SGI f77 compatibility
5215    o verification/lab_sea
5216      - added description of sea-ice model
5217      - added missing matlab routines
5218      - added test of thermodynamics parallelization
5219    
5220    checkpoint47a_post (2002/11/23)
5221    o new pkg: aim_v23
5222     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
5223       for now, keep the same surface forcing as before.
5224     - Part-Cell implemented into AIM; check that Heat & Water are conserved
5225     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
5226     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
5227    o add diagnostic of surface correction term in monitor output
5228    
5229    o bulk_force and therm_seaice
5230    - Two packages:  bulk_force (Bulk forcing)
5231      and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
5232    - Earlier integration from Stephaine Dutkiewicz
5233      and Patrick Heimbach.
5234    - Two ifdef statements for compile time,
5235       ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
5236    
5237    checkpoint47 (2002/11/15)
5238    differentiable version of checkpoint46n_post
5239    o bug fix in quasihydrostaticterms
5240    o * "clean" adjoint code (in terms of extensive recomputations)
5241        can now be obtained for all GMREDI options (i.e. for
5242        - GM_VISBECK_VARIABLE_K
5243        - GM_NON_UNITY_DIAGONAL
5244        - GM_EXTRA_DIAGONAL
5245        - GM_BOLUS_ADVEC )
5246      * However, wrong gradient check problem remains unsolved.
5247      * New CPP options have been introduced for different
5248        tapering schemes
5249    o external_fields_load now part of differentiation list
5250    o pressure needs multiple storing;
5251      would be nice to have store_pressure at beginning or
5252      end of forward_step, e.g. by having phiHyd global (5-dim.)
5253      (NB: pressure is needed for certain cases in find_rho,
5254      which is also invoked through convective_adjustment).
5255    o recomputations in find_rho for cases
5256     'JMD95'/'UNESCO' or 'MDJWF' are OK.
5257    o #define ATMOSPHERIC_LOADING should be differentiable
5258    o ini_forcing shifted to begining of initialise_varia
5259    o Incorporating QNVS line search routines into MITgcm
5260      (this is separate code, and therefore not under pkg)
5261      lsopt/, optim/
5262    o Updated verification/carbon/
5263      - #define GM_VISBECK_VARIABLE_K
5264      - GM_taper_scheme    = 'ldd97'    
5265    
5266    checkpoint46n_post (2002/11/12)
5267    Merging from release1_p8:
5268    o verification/natl_box:
5269      updating new external_fields_load routine
5270    o New package: pkg/seaice
5271      Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
5272      The sea-ice code is based on Hibler (1979-1980).
5273      Two sea-ice dynamic solvers, ADI and LSR, are included.
5274      In addition to computing prognostic sea-ice variables and diagnosing
5275      the forcing/external data fields that drive the ocean model,
5276      SEAICE_MODEL also sets theta to the freezing point under sea-ice.
5277      The implied surface heat flux is then stored in variable
5278      surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
5279      kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
5280      non-local transport term.  Because this call precedes model
5281      thermodynamics, temperature under sea-ice may not be "exactly" at
5282      the freezing point by the time theta is dumped or time-averaged.
5283      N.B.: fairly large differences in accuracy occur across
5284            different platforms/compilers; comparison between
5285            g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
5286            generated output gives:
5287       T           S           U           V
5288      C D M    c        m  s        m  s        m  s        m  s
5289      n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
5290      f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
5291      g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
5292    
5293      Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
5294    o GAD:
5295      - generated new common blocks to account for call of
5296        same gad routines with differing traceridentities
5297        (needed to modify tracerIdentity indices in GAD.h)
5298      - generated separate common blocks for case useCubedSphereExchange
5299        (Department of Futurology)
5300      - parameter lists to gmredi_?transport: added tracerIdentity
5301      - added new key indices to tamc.h
5302    o external_fields_load:
5303      - added this routine to TAF list
5304      - needed to make some common blocks global and additional storing
5305        along the same lines as exf package (checkpoint_lev?_directives.h)
5306    o exf:
5307      updated external forcing package
5308      - bug fixes carried over from ecco-branch
5309        (missing OBCS_OPTIONS.h in two routines)
5310      - enable easy to use "no forcing".
5311      - added exf I/O for atmospheric loading
5312      - added exf I/O for runoff data
5313      - transfered scaling between exf <-> MITgcm to exf namelist
5314    o Adding new verification experiment global_with_exf.
5315      This verification experiment is almost identical to the
5316      global_ocean.90x40x15 experiment, except that it uses
5317      the exf (and cal) package instead of the
5318      external_fields_load routine (cf README file).
5319    
5320    checkpoint46m_post (2002/11/07)
5321    o modified testscript to return -- when there are no lines of "%MON" output
5322    o added new flag "quasiHydrostatic" for QH mode
5323      and new routine quasihydrostaticterms()
5324    o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
5325      New routine: mom_u_coriolis_nh()
5326    o fixed sign of non-hydrostatic metric terms in u and v equations.
5327      Depend on correct sign of gravitySign.
5328    o added work.pc* to .cvsignore in aim directories using ifc
5329    o introduced flag for controllin non-hydrostatic metric terms
5330    o removed gravitySign from PARM04
5331    o switched to g77/ifc from pgf77 in aim experiments
5332    
5333    checkpoint46l_post (2002/11/01)
5334    o made convective adjustment work with pressure coordinates:
5335     - changed the direction of k-loop in convective_adjustment.F for the
5336       case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
5337     - adjusted the reference pressure k-index in convective_adjustment.F
5338     - adjusted the convection condition in convect.F (in analogy to
5339       calc_ivdc.F)
5340     - convective_adjustment no longer computes anything on the halos
5341     - removed the warnings about negative salinity from find_rho.F and
5342       find_alpha.F; instead the new routine look_for_neg_salinity, called
5343       at the beginning of find_rho, find_alpha, and find_beta, does a
5344       check of the entire slice, if CPP-option
5345       CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
5346    checkpoint46l_pre (2002/10/23)
5347    
5348    checkpoint46k_post (2002/10/23)
5349    o fixed the verification/global_ocean.90x40x15 experiment:
5350     - new bathymetry (the world according to A., JMC, and M.)
5351     - new initial fields and forcing fields (*.bin files)
5352     - new POLY3.COEFFS (for the next release one should switch to a full
5353       equation of state: JMD95P or MDJWF)
5354     - fixed several errors and redundancies in the data file
5355     - experiment uses looped cells
5356     - added matlab directory with diagnostic scripts for plotting of output
5357    
5358    o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
5359     - read AIM physics parameters from a file (data.aimphys)
5360     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
5361    
5362    checkpoint46j_post (2002/10/07)
5363    o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
5364    o move wVel computation at the end of the time step, in S/R integr_continuity
5365    o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
5366    o update timeave pkg for wVel diagnostic.
5367    checkpoint46j_pre (2002/09/27)
5368    
5369    checkpoint46i_post (2002/09/25)
5370    o Clean up AIM package (and keep the results unchanged):
5371      include CPP_OPTION and use IMPLICT NONE in all routines ;
5372      declare all the variables _RL ; use _d 0 for all numerical constants.
5373      use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
5374    
5375    checkpoint46h_post (2002/09/25)
5376    o cleaned up the use of rhoNil and rhoConst.
5377      - rhoNil should only appear in the LINEAR equation of state, everywhere
5378        else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
5379        and the dynamical equations are all divided by rhoConst
5380    o introduced new parameter rhoConstFresh, a reference density of fresh
5381      water, to remove the fresh water flux's dependence on rhoNil. The default
5382      value is 999.8 kg/m^3
5383    o cleanup up external_forcing.F and external_forcing_surf.F
5384      - can now be used by both OCEANIC and OCEANICP
5385    checkpoint46h_pre (2002/09/18)
5386    
5387     Added code to convert surface volume flux (fresh water) into
5388     a mass flux when using P coordinates in the ocean (OCEANICP).
5389     Note: It assumes you have set rho0=rhoConst=density of fresh water.
5390    
5391    checkpoint46g_post (2002/09/18)
5392    o Include a new diagnostic variable phiHydLow for the ocean model
5393      - in z-coordinates, it is the bottom pressure anomaly
5394      - in p-coordinates, it is the sea surface elevation
5395      - in both cases, these variable have global drift, reflecting the mass
5396        drift in z-coordinates and the volume drift in p-coordinates
5397      - included time averaging for phiHydLow, be aware of the drift!
5398    o depth-dependent computation of Bo_surf for pressure coordinates
5399      in the ocean (buoyancyRelation='OCEANICP')
5400      - requires a new routine (FIND_RHO_SCALAR) to compute density with only
5401        Theta, Salinity, and Pressure in the parameter list. This routine is
5402        presently contained in find_rho.F. This routine does not give the
5403        correct density for 'POLY3', which would be a z-dependent reference
5404        density.
5405    o cleaned up find_rho
5406      - removed obsolete 'eqn' from the parameter list.
5407    o added two new verification experiments: gop and goz
5408      (4x4 degree global ocean, 15 layers in pressure and height coordinates)
5409    checkpoint46g_pre (2002/09/16)
5410    
5411    checkpoint46f_post (2002/09/16)
5412    o Enable tangent linear (forward mode) gradient checks:
5413      - extended active file handling to g_... files
5414      - added TANGENT_SIMULATION to theSimulationMode
5415      - extended grdchk package accordingly
5416    o added tangent linear setup in verification/carbon/code_ftl
5417    o added adjoint setup in verification/front_relax/code_ad
5418    
5419    checkpoint46e_post (2002/09/05)
5420    o Added new equation of state -> MDJWF
5421      - EOS of McDougall et al., 2002, JAOT, submitted
5422      - caveat: the equation of state is only valid for a smaller (more
5423        realistic?) range of values than JMD95P/Z and UNESCO
5424      - added masks to the calculation of pressure in store_pressure
5425      - added more check values for density in check_eos (ini_eos.F), some of
5426        the old check values are out of the range of the MDJWF-eos, so don't
5427        expect perfect matches for those
5428    checkpoint46e_pre (2002/08/19)
5429    
5430    checkpoint46d_post (2002/08/19)
5431    o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
5432      'OCEANICP', also initialised field pressure correctly in ini_eos in the
5433      case of pressure coordinates. eosType='JMD95Z' in
5434      combination with buoyancyRelation='OCEANICP' now causes an error.
5435    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
5436      in find_alpha/beta.
5437    checkpoint46d_pre (2002/08/15)
5438    
5439    o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
5440      so that JMD95Z and JMD95P give approptiate static stability in find_rho.
5441    
5442    checkpoint46c_post (2002/08/15)
5443    o Changes necessary for ocean in p-coordinates
5444     -  Added new buoyancy relation = 'OCEANICP'
5445     -  Added new parameters = gravitySign (this used to be contained inside
5446        the factor dRdZ which I added when we first switched to R coordinates).
5447     X GM/Redi is not compatible (yet)
5448     X bottom drag and no-slip need to be debugged.
5449    checkpoint46c_pre (2002/08/07)
5450    
5451    checkpoint46b_post (2002/08/07)
5452    o Added new equation of state -> JMD95Z and JMD95P
5453      - EOS of Jackett and McDougall, 1995, JAOT
5454      - moved all EOS parameters into EOS.h
5455      - new routines ini_eos.F, store_pressure.F
5456    o Added UNESCO EOS, but not recommended because it requires
5457      in-situ temperature (see JMD95)
5458    o Modified formatting for knudsen2.f in utils/knudsen2 and added
5459      unesco.f to be used with POLY3
5460    checkpoint46b_pre (2002/07/31)
5461    
5462    checkpoint46a_post (2002/07/31)
5463    o Added (atmospheric) pressure loading
5464      - new field in FFIELDS.h, etc...
5465      - new cpp flag ATMOSPHERIC_LOADING
5466    o Changed hFacC to _hFacC in calc_phi_hyd.F
5467    o Added SHORTWAVE_HEATING to some files for consistency
5468    checkpoint46a_pre (2002/07/13)
5469    
5470    checkpoint46 (2002/07/13)
5471    further merges from release1_p5
5472    o new ctrl package
5473      - adopted from ECCO environment to enable optimization
5474      - added Eliassen Palm fluxes to controls
5475    o added Eliassen Palm flux controls to gradient check package
5476    o cost package
5477      - Compatible with new ctrl package
5478      - added Eliassen Palm cost hooks
5479      - modif's of existing cost functions
5480    o Adjoint-related bug fixes in kpp:
5481      - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
5482      - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
5483    o autodiff package
5484      - flow directives:
5485        + new for S/R do_the_model_io
5486        + enhanced for S/R checkpoint
5487        + new gmredi.flow
5488      - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
5489        disable adcommon.h/g_common.h by default.
5490      - fixed problem for adjoint of global_max
5491    o modified verification/carbon/
5492    o New setup for adjoint of global_ocean
5493    o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
5494    o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
5495    o incorporated hooks for sponge layer code (external_forcing.F)
5496    
5497    checkpoint45d_post (2002/07/12)
5498    o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
5499    o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
5500      (affects plume_on_slope "cg2d" output)
5501    o add new parameter deltaTfreesurf for free-surface time stepping
5502    o exchange gT,gS when using staggerTimeStep & GM & Oly<4
5503    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
5504    o change phiMin in exp1 (to agree with documentation)
5505    o add new flags:
5506     - T,S forcing inside/outside Adams-Bashforth
5507     - turn off temp,salt advection and/or forcing
5508     - for each tracer, define internal flag for multiDimAdvection & A-B
5509    o monitor: change definition of KE to check conservation of Energy
5510    
5511    checkpoint45c_post (2002/05/30)
5512    o Removed f90 comments ("!")
5513    o Modified initialisations to enable exf package for MITgcm
5514      (without invoking ECCO_PACKAGE).
5515    o modifications to gradient check package (Martin Losch)
5516      - enable centered differences
5517      - modified format of standard output
5518    
5519    checkpoint45b_post (2002/05/30)
5520    o cleaned exchange calls in cg2d
5521    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
5522    o included CPP option SINGLE_LAYER_MODE in thermodynamics
5523      to configure barotropic setup (Martin Losch)
5524    o moved some initialisations within bi,bj loop in dynamics
5525      (TAF flow dependency)
5526    o in initialise_varia, moved call packages_init_variables
5527      before convective_adjustment_init
5528      (corresponding adjustment of TAF tape initialisation).
5529    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
5530    
5531    checkpoint45a_post (2002/05/01)
5532    o compute Rho over the whole domain (extend iMin,jMin indices)
5533    o specific exchange for X-slice domain (case Ny=1)
5534    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
5535    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
5536    
5537    checkpoint44h_post = checkpoint45
5538    o Fix to restore differentiability:
5539      place at which packages_init_variables is called in
5540      initialise_varia is crucial for reverse control flow.
5541    o modifications in GMRedi to enable stable adjoint
5542      (corresponding modif's in thermodynamics, dynamics)
5543    o added missing hook for sponge layer code in external_forcing
5544    o modified test cost functions
5545    o storing in gad_advection (plus removal of write(0,*)!
5546    o missing headers TR1.h added in convective_adjustment routines
5547    o errorMessageUnit set non-equal zero in eeboot
5548      (conflict on some platforms, e.g. IBM SP3)
5549    o modified carbon verif.
5550    
5551    checkpoint44h_pre (2002/03/14)
5552    o vertical grid option: allow to put the Interface at the middle between
5553      2 cell-centers ; replace delZ in pkg/kpp by drF.
5554    o GM Advective form: Tracers are advected using the residual transport (=
5555      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
5556    
5557    checkpoint44g_post (2002/03/05)
5558  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
5559    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
5560    
# Line 68  o merge of relevant stuff from the ecco- Line 5619  o merge of relevant stuff from the ecco-
5619  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
5620  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
5621    
5622  checkpoint44  checkpoint44 (2002/01/18)
5623  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
5624  o select when filters are applied ; add options to zonal_filter (data.zonfilt)  o select when filters are applied ; add options to zonal_filter (data.zonfilt)
5625  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)  o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
# Line 76  o update AIM experiments (NCEP input fil Line 5627  o update AIM experiments (NCEP input fil
5627  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
5628  o added some stuff for AD  o added some stuff for AD
5629    
5630  checkpoint43  checkpoint43 (2001/09/28)
5631  o added two new advection tests  o added two new advection tests
5632  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
5633  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
5634  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
5635    
5636  checkpoint42  checkpoint42 (2001/09/27)
5637    Fixed AD-related problems:    Fixed AD-related problems:
5638  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
5639    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 94  o Modified store directives for split of Line 5645  o Modified store directives for split of
5645    for the case ALLOW_KPP    for the case ALLOW_KPP
5646  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
5647    
5648  checkpoint41  checkpoint41 (2001/09/27)
5649  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
5650    to work with protex    to work with protex
5651    
5652  checkpoint40  checkpoint40 (2001/09/27)
5653  o moved calc_gs, calc_gt and calc_tr1 back to model/src  o moved calc_gs, calc_gt and calc_tr1 back to model/src
5654  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
5655  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 107  o more mods for non-linear free-surface Line 5658  o more mods for non-linear free-surface
5658  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
5659  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
5660    
5661  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
5662  o added DST advection schemes  o added DST advection schemes
5663  o fix MPI bug on SGI's  o fix MPI bug on SGI's
5664  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 117  o changes to commenting of arguments for Line 5668  o changes to commenting of arguments for
5668  o added/updated many matlab scripts  o added/updated many matlab scripts
5669  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
5670        
5671  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
5672  o new package rw/  o new package rw/
5673    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
5674    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 136  o TAMC-related update to cope with mom_f Line 5687  o TAMC-related update to cope with mom_f
5687    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
5688    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
5689    
5690  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
5691  o bug fix in dynamics.F  o bug fix in dynamics.F
5692    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
5693  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
5694  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
5695    related to TAF    related to TAF
5696    
5697  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
5698  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
5699  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
5700    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 151  o corresponding split of calc_diffusivit Line 5702  o corresponding split of calc_diffusivit
5702  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
5703  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
5704    
5705  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
5706  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
5707    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
5708  o re-generated *all* output since almost all output is modified by this  o re-generated *all* output since almost all output is modified by this
# Line 165  o added new expt "solid-body.cs-32x32x1" Line 5716  o added new expt "solid-body.cs-32x32x1"
5716    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
5717      is not necessarily any better than the current one...      is not necessarily any better than the current one...
5718    
5719  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
5720  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
5721    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
5722  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 173  o extended iMin,jMin range for calc_comm Line 5724  o extended iMin,jMin range for calc_comm
5724  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
5725  o a few minor updates and fixes  o a few minor updates and fixes
5726    
5727  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
5728  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
5729  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
5730  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
5731    
5732  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
5733  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
5734  o Added gradient check package  o Added gradient check package
5735  o Added routines for passive tracer handling  o Added routines for passive tracer handling
5736  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
5737    
5738  checkpoint39  checkpoint39 (2001/05/14)
5739   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
5740     (mainly missing or wrong directives)     (mainly missing or wrong directives)
5741   o Corrected common blocks when fooling TAMC to produce adjoint I/O   o Corrected common blocks when fooling TAMC to produce adjoint I/O
# Line 198  checkpoint39 Line 5749  checkpoint39
5749           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
5750   o disabled some packages by default in genmake   o disabled some packages by default in genmake
5751    
5752  checkpoint38  checkpoint38 (2001/04/10)
5753   o see notes_c37_adj.txt   o see notes_c37_adj.txt
5754   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
5755   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 206  checkpoint38 Line 5757  checkpoint38
5757     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
5758   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
5759    
5760  checkpoint37  checkpoint37 (2001/03/13)
5761   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
5762     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
5763      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 223  checkpoint37 Line 5774  checkpoint37
5774   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
5775   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
5776    
5777  checkpoint36  checkpoint36 (2001/02/20)
5778   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
5779   o recover Time-Average diagnostics   o recover Time-Average diagnostics
5780   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
5781   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
5782    
5783  checkpoint35  checkpoint35 (2001/02/08)
5784   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
5785   o allows staggered time-stepping   o allows staggered time-stepping
5786   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
5787   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
5788    
5789  checkpoint34  checkpoint34 (2001/01/30)
5790   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
5791   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
5792     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 246  checkpoint34 Line 5797  checkpoint34
5797   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
5798   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
5799    
5800  checkpoint33  checkpoint33 (2000/11/30)
5801   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
5802   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
5803     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 264  checkpoint33 Line 5815  checkpoint33
5815       possibly use them.       possibly use them.
5816   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
5817    
5818  checkpoint32  checkpoint32 (2000/11/13)
5819   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
5820     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
5821   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 275  checkpoint32 Line 5826  checkpoint32
5826   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
5827   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
5828    
5829  checkpoint31  checkpoint31 (2000/09/11)
5830   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
5831     -> new routines packages_...F     -> new routines packages_...F
5832     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 292  checkpoint31 Line 5843  checkpoint31
5843     - not yet tested for GMRedi.     - not yet tested for GMRedi.
5844     - not yet tested for KPP.     - not yet tested for KPP.
5845    
5846  checkpoint30  checkpoint30 (2000/07/13)
5847   o Updates for OBCs   o Updates for OBCs
5848   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
5849   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 301  checkpoint30 Line 5852  checkpoint30
5852   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)   o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
5853     and entry for T90 in genmake     and entry for T90 in genmake
5854    
5855  checkpoint29  checkpoint29 (2000/06/21)
5856   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
5857    
5858  checkpoint28  checkpoint28 (2000/06/09)
5859   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
5860   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
5861   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 317  checkpoint28 Line 5868  checkpoint28
5868     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
5869   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
5870    
5871  checkpoint27  checkpoint27 (2000/04/10)
5872   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
5873     formulation works properly with variable resolution.     formulation works properly with variable resolution.
5874   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 325  checkpoint27 Line 5876  checkpoint27
5876   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
5877     in new routine ini_psurf()     in new routine ini_psurf()
5878    
5879  checkpoint26  checkpoint26 (2000/04/05)
5880   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
5881     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
5882   o fixed macros like _ADT to work with both versions of Linux cpp   o fixed macros like _ADT to work with both versions of Linux cpp
# Line 335  checkpoint26 Line 5886  checkpoint26
5886     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
5887   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
5888    
5889  checkpoint25  checkpoint25 (2000/03/15)
5890   o updates for OBCs and NH   o updates for OBCs and NH
5891   o dramatically reduced memory usage   o dramatically reduced memory usage
5892   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 346  checkpoint25 Line 5897  checkpoint25
5897      an explicit free-surface option)      an explicit free-surface option)
5898   o initial state input files for U and V   o initial state input files for U and V
5899    
5900  checkpoint24  checkpoint24 (1999/08/02)
5901   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
5902   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
5903   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
5904    
5905  checkpoint23  checkpoint23 (1999/05/26)
5906   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
5907   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
5908    
5909  checkpoint22  checkpoint22 (1999/05/18)
5910   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
5911   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
5912    
5913  checkpoint21  checkpoint21 (1999/05/18)
5914   o Introduced new I/O package that supports direct-access records (mdsio.F)   o Introduced new I/O package that supports direct-access records (mdsio.F)
5915   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
5916   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
5917   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
5918    
5919  checkpoint20  checkpoint20 (1999/03/22)
5920   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
5921   o Added non-hydrostatic code   o Added non-hydrostatic code
5922   o Fixed some input data   o Fixed some input data
5923   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
5924    
5925  checkpoint19  checkpoint19 (1998/12/15)
5926   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
5927   o Added new code for open boundaries.   o Added new code for open boundaries.
5928   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 379  checkpoint19 Line 5930  checkpoint19
5930   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
5931   o Split default parameters out of ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
5932    
5933  checkpoint18  checkpoint18 (1998/11/30)
5934   o Further changes for optional code generation with   o Further changes for optional code generation with
5935     CPP - ugh!     CPP - ugh!
5936    
5937  checkpoint17  checkpoint17 (1998/11/03)
5938   o Beginning to incorporating modularity   o Beginning to incorporating modularity
5939     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
5940   o Small changes for TAMC complinace   o Small changes for TAMC complinace
5941   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
5942     configuration "exp0".     configuration "exp0".
5943    
5944  checkpoint16  checkpoint16 (1998/10/28)
5945   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
5946     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
5947     assignment is an addition.     assignment is an addition.
# Line 398  checkpoint16 Line 5949  checkpoint16
5949     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
5950     limit ).     limit ).
5951    
5952  checkpoint15  checkpoint15 (1998/09/29)
5953   Rewrote exchange routines to allow   Rewrote exchange routines to allow
5954   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
5955   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 407  checkpoint15 Line 5958  checkpoint15
5958     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
5959     communication method.     communication method.
5960    
5961  checkpoint14  checkpoint14 (1998/09/09)
5962   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
5963   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
5964    
5965  checkpoint13  checkpoint13 (1998/07/17)
5966   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
5967   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
5968   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 426  branch-point-rdot Line 5977  branch-point-rdot
5977   I don't want to commit the rDot to the main-trunk until   I don't want to commit the rDot to the main-trunk until
5978   we've actually tested it...   we've actually tested it...
5979    
5980  checkpoint12  checkpoint12 (1998/07/08)
5981   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
5982   configure script).   configure script).
5983   Released to testers.   Released to testers.
5984    
5985  checkpoint11  checkpoint11 (1998/07/02)
5986   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
5987   and ini_masks_etc().   and ini_masks_etc().
5988    
5989  checkpoint10  checkpoint10 (1998/07/01)
5990   Introduced the configure script.   Introduced the configure script.
5991   Separated out the diags package.   Separated out the diags package.
5992   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
5993   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
5994    
5995  checkpoint9  checkpoint9 (1998/06/22)
5996   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
5997   General tidy-up.   General tidy-up.
5998   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
5999    
6000  checkpoint8  checkpoint8 (1998/06/22)
6001   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
6002   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
6003    
# Line 456  checkpoint7-4degree-ref Line 6007  checkpoint7-4degree-ref
6007   model etc..   model etc..
6008   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
6009    
6010  checkpoint7  checkpoint7 (1998/06/15)
6011   Created by cnh   Created by cnh
6012   Simple 4 degree global simulation   Simple 4 degree global simulation
6013   configuration.   configuration.
# Line 464  checkpoint7 Line 6015  checkpoint7
6015   hydrography, bathymetry etc   hydrography, bathymetry etc
6016   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
6017    
6018  checkpoint6  checkpoint6 (1998/06/08)
6019   Created by cnh   Created by cnh
6020   merged checkpoint5 with CD and   merged checkpoint5 with CD and
6021   spherical polar code.   spherical polar code.
6022   Still some problems with GM Redi   Still some problems with GM Redi
6023   abd full topography.   abd full topography.
6024    
6025  checkpoint5  checkpoint5 (1998/06/08)
6026   Created by AJA   Created by AJA
6027   contains updates to GM Redi   contains updates to GM Redi
6028   and reordered timestepping loop   and reordered timestepping loop
6029   for Implicit Diffusion.   for Implicit Diffusion.
6030    
6031  checkpoint4  checkpoint4 (1998/05/30)
6032   Created by cnh   Created by cnh
6033   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
6034   grid variations are limited.   grid variations are limited.
6035   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
6036   for generation.   for generation.
6037    
6038  checkpoint3  checkpoint3 (1998/05/26)
6039   Created by cnh   Created by cnh
6040   Added extra flags for runtime options   Added extra flags for runtime options
6041   Added this file   Added this file

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