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revision 1.255 by heimbach, Wed Feb 18 22:34:52 2004 UTC revision 1.1503 by jmc, Thu Sep 22 20:12:10 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  checkpoint52j_post  o pkg/seaice (LSR):
8      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
9      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
10        * identical results with non-CS topology (but save up to half of EXCH calls)
11        * no much changes in cs-32 verification tests since no ice at face edges
12         (differences due to convergence criteria, since nb of iterations changed)
13        * expect some differences on lat-lon-cap grid.
14        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
15    o pkg/exch2:
16      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
17        many tiles); until alternative coding is added, just add a stop.
18    o pkg/kpp:
19      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
20        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
21    o optfiles:
22      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
23        into corresponding standard one, which now support different build:
24        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
25      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
26    o pkg/obcs (seaice):
27      - add missing EXCH for uIce,vIce after applying OBCS;
28      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
29        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
30        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
31      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
32      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
33        and eedata.mth for MPI and mutlti-threaded testing.
34    o pkg/flt:
35      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
36      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
37      - fix pickup and trajectories + profiles output with multi-threads;
38      - add parameter to select group of fields to write along trajectory and
39        profile (default unchanged);
40      - only call PORT_RAND* function when flt_noise <> 0;
41      - add multi-threaded test for verification exp. flt_example.
42    o eesupp/src:
43      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
44      - USE_OMP_THREADING: check that number of threads (from eedata) matches
45        actual number (from env.var. setting).
46    o pkg/ebm:
47      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
48      - add multi-threaded test for verification exp. global_ocean_ebm
49    
50    checkpoint63b (2011/08/29)
51    o pkg/ebm:
52      - fix sign of runoff;
53      - update directly forcing fields (Qnet,EmPmR) to use standard
54        external_forcing_surf.F (remove ebm_forcing_surf.F);
55      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
56      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
57        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
58      - update global_ocean_ebm parameters file data and update output (fwd+ad).
59    o verification/matrix_example:
60      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
61        MPI and mutlti-threaded testing.
62    o pkg/matrix:
63      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
64      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
65      - fix for multi-threaded (remove DATA statement);
66      - use standard DIFFERENT_MULTIPLE function;
67      - add MATRIX_OPTIONS.h
68    o verification/matrix_example:
69       To allow to split the domain in several tiles, change the domain size
70        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
71        Western side) of land points.
72    o (*_)write_pickup:
73      - fix few bugs in mypackage_read/write_pickup.F
74      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
75        array of length 1 (was caught by compiler syntax-check).
76    o pkg/diagnostics (velocity potential solver):
77      - fix initialisation of main diagonal matrix (for overlap values)
78    o tools/build_options:
79      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
80        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
81      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
82        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
83        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
84        and use "-devel" testreport option for standard testing on baudelaire.
85    o pkg/grdchk:
86      - Assume that all gradient-check position are within the same tile
87        corresponding to global indices (iGloTile,jGloTile) and that
88        positions (i,j indices or nbeg) are local to this tile;
89      - set tile local-indices and proc. number according to tile global-indices;
90      - remove grdchkwhichproc from namelist (retired param);
91      - send adjoint gradient to all procs so that all procs print it to STDOUT;
92      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
93    o adding package bbl (Bottom Boundary Layer)
94      description in MITgcm/pkg/bbl/bbl_description.tex
95      example/test experiment in MITgcm_contrib/bbl
96    o adjoint verifications
97      - changed 5 experiments to multi-tiles
98        * global_ocean.90x40x15
99        * obcs_ctrl
100        * offline_exf_seaice
101        * tutorial_dic_adjoffline
102        * tutorial_tracer_adjsens
103        changed reference output for those that crossed tile boundaries
104        (changed choices of gradient check positions)
105      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
106      - temporary bug fix in grdchk_loc.F for obcs
107    o genmake2 & testreport
108      - add target "obj" (just for OBJFILES files) to Makefile;
109      - add option to specify FEXTRAFLAGS on command line.
110    o pkg/mypackage:
111      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
112    
113    checkpoint63a (2011/08/02)
114    o pkg/diagnostics (velocity potential):
115      - fix velocity-potential calculation when using OBCS: balance net inflow
116        at each level (new S/R OBCS_DIAG_BALANCE).
117      - fix some of the problems with OBCS in stream-function calculation.
118    o pkg/exf/exf_readparms.F
119      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
120        EXF_NML_OBCS) more consistent, so that you need not have these lists
121        in data.exf when they are not used.
122    o optim/optim_readdata.F:
123      - add some output about obcs variables that might help debugging
124      - add a check about nvarlength
125    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
126    o pkg/diagnostics (velocity potential):
127      - fix mask for OBCS (still problems in stream-function with OBCS);
128      - add specific parameter (default = main code CG2D params) for solver;
129      - in case of poor convergence, use solution corresponding to lowest residual.
130    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
131      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
132      and should be avoided where possible.
133    o model/src (rStar):
134      - include r* effect on reference-state (PhiRef) in totPhiHyd
135        (so that it's really the potential anomaly at the cell center);
136        affect solution only if z* with full pressure in EOS.
137      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
138        update output (because of z* in totPhiHyd and viscA4 changes);
139      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
140        @ constant r) until interpolation at constant r is implemented.
141    o pkg/diagnostics
142      - fix RCENTER diagnostics in case cell center is not at interface middle
143    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
144      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
145      that THETA and SALT are "conservative temperature" and "absolute
146      salinity"
147    o pkg/ctrl
148      - fix computation of endrec in s/r ctrl_init_rec
149      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
150    o pkg/seaice/seaice_growth.F
151      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
152        remove then obsolete STORE directives
153      - fix STORE directives for tice and tices, so that only the
154        appropriate part of the fields are stored (and not the entire
155        field); update global_ocean.cs32x15.seaice AD output.
156      - cosmetic changes: adjust CPP flags and indentation for better
157        legibilty
158    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
159      Chris Wilson)
160    o pkg/gmredi:
161       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
162       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
163    
164    checkpoint63  (2011/07/11)
165    o pkg/exch2:
166     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
167     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
168       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
169       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
170    o pkg/diagnostics:
171     - deal with pairs of post-processed diags which are computed together; in
172       particular, re-order list of diags within 1 file to save 2nd computation.
173     - add S/R to compute velocity stream-function (called after velocity-potential
174       calculation) from divergence free transport -> new diagnostics "PsiVEL".
175     - add parameter to select grid-point location where PsiVEL == 0.
176    o eesupp/src:
177       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
178       (specific S/R needed with exch2 topology - for now, just print an error msg)
179    o pkg/shelfice
180     - Implement friction velocity-dependent transfer coefficients following
181       Holland and Jenkins, JPO, 1999
182       Original code by M. Losch with small modifs.
183       Enable with CPP option SHI_ALLOW_GAMMAFRICT
184       and runtime flag SHELFICEuseGammaFrict
185    o verification lab_sea & global_ocean.cs32x15:
186     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
187       does not miss some dependencies (but is slower) and also works with many files
188       (default makedepend limitation for AD built).
189     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
190    o pkg/diagnostics:
191     - add run-time parameter "useMissingValue" (def=False) to fill land-point
192        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
193       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
194     - Extend the use of "missing_value" setting from data.diagnostics for the case
195       of counter-diagnostics (where fraction-weight is zero). This applies both to
196       MNC and MDS output files.
197    o pkg/seaice/seaice_growth.F:
198      - add 'a priori' cap of latent heat flux based on actual mass considerations
199        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
200        non-legacy seaice_solve4temp.
201      - add diagnostic of the residual sublimation freshwater flux (the freshwater
202        flux taken from the ocean if the total actual latent heat fluxes exceed
203        the maximum)
204      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
205       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
206      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
207       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
208      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
209      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
210    o verification 1D_ocean_ice_column:
211       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
212       update results
213    o pkg/diagnostics:
214     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
215       which are not filled-up but computed from other diags ; In this case, the mate
216       diag points to the primary (filled-up) diag to used for post processing.
217     - Update Velocity-potential computation using post-processed diag framework.
218     ==> Change the ordering of fields and time-periods in MDS output file
219       when using periodic averaging: now writes one time record with the full set
220       of fields for this time period, then the next time reccord (it used to be
221       one field with the full set of time records then the next field).
222         Note: this is now similar to NetCDF (MNC) output file. <==
223    
224    checkpoint62z (2011/06/21)
225    o adjoint monitor:
226     - Add adjoint monitor output for packages exf, seaice
227       and update relevant testreport output
228    o pkg/seaice:
229     - re-order diags inits so that they appear in order in available_diagnostics.log
230     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
231       area/heff/hsnow preceeding thermodynamic growth/melt.
232     - modified diag: SIdA; output actual effect, as the description states.
233     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
234     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
235       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
236        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
237     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
238     - added diagnostics for seaice generic tracers (SItr*).
239     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
240     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
241     I. Fenty: 18-Jun-2011:
242     Minor changes to seaice package:
243     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
244        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
245       - Differentiated "regularization variables" from "floor variables"
246        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
247        * hiceMin became SEAICE_hice_reg (old hiceMin)
248          (with _reg meaning regularization variable)
249       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
250        so as to ensure energy conservation when going between phases
251      - A22 was not used anywhere
252     2) Changed regularization procedure for heffActual and hsnowActual to ensure
253        well-boundedness and smooth adjoint in seaice_growth.F
254     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
255        because the old regularization always set heffActual >= 0.05 cm
256     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
257        on AREA when HEFF > 0.
258      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
259        requiring that DISABLE_AREA_FLOOR *not* be defined
260     Affected verifications:
261      - 1D_ocean_ice_column (output.txt output_adm.txt)
262      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
263    o pkg/diagnostics:
264      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
265      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
266        (was _RL, now integer) with option = 0 to retrieve all levels.
267      - add pieces of code to compute velocity potential at each level (new diagnostics
268        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
269        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
270      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
271        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
272        and in diagnostics_fract_fill.F (do not need a valid pointer for the
273        diagnostics counter-mate); check that definition of counter-diagnostic
274        includes a valid counter-mate (in diagnostics_set_levels.F).
275    o model/src (rStar):
276      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
277        affect solution only if z* with full pressure in EOS;
278        update output of test-exp global_ocean.90x40x15.
279    o pkg/seaice:
280      - introduce siEps=1e-5 parameter
281      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
282      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
283      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
284        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
285        as well as ice cover age and ridging index (attached to AREA).
286        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
287        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
288        Up to SItrMaxNum=3 tracers can be used simultaneously.
289    o pkg/salt_plume:
290      -introduce SPsalFRAC run time parameter that sets the fraction of the
291       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
292       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
293    o model debug options:
294      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
295        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
296      - Refine debug-msg printing selection (3 new levels):
297        debugMode  : controls printing of debug messages (sequence of S/R calls).
298        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
299         debLevZero =  0 ; /* level of disabled aux. msg printing */
300         debLevA =  1 ; /* level of minimum  aux. msg printing */
301         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
302         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
303         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
304         debLevE =  5 ; /* level of extensive debug printing */
305        New debugLevel default: with default debugMode value (=F),
306          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
307          and if debugMode=T, default debugLevel = 4 (debLevD).
308        Relation with previous settings:
309         debLevB (=2) corresponds to former debLevA (=1)
310         debLevD (=4) corresponds to former debLevB (=2)
311        Note:
312         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
313         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
314            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
315      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
316        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
317    o pkg/obcs:
318      - change OBCSfixTopo default from True to False (should not change the results);
319        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
320    o pkg/thsice:
321      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
322        2nd layer seaice sublimation (unlikely to happen)
323      - use Interior mask for OBCS in thsice_advection.F (similar to what is
324        done in gad_advection & seaice_advection).
325    o adjoint:
326      bug fix spotted by Gael Forget:
327      seaice_advection and thsice_advection still had
328      legacy CPP options to avoid CS corner updates for adjoint
329    o pkg/seaice:
330      => Change some of the defaults (2011/05/29):
331         - change SEAICEuseFluxForm default (from False to True)
332         - change DIFF1 default (from 0.004 m/s to 0. m/s)
333         And print warnings if DIFF1 is not set in data.seaice and centered
334          avection scheme is used without any diffusion.
335      also:
336      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
337      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
338      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
339        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
340        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
341      update results of test exp.:
342         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
343             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
344             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
345         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
346         seaice_obcs: output (SEAICEuseFluxForm=T)
347      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
348          for standard fwd & AD lab_sea tests (to keep the same output).
349    o pkg/seaice/seaice_growth.F:
350      - use Ian Fenty's capping formulas for actual ice
351      thickness thoughout EVOLUTION branch.
352      - put treatment pathological case #2) in CPP brackets
353      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
354      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
355    o pkg/seaice:
356      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
357      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
358      also pass fac as a param, which can be 1. (to update the tendency
359      field) or the time step (to update the field itself).
360      - seaice_advdiff.F: for multidim, call seaice_diffusion with
361      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
362      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
363      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
364      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
365    o pkg/seaice:
366      diffusion with centered advection scheme (diffus.F & advect.F):
367      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
368        to just compute the laplacian of input-field.
369      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
370      - fix flux-form version in diffus.F to conserve tracer.
371      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
372       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
373    
374    checkpoint62y (2011/05/26)
375    o pkg/seaice:
376     - seaice_growth.F : in EVOLUTION branch, always include
377       a_QSWbyATM_cover in qnet (as it should be).
378     - verification/global_ocean.cs32x15 : update results accordingly
379       (output.seaice.txt output_adm.seaice.txt).
380    o pkg/seaice + obcs:
381     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
382       equivalent of assuming no tracer gradient outside the OB region.
383       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
384     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
385       after changes above);
386     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
387       only at OB location (instead of over a band of OLx width).
388    o pkg/seaice:
389     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
390       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
391    o pkg/obcs:
392      - split header file "OBCS.h" into 4 separated files:
393        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
394       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
395         (contain no conditional statement which depends on OBCS options).
396      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
397        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
398    o ctrl, cost, grdchk & autodiff pkgs:
399      - make options file more standard (like other {PKG}_OPTIONS.h file but
400        with AD_CONFIG.h); clean-up some of the included header files.
401    o pkg/obcs:
402      - do not mask tracer when applying OB (tracer == 0 could generate problems)
403      - apply tracer OB values to tracer field only at OB location (instead of
404        over a band of OLx width)
405      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
406      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
407        obcs_apply_tloc.F & obcs_apply_sloc.F
408    o obcs in model/src:
409      - call OBCS_APPLY_W only if NonHydrostatic.
410      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
411      - reset dEtaHdt and wVel to zero outside OB interior region ;
412      - leave tracer unchanged outside OB interior region: This has no effect
413        on the solution but just to prevent unrealistic tracer value outside OB.
414      - zero out velocity outside OB interior region: This has no effect on
415        the solution but just to prevent unrealistic velocity outside OB.
416    o obcs and non-lin free-surf:
417       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
418       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
419       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
420       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
421       update results of test-exp. exp4(nlfs).
422    o exp4 (nlfs) test-exp:
423       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
424       with NonLin-FreeSurf); update output.nlfs.txt
425    o obcs and 2d/3d solver norm:
426       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
427       and outside OB interior region (will allow to place OB further inside the
428       domain). Depending on the domain, can affects cg2d-Norm (previous
429       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
430       and cg3d-Norm (previous Norm was computed before canceling OB terms),
431       e.g. in tutorial_plume_on_slope.
432      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
433    o pkg rbcs:
434      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
435      - add capability to apply relaxation to horizontal velocity uVel & vVel.
436    o pkg/grdchk: add gradient check for control variable xx_shifwflx
437    o pkg/shelfice/shelfice_init_fixed.F
438      fix CPP-flag combinations
439    o pkg/seaice: Merge iceage code of Pierre Rampal
440      * update/change/correct ice age calculations
441      * add age updates for pathological cases
442      Probably needs more testing...
443    
444    checkpoint62x (2011/05/13)
445    o pkg/mom_vecinv:
446       high-order vorticity scheme: use interior masks (maskInW & S)
447       to zero-out (outside OB) gradient of vorticity.
448    o verification exp.:
449       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
450       hs94.128x64x5 and seaice_obcs ; update results.
451    o pkg/obcs:
452      fix bug in OBeta for YZ sections in obcs_exf_load.F
453    o pkg/ctrl, pkg/shelfice, and optim:
454      - add new control variable xx_shifwflx (fresh water flux underneath ice
455        shelves). This is almost as tedious as obcs-ctrl, because the
456        variables needs its own mask.
457      - add a cost function term that penalizes the deviation of xx_shifwflx
458        from the first guess (zero) in analogy to other control variables
459    o pkg/shelfice:
460      - start basic adjoint
461    o pkg/ctrl:
462      - remove extra 2D field "for good measure" when initializing in
463        ctrl_set_globfld_[xy/xz/yz].F
464      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
465      - improve error messages in ctrl_set_unpack_*
466    o OBC implementation in momentum:
467       use interior masks (maskInC,W & S) in momentum S/R:
468       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
469       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
470       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
471       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
472       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
473        (and also with Leith/Smagorinsky harmonic-viscosity).
474       Update output of experiment dome and exp4 (+nlfs).
475    o exp4 test-exp:
476      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
477        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
478        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
479        time-varying OB at Western-side for wVel (NonHyd); update output.
480      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
481        and biharmonic-viscosity ; also use prescribed time varying OB.
482    o pkg/obcs:
483      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
484    o model/src:
485      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
486      - initialise startTime & nIter0 with unlikely values: allows to set one
487        from the other without ambiguity.
488    o seaice_obcs test-exp.:
489      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
490    o pkg/obcs:
491      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
492        no longer needed with maskInC,W,S in pkg/generic_advdiff.
493    o pkg/seaice:
494      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
495        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
496      - fixed bug in the initialization of sea ice salinity variable HSALT
497        in seaice_init_varia.F  (removed dependence on ICE2WATR)
498    o fizhi-cs test exp.:
499       switch reference output convention for these 2 non-standard test-exp,
500        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
501          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
502       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
503    o model/inc:
504      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
505        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
506    o pkg/seaice:
507      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
508    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
509      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
510        and initial HSALT
511    
512    checkpoint62w (2011/04/26)
513    o pkg/mom_fluxform:
514      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
515      - use parameter "sideDragFactor" in no-slip BC side-drag part.
516      - update output of exp. global_ocean.90x40x15
517    o pkg/mom_vecinv:
518      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
519    o update seaice exp.:
520      use more consistent parameter values (remove "backward compatability only":
521       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
522      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
523       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
524    o update test-exp global_ocean.90x40x15:
525      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
526      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
527      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
528      o turn on zStar & viscA4 in standard set-up (dir input/)
529        and update output files: output.txt & output.dwnslp.txt
530    o new AD-test experiment: obcs_ctrl
531      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
532    o pkg/dic:
533      fix two bugs in handling water vapour pressure in carbonate chemistry
534      and air-sea fluxes. Found by Val Bennington and Galen McKinley
535      (add DIC Option = WATERVAP_BUG to recover old results)
536      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
537    o adding allowInteriorFreezing option to check for water below freezing point
538      at depth and bring the negative heat anomaly to the surface level
539    o pkgs _fields_load:
540      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
541      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
542        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
543        rbcs to get interpolation weights and time reccord number.
544      - fix multi-threading in aim_fields_load.F
545      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
546    o external_fields_load:
547      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
548       interpolation weights) to use in a periodic time-series ; do not divide by
549       time-step to convert to integer:
550       - this fixes case where externForcingPeriod is not multiple of time-step
551          (Thanks to Christopher L. Wolfe)
552       - this fixes case where externForcingPeriod is an odd multiple of time-step
553         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
554      store index of time-record which is currently loaded:
555       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
556       - needed for the adjoint but not yet used because of extensive recomputations;
557         (to be fixed soon)
558    
559    checkpoint62v (2011/04/02)
560    o verification/1D_ocean_ice_column added to test Ian Fenty's
561      pkg/seaice_growth.F modifications for improving sea ice code differentiability
562    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
563      (new velocity statistics after changing maskInW & maskInS definition)
564    o pkg/generic_advdiff with OBCS:
565      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
566      equivalent to assumption of no tracer gradient outside the OB region.
567      This will affect the results if using obcs+biharmonic diffusion.
568      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
569    o pkg/obcs:
570      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
571      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
572      in Interior region. No impact on solution but affects Velocity monitor stats.
573    o pkg/ptracers (adjoint)
574      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
575      tape file for each tracer
576    o model/inc/src and pkg/autodiff: add parameters that allow to turn
577      of parts of the adjoint code at run time. For now, there are only
578      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
579      parameters are set in data.pkg.
580      This is the lazy coward's version of doing this, but still useful for
581      debugging. In order to do it right, everything needs to be moved to
582      pkg/autodiff.
583    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
584      the end; this fixes the adjoint balancing code for open boundaries.
585    o pkg/ctrl:
586      - change behavior of xx_${varname}period to be analogous to exf-conventions:
587        xx_${varname}period =   0.,  means time-independent control part
588        xx_${varname}period = -12., means one-year-periodic monthly control part
589      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
590        clean up ctrl_init a little, remove unused variables
591      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
592      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
593    
594    checkpoint62u (2011/03/15)
595    o model/src:
596      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
597        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
598      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
599        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
600    o pkg/ctrl/obcs/ecco:
601      - remove obsolete, unused, and partially broken code:
602        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
603        ALLOW_CTRL_OBCS_BALANCE
604      - put a stop statement into ecco/cost_obcsvol.F, but also add
605        cost_obcsvol to ecco_ad_diff.list
606    o pkg/ecco: fix counting cost function contributions for obcs (code
607      by Matt M.) and diffkr for diagnostics
608    o pkg/ecco, pkg/ctrl, pkg/grdchk:
609      add cost penalty terms for initial uvel, vvel, eta controls
610      and I/O for prior error files
611    o pkg/mdsio:
612       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
613       (new argument) to check for tiled file in mdsioLocalDir : this fix the
614       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
615    o pkg/ctrl:
616     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
617       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
618       unused and superfluous variables
619     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
620    o pkg/ecco
621     - enable adjoint of Stevens OB
622    o pkg/ctrl/ecco/grdchk:
623      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
624        Fortunately, we do not have any tests for the numerous cpp-flagged
625        option of "obcs as control parameters" so we will never know
626        if this is an improvement (but at least now things compile).
627      - remove an obsolete initialization from ecco_cost_init_barfiles.F
628      - fix some problems within never used ifdefs to make the code compile
629    o pkg/obcs:
630     - Refine Interior mask definition to work with more complex OB (e.g.
631       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
632       read in Interior mask from file. Check if Interior mask is consistent
633       with OB list of indices.
634    o pkg/seaice
635     - beginning code for a seaice tracer package,
636       but currently only used for seaice age: SEAICE_AGE
637       SEAICE_num = 4
638       iTracer = 1: area-weighted ice age
639               = 2: volume-weighted ice age
640               = 3, 4: template for one-year vs. multi-year ice
641       data.seaice has new namelist SEAICE_PARM03 for arrays related to
642       SEAICE_num
643    
644    checkpoint62t (2011/03/05)
645    o pkg/obcs:
646     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
647       then normal component. This ensures that the normal component is set
648       correctly even when it conficts with tangential setting from an other OB.
649       Affects results of test-experiment seaice_obcs: update the output.txt
650    o pkg/obcs:
651     - add code to monitor statistics of dynamical fields at OB.
652     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
653       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
654       - change default: balance the Net inflow through all OB (instead of balancing
655         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
656     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
657       to match Nortern OB inflow (OBCS_balanceFacN=0).
658    o pkg/seaice:
659     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
660    o pkg/seaice (seaice_growth v 1.113):
661     - reverting seaice_growth to v 1.111 in order to have code with exact bit
662       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
663       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
664       runtime flag SEAICEareaFormula is kept but is inactive
665    o model/src:
666     - add new param to scale curvilinear grid distance and area when using
667       a different sphere radius from the grid-files.
668     - test/check multi-threads EXCH applied to local variable (cg2d_x)
669    o adjoint:
670     - enable adjoint of Stevens OB
671     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
672       (a bit delicate because of potentially modified adj. common block structure;
673       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
674    
675    checkpoint62s (2011/02/15)
676    o pkg/seaice (seaice_growth v 1.112):
677     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
678       computing the ice cover tendency from effective thickness tendencies. Include
679       Ian Fenty's formula.
680     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
681       SEAICEareaFormula.
682     - simplify notations for the various d_HEFF/d_AREA terms.
683    o pkg/gmredi:
684     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
685       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
686       add a verification test-run (front_relax.bvp) to test GM_useBVP.
687    o pkg/seaice (seaice_growth v 1.111):
688     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
689     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
690       also melt ice.
691    o pkg/seaice:
692     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
693     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
694    o pkg/cheapaml:
695     - from Nico Wienders: New version of this package.
696    o pkg/flt:
697     - add CPP options to prevent floats to re-enter the opposite side of
698       a periodic domain (default: keep periodicity)
699    o pkg/gmredi:
700     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
701       (needed for multi-dim advection).
702     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
703    o model/src:
704     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
705    o tutorial_tracer_adjsens
706     - extend to NLFS and replace maskC by hFacC
707       (change reference output accordingly)
708    
709    checkpoint62r (2011/01/24)
710    o testreport:
711     - add option -deloutp (-do) to remove output file after successful run
712     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
713       extract exact list of procs from this file ; adjust COMMAND by
714       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
715    o pkg/ecco: replace old ineffective way of penalizing deviations from
716      first guess (of obcs) with code by Matt Mazloff
717    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
718      exf/cal
719      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
720        and handle case of obcs?period == 0
721        Not affected by these changes: There is still an inconsistency in
722        the computation of start/endrec for the obcs variables for ALLOW_CAL
723        defined (see comment by Menemenlis, 7-Mar-2003)
724      - make S/R ctrl_get_gen_rec return something meaningful even if
725        ALLOW_CAL is not defined
726      - ctrl_getobcs?: simplify code so that it does not need to use
727                       S/R exf_swapfields
728    o testreport:
729       allow to test MPI with different number of processors for each experiment:
730       create file "SIZE.h.mpi" in each build dir.
731       Note: update of "-command" argument not yet implemented.
732    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
733      alleviate the need for additional 3D tapes when using
734      the non-inear free surface in the adjoint. This is done
735      by adding an 'update' of hfacc etc. to their current
736      value at the beginning of forward_step.F.
737    o pkg/seaice
738      seaice_lsr: move stress-divergence computations out of outer pseudo-
739      timestepping loop
740    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
741      up, so that the calls of the ctrl_* subroutines are really at the end
742      of the routine.
743    o pkg/gmredi:
744      allow to specify a 2-D horizontal map and a 1-D vertical profil
745      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
746    o pkg/seaice:
747      move lsr iterations from seaice_dynsolver to seaice_lsr.
748    o pkg/seaice:
749      reduce memory footprint of seaice mutldim advection tapes,
750      by using a 2D tape independent of the generic_advdiff ones,
751      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
752    
753    checkpoint62q (2010/12/29)
754    o model/src:
755      - check horizontal grid-spacing for unset or zero/negative values.
756      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
757    o pkg/flt:
758      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
759      - precision of input and output files set according to readBinaryPrec
760        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
761      - initial float position from tiled file was not converted to index space
762        (looks like a bug): fixed to make it similar to initial pos. global file.
763    o global_ocean.cs32x15:
764       change SIZE.h of AD set-up to get same tiling as with MPI.
765       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
766    o model/src:
767       add flag to control printing of domain fields (bathymetry, hFac ...) in
768       ini_mask_etc (call to plot_fieds_xy*).
769    o pkg/thsice:
770       if useEXF, some forcing fields are not valid in overlap: fixed by computing
771       over the interior only + apply EXCH at the end (like with SEAICE advection).
772    o pkg/mdsio:
773      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
774        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
775      - change barrier call for safe multi-threads access to 3-D shared buffer.
776      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
777      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
778        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
779    o pkg/flt:
780      - add fourth-order Runge-Kutta integration
781      - add basic exch2 support (only 1 facet supported so far!)
782    o pkg/mdsio+rw:
783      new S/R to read local (or tile independent) vector (read counterpart of
784       mds_writevec_loc, and front-end write_glvec_rl/rs).
785    o global_ocean.cs32x15: additional input_ad.seaice experiment
786        that uses pkg/seaice rather than pkg/thsice.
787        (using multidim advection for seaice)
788    o towards more F95 syntax for array specification in namelist:
789      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
790        of all verification experiments.
791           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
792          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
793      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
794    o global_ocean.cs32x15: additional input.seaice experiment
795        that uses pkg/seaice rather than pkg/thsice.
796    
797    checkpoint62p (2010/12/17)
798    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
799        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
800    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
801        allow for use of multim. advection in seaice adjoint.
802    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
803      - first attempt to close budgets by taking into account the freshwater
804        flux implied by the sublimation of snow and ice. So far only the
805        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
806        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
807    o eesupp/src:
808      new S/R with new option (NML_EXTENDED_F77) to change array specification
809      from F95 standard to commonly accepted extended F77 form.
810      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
811      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
812      for less tolerant f77 compiler (e.g., pgf77, g77).
813    o globalFiles:
814      commented out in parameter file "data" since it's not safe with MPI
815      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
816      in this case); no longer commented out in restart test (tst_2+2).
817    o add adTapeDir to specify a special directory where adjoint tapes are
818      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
819      and cannot be used together with mdsioLocalDir.
820    o nesting pkgs:
821      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
822      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
823      - add parameter files + utils dir + output from short run on beagle.
824    o pkg/seaice:
825        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
826    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
827      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
828    
829    checkpoint62o (2010/11/25)
830    o pkg/exf:
831      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
832    o pkg/seaice:
833      - seaice_ocean_stress: split a loop for better vectorization of the
834        adjoint code
835      - seaice_growth.F: fix bug in conservation of freshwater connected to
836        capping of heff, put contribution into d_HEFFbyNEG
837      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
838        by something more sensible (parameters that are what their name implies)
839      - change some defaults, so that by default exf-parameters are used for
840        things like rhoAir, cpAir,latent/sensible heat parameters, in order
841        to reproduce the old results, many data.seaice now contain funny values
842        for cpAir and latent heat of sublimation
843    o packages_readparms.F: move exf_readparms up in line so that
844        exf-parameters are visible for other packages (e.g. seaice)
845    o debugMode & debugLevel=2:
846      - differentiate between debugMode & debugLevel=2:
847        debugMode: controls printing of debug messages (sequence of S/R calls).
848        debugLevel: controls printing of algorithm intermediate results and stats.
849      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
850        => allows to print debug-stats without all sequence of call messages.
851      - switch control of debug print from debugLevel to debugMode in many S/R.
852    o pkg/obcs (obcs-sponge):
853        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
854        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
855    o pkg/generic_advdiff:
856      - record overlap minimum size for each advection scheme;
857      - refine criteria on overlap minimum size;
858      - check and stop (in gad_check) if overlap size is too small.
859    o pkg/obcs:
860      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
861        once, in ptracers_implicit.F)
862      - with seaice: remove test on empty file name in obcs_apply_seaice (always
863        apply OB values when tile has OB)
864    o model/src, coriolis setting:
865      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
866        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
867        files (selectCoriMap=3) with any grid.
868      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
869    o pkg/seaice/seaice_growth.F:
870        a few cosmetic changes that reduce the number of lines of code
871    o pkg/obcs: add boundary conditions following Stevens (1990)
872      - the code follows old MOM/NAOSIM code
873      - so far it is only implemented for the eastern and western boundaries
874        and NOT for pTracers
875    o pkg/rbcs:
876      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
877        beginning of the first rbcs forcing period.
878      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
879        offline package, i.e., one file per time, labeled by iteration number;
880        deltaTrbcs sets the timestep with which the data was generated;
881        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
882      - rbcsForcingCycle=0 makes forcing non-cyclic.
883      - make arithmetic safe for negative times and odd forcing periods.
884    
885    checkpoint62n (2010/11/09)
886    o pkg/seaice:
887        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
888    o pkg/obcs:
889       New S/R to copy tracer value from the OB location to narrow band region
890        (width = same as overlap) beyond the OB: preserve OB value (needed for
891        high-order scheme) which were overwritten by EXCH call if in overlap
892        region. Applied to theta, salt, ptracer and advected seaice variables.
893       With seaice: use maskInC in similar way as in gad_advection.F,
894        in seaice_advection.F and advect.F.
895       Update output of experiment seaice_obcs and change exp4 to test OBCS with
896        4th order Adv.Scheme. for pasive salt and ptracer.
897    o tools/genmake2:
898      - when looking for an optfile (not specified), only search for Fortran compiler
899        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
900      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
901        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
902      - set default for CPP to "cpp -traditional -P" (was the case without specifying
903        an optfile, but otherwise default was just "cpp".
904      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
905      - when "CC" is not set in the optfile, look for possible C compiler
906        (instead of just setting CC=cc)
907      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
908        => add a ".F" to ".o" rule for source files with no "#include" (such as
909           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
910      - move gfortran before g77 in list of possible Fortran compiler (consistent
911        with reference compiler switch from g77 to gfortran)
912    o pkg/seaice:
913      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
914        seaice_check that stops the model, when the CPP flag is used.
915      o seaice_growth.F: make capping of ice volume conserving by returning the
916        capped ice as freshwater to EmPmR. This does not change the verification
917        experiments but will change runs where the capping is acutally active
918    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
919      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
920         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
921         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
922    o tools/genmake2:
923      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
924      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
925      - clean previous genmake log files before anything else.
926      - change Makefile to remove testreport log files (*.tr_log) and genmake log
927        files only with "CLEAN" target (instead of "Clean");
928    o pkg/generic_advdiff:
929      Change OBCS in multiDim advection (gad_advection.F):
930       Use maskInC to prevent intermediate update of tracer-field in OB regions,
931       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
932       which were applying future time-step OB values.
933      This way, all explicit calculations use current-time-step OB values
934       (simpler and more consistent).
935      Affects results when set-up uses time-varying OBC and multi-dim advection;
936       update output of experiment seaice_obcs.
937    o pkg/seaice:
938      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
939       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
940         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
941      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
942       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
943       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
944    o pkg aim (2010/10/26):
945      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
946        formulation with obliquity, eccentricity, ... as run-time parameters,
947      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
948        upward shortwave radition at the surface (all-sky and clear-sky).
949    o pkg/obcs:
950      - writing sections with globalFiles=T does not work: switch to tiled-files
951        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
952      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
953      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
954    
955    checkpoint62m (2010/10/21)
956    o pkg/seaice: vectorize seaice_solve4temp.F
957      - move iterations loops outside of i/j-loops
958      - requires 2D arrays for TB and effConduct
959      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
960        modified in this routine
961      - a little bit of clean up, adjusting indentation, etc.
962      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
963        performance and '**TWO' by '**2' (because TWO is a float),
964        replaced ONE, ZERO
965    o eesupp/src:
966       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
967    o pkg/seaice/seaice_growth.F
968      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
969      merging process. The merged routine has two branches, and one activates the 'evolution'
970      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
971      In summary, here is what the '10/10 revision' did consist of
972        part 1: seaice_growth.F revisions 1.71 to 1.75
973          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
974            The emphasis here was on improving readability (e.g. by trying to use meaningful
975            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
976        part 1.5:
977          - revising the lab_sea experiment to make it a more useful (i.e. stable
978            and representative of an actual model run). This was done by generating a
979            (winter) pickup to start from, switching back the main experiment dynamic
980            solver from evp to lsr, having one of the experiments use the free drift solution.
981        part 2: seaice_growth.F revisions 1.76 to 1.85
982          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
983          - Sorting out the various fields units and sign (set early on and reset at the end)
984            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
985            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
986          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
987            and simplifying logical expressions to further improve readibility.
988        part 3: seaice_growth.F revisions 1.86 to 1.89
989          - Re-organize the blocks of code more logically.
990          - Merging the '_if.F' pieces that add something new.
991    o pkg/thsice:
992      - vectorize thsice_solve4temp and thsice_get_exf.
993        Problem: thsice_solve4temp has an unvectorizable statement that
994        might also be problematic for TAF
995      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
996        does not change the verifcation experiment, but will change all
997        experiments that have this flag undefined (not tested in verification);
998        a little reorganization to save a few 2D fields and recomputations
999      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
1000      - 2nd step:  fix some store dirs
1001        o seems to work somewhat, i.e. using ifort but not g77
1002        o likely cause are incomplete init. or recomputation
1003        o start verification/global_ocean.cs32x15/input_ad.thsice
1004    o pkg/obcs: add support for exch2
1005      - the position of the boundary and prescribed values are specified using
1006        a global domain with exch2 facets stacked
1007        - in x for N,S boundaries (like W2_mapIO=-1)
1008        - in y for E,W boundaries (so E,W boundaries do not overlap)
1009    o pkg/mdsio: add support for writing global sections with exch2
1010        file layout is as for obcs described above:
1011        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
1012        - for y-z sections, facets are stacked in y
1013    o pkg/thsice:
1014       - change a few routines for better vectorization: thsice_albedo.F,
1015         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
1016         not affected, but in particular the latter routine has changed
1017         dramatically (not necessarily easier to read now).
1018       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
1019       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
1020    o verification/lab_sea:
1021      - overhaul of the forward model experiments. The main motivation
1022        for this revision is that lab_sea has proven quite fragile (when
1023        changing the sea-ice code, and switching platforms) to a point
1024        when failures were very hard to attribute to specific code problems.
1025      - the suspected reason for this fragility is noise amplification by evp so,
1026        to start with, we decided to replace evp with lsr in the main experiment.
1027      - the input.lsr experiment thus became obsolete and was removed.
1028      - it was replaced with the input.fd experiment that uses an
1029        analytical "free drift" solution as the ice velocity field.
1030      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
1031        will hopefully allow us to discriminate problems due to dynamic solvers
1032        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
1033        us to test additional options, along with the salt plume package.
1034      - Finally a pickup was generated (at the end of a one year run) to
1035        make the tests more representative of an actual model run. Previously
1036        the tests starting point was a 1m thickness of ice everywhere.
1037    o pkg/seaice:
1038      - introducing S\R seaice_freedrift.F that compute the
1039        analytical solution to an approximate ice momentum
1040        equation (i.e. the simple stress/coriolis balance).
1041      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
1042        of the free drift velocity field, and enable its use.
1043        To actually use the free drift solution as the model ice
1044        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
1045    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
1046    
1047    checkpoint62l (2010/10/04)
1048    o pkg/seaice:
1049      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
1050      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
1051       version (with USE_ORIGINAL_SBI undef);
1052    o add hooks for new packages OASIS, the package will follow
1053      (hooks exclude the seaice pkg for now)
1054    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
1055      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
1056      rather than mdsio_readvector.F/mdsio_writevector.F, within
1057      adread_adwrite.F to read/write adjoint-related tapes to disk.
1058    o eesupp and pkg/mdsio: ALLOW_WHIO
1059      Option to write/read 2D fields to files including tiles halos.
1060      The main purpose is for adjoint related "tape I/O".
1061      The secondary purpose is for debugging phases.
1062      A word on those rather specifically intended purposes.
1063      The code was meant to be stripped down to the bare minimum.
1064      Typically, there is a unique and basic mapping to the global
1065      buffer (tile by tile, then proc by proc, then level by level), and
1066      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
1067      meant to generate user friendly outputs of various shapes and forms.
1068      Rather it is intended, for the knowledgeabale developers,
1069      to be largely independent of the many mdsio options, to allow
1070      outputs of tiles+halos in debugging phases and in adjoint runs,
1071      and to allow some flexibility in tuning (adoint) I/O depending on each
1072      file system behavior. With regard to tuning, most of the potential knobs
1073      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1074      to specify directories, to specify the typical size of I/O calls, etc.)
1075      are not yet included, and will be added if they prove useful.
1076    o pkg/seaice:
1077       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1078    o pkg/seaice:
1079       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1080       code (seaice_budget_ice_if.F) which enable to recover old standard
1081       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1082       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1083    o model/src (rStar):
1084       use simple average (not area weighted) of rStarFac at U,V point when using
1085       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1086       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1087    
1088    checkpoint62k (2010/09/17)
1089    o adjoint
1090       * changed verification/global_ocean.cs32x15 ; adjoint now tests
1091         Adams-Bashforth 3 + NLFS + RSTAR
1092       * some more modifs required for ECCO-GODAE v4
1093    o pkg/seaice
1094       add SEAICE_AGE_VOL option to use volume instead of area for
1095       integrating SEAICE_AGE
1096    o model/src:
1097       first check-in of sigma & hybrid-sigma coordinate code ; also includes
1098       non-linear free-surface parts ; but pressure-gradient not yet coded.
1099    o pkg/ptracers:
1100       option for ptracer to convert Salt Relax into additional EmP.
1101        tested in exp. global_ocean.90x40x15.dwnslp (update output)
1102    
1103    checkpoint62j (2010/08/25)
1104    o pkg/ggl90:
1105       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
1106    o pkg/dic: car_flux.F, phos_flux.F
1107      - reduce number of exp-calls in order to improve performance
1108      - clean up a little (replace fields by their macros, etc., fix
1109        typo in CPP-flag)
1110    o pkg/ggl90: minor changes
1111      - GGL90diffKrS was removed --> always use GGL90diffKr
1112      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1113      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1114        (commented out for now)
1115      - change in max/min operations to ensure that smoothing is ok
1116      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1117      - always use diffKrNrT as background profile (i.e. never use diffKr field)
1118    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1119    o pkg/dic:
1120      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1121        vectorization
1122      - small bug fix in insol for the unlikely case of a cartesian grid
1123      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1124        + now vectorize, which also removes adjoint recomputations;
1125        + replace integer maksp1 by _RL maskp1
1126        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1127    
1128    checkpoint62i (2010/07/21)
1129    o pkg/flt:
1130      - with OBCS: stop floats which enter the OB region
1131    o model/src:
1132      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1133        for implicit vertical advection.
1134    o pkg/seaice:
1135     - account for melting in seaice age evolution.
1136     - remove double counting of seaice ridging effect on seaice age.
1137    
1138    checkpoint62h (2010/06/18)
1139    o pkg/exch2:
1140     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1141    o tools/genmake2
1142      - remove "-pdefault" option: redundant with the use of "packages.conf";
1143      - remove file pkg/pkg_default : set the default as a pkg group
1144        ("default_pkg_list") defined in pkg/pkg_groups;
1145      - fix for case pkg/pkg_depend is missing (was hanging before);
1146      - add option "-pgroups" to specify a different pkg_groups than the default.
1147    o verification/adjustment.cs-32x32x1:
1148       add a "minimal" set-up test (code_min & input_min) which only compiles
1149       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1150    o tools/genmake2
1151      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1152      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1153    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1154      files are nearly the same anyway.
1155      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1156       - redefinition of tau(i,i) (by a factor of ustar)
1157       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1158       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1159       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1160       - replace
1161         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1162         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1163         by
1164         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1165         (changes results)
1166       -> exf_bulkformulae v1.22,
1167          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1168          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1169                    output.txt 1.63
1170           offline_exf_seaice: output.seaicetd.txt 1.7
1171           seaice_obcs: output.txt 1.10)
1172      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1173       -> exf_bulkformulae v1.23,
1174          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1175          and global_ocean.cs32x15.icedyn (only 11 matching digits)
1176      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1177    o adjoint of exch-1:
1178     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1179       (note: was already like this when using EXCH-2) and remove flow dir
1180       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1181     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1182     - update pkg/exch2 diff list.
1183    
1184    checkpoint62g (2010/05/19)
1185    o eesupp/src (exch-1):
1186     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1187       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1188       (renamed to exch1_*rx_cube.F).
1189     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1190       to call new exch1 S/R ; update Makefile and .cvsignore.
1191     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1192       exch2_xy_rx later)
1193      Note: after updating your code, need to run "make clean" in eesupp/src
1194    o test experiment bottom_ctrl_5x5:
1195       new output_adm.txt with fewer grdchk & less monitor output.
1196    o model/src:
1197      remove the call to ini_cori in initialise_varia.F (just keep the usual one
1198       in initialise_fixed.F). More consistent with coriolis & horizontal grid
1199       beeing treated in the same way (ini_grid is not called a 2nd time).
1200    o pkg/exf:
1201      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1202      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1203      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1204      - cosmetic changes to exf_bulkformulae.F to make it look more like
1205        exf_bulk_largeyeager04.F
1206    o eesupp/src (exch-1):
1207      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1208      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1209        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1210        (even without using MPI).
1211      - Message mode: move RecvAck setting (indicator of buffer being ready)
1212        from send_put to recv_get S/R (was useless before, but not sure if
1213        it's much more useful now);
1214      - Switch the order of sync: MPI-proc 1rst and then threads;
1215      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1216      - fix AD code for communication mode ='get' (but not used).
1217    o model/src:
1218      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1219      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1220    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1221    o pkg/ctrl: require a specific set of control variables and exf-flags for
1222      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1223    o model/src:
1224     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1225       1rst forward sweep, to avoid over-writing output files during recomputations
1226       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1227     b) 2nd version:
1228      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1229      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1230         writePickupAtEnd) + seaice & ptracers output;
1231      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1232    o model/src:
1233      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1234    o pkg/exch2:
1235      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1236      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1237    o pkg/autodiff & exch2:
1238      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1239      (for now, only if ALLOW_EXCH2 is defined).
1240    o pkg/autodiff:
1241      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1242        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1243       + clean-up comments (_RS is not always real*4)
1244      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1245      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1246        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1247    o testreport (AD-tests):
1248      no longer link files from dir "../input" (1rst link files from
1249      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1250    
1251    checkpoint62f (2010/04/29)
1252    o model/src/the_main_loop.F:
1253      adjust store directives for seaice evp and multicategory according to
1254      pkg/ecco/the_main_loop.F
1255    o adjoint:
1256      global_sum_ad was incomplete (noted many times by many people ;)
1257      nice description by Jean U. as follows:
1258      * allreduce(var) in global_sum.F can be interpreted as
1259        reduce(sum) followed by broadcast of sum.
1260      * The adjoint of that is
1261        sum(adjoint) followed by broadcast(summed adjoint value)
1262        or in other words, allreduce(sum, adjoint vars)
1263      We were missing the sum(adjoint)!
1264      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1265      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1266      The fix should produce 16-digit accuracy between
1267      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1268      multi-CPU single-tile (e.g. nSx=1, nPx-2)
1269      We'll probably change this yet again shortly
1270    o eesupp/src:
1271      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1272    o pkg/icefront
1273      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1274        specification of addmass array based on a 2D field, which is added
1275        at bottommost wet level at each horizontal location.
1276    o model/src:
1277     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1278     layout; (not always compatible with delX,delY setting; commented out for now).
1279    o pkg/exch2:
1280     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1281     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1282    
1283    checkpoint62e (2010/04/15)
1284    o pkg/obcs:
1285      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1286    o pkg/dic:
1287      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1288        (note: not presently tested in any forward verification exp.)
1289       update tutorial_global_oce_biogeo AD output file.
1290    o pkg/exf:
1291      - account for the variation of albedo as a function of zenith angle
1292        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1293    o build_options:
1294     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1295    o pkg/dic:
1296      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1297      - use binary pickup file for restart;
1298      - initialise atmos-CO2 box from dic_pCO2 parameter;
1299      - fix multi-threaded.
1300    o pkg/rbcs:
1301     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1302       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1303     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1304       and update output.txt
1305    o pkg/kpp:
1306     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1307     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1308       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1309       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1310     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1311       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1312    o pkg/offline:
1313      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1314      (bug was added in version 1.10 on 2007-08-23).
1315    o pkg/offline:
1316      - no need to specify periodicExternalForcing, etc ... to use offline pack
1317      - offline input files no longer just single prec --> parameter offlineLoadPrec
1318    o verification/lab_sea:
1319      change AD test to multi-tile setup and update all 4 AD output.
1320      NOTE: while cost function values remain very similar,
1321      gradients are very different, although gradient checks are self-consistent
1322      Should try to get to the bottom of this (cost function summation order?)
1323    o pkg/dic:
1324      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1325      a weakness of TAF that drops part of double precision in log10 derivative.
1326      <= changes removed since problem has been fixed in current TAF version 1.9.71
1327      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1328    o pkg/ecco:
1329      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1330      update all 4 lab_sea AD output.
1331    
1332    checkpoint62d (2010/03/22)
1333    o build_options:
1334      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1335    o remove unbalanced quote (single or double) in commented line of source code
1336      (may cause some warning with some preprocessor/makedepend versions).
1337    o pkg/seaice:
1338      fix seaice_model.F for adjoint (gael) and update AD results of experiments
1339       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1340    o testreport:
1341      add option '-runonly' (short: '-ro') to just do the run part (without make).
1342    o eesupp: remove JAM communication code (obsolete).
1343    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1344      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1345      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1346      (update also the output).
1347    
1348    checkpoint62c (2010/03/02)
1349    o tools/build_options :
1350       move (some) old optfiles from build_options/ to build_options/unsupported/
1351    o model/src and pkg/exf
1352       surface relaxation -- separating data and data.exf options
1353       The point is to ensure that we specify the surface relaxation
1354       either in data or in data.exf (but not half and half) and to
1355       avoid an accidental relaxation to 0 (which happened if a time
1356       scale was specified but the file name was left empty)
1357    o model/src model/inc and pkg/mom_common
1358       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1359       => addition to the viscosity field as computed by others schemes
1360    o tools/build_options:
1361      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1362        but keep the former optfile for few weeks for smooth transition
1363    o pkg/ecco
1364      - allow user defined cost function contributions
1365         CPP: ALLOW_USERCOST_CONTRIBUTION
1366         USAGE: compute contributions in cost_usercost_all.F
1367      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1368          the two options are complementary.
1369    o pkg/smooth
1370      - migration from contrib to the main repository
1371    
1372    checkpoint62b (2010/01/26)
1373    o pkg/monitor:
1374      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1375        (in case someone forgot to update customized pieces of code)
1376    o nonHydrostatic:
1377      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1378      - add a simple 2-D experiment (short_surf_wave) to test it.
1379    o pkg/icefront:
1380       adding the shell of, and the hooks to, a new package that
1381       will model melting and freezing of vertical glacier ice fronts
1382    o momentum:
1383      add diagnostics of momentum tendency from Hydrostatic pressure gradient
1384       (without surf.pressure term: would need a 2nd filling since implicit term).
1385    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1386      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1387      cannot deal with the former
1388    o cleaning:
1389      - remove all (except OpenAD) old TLM output from results_ad dirs.
1390      - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1391      - comment out maskH definition (replaced by maskInC)
1392    o pkg/monitor:
1393      - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1394        & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1395    
1396    checkpoint62a (2010/01/15)
1397    o model/src:
1398      - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1399    o pkg/diagnostics:
1400      - add optional level number diagnostics (i.e., level number to be define
1401        explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
1402      - strictly check for valid parser-code(10) ;
1403      - check if adding diag to the list from the right place.
1404    o pkg/longstep:
1405      - change parameters and fix tracer conservation with rstar/nonlinear free surface
1406    o diagnostics:
1407     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
1408       S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
1409    o pkg/diagnostics:
1410     - Add option for writing vertical integral (sum of selected levels) of an output
1411        field instead of writing output field levels. Activate this option on a per
1412        output-file basis, by setting the 2nd character of fileflag to 'I'.
1413     - Add field-specific information relative to level integral in 3rd postion
1414        of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
1415        vertically (x level-thickness x hFac), "r"=same but without hFac.
1416    o do_the_model_io:
1417      - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
1418        in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
1419        writing pickups and stopping.
1420    o pkg/diagnostics (for now, only with mdsio):
1421      - write time information to meta file (and modify accordingly rdmds.m) :
1422        time-averaged diagnostics output: write starting and ending time of the
1423        time-averaging interval ; snap-shot diagnostics output remains unchanged;
1424    o pkg/timeave:
1425      - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
1426        always Nr), now assumed to be equal to number of levels of averaged field;
1427        only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
1428    o pkg/sbo:
1429      - fix ocean bottom pressure global-average & 2-D time-ave output (was
1430        neither initialised nor filled).
1431      - add starting iteration in suffix of global-average output file
1432        (to avoid over-writing the file after a restart)
1433      - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
1434    o time-average:
1435      - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
1436        (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
1437         ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
1438        this fix DIC_COST cumulative-time array (previously: bi,bj,k)
1439      - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
1440      - fix missing accumulation for pkg/opps.
1441      - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
1442         (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
1443      - fix initialisation of time-ave vars and do only full time-step increment
1444        (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
1445    o pkg/layers:
1446      - use standard RW pkg S/R to write the output
1447        and remove local write_fld version (which had a problem).
1448      - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
1449      - fix LAYERS_CALC argument list.
1450    o pkg/timeave:
1451      - store cumulative-time in a simple tiled array (drop the level index)
1452      - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
1453    o pkg/ocn,aim_compon_interf
1454      - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
1455    
1456    checkpoint62  (2009/12/23)
1457    o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
1458        (was not previously tested in any other exp.)
1459    o pkg/monitor:
1460      - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
1461        mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
1462        (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
1463      - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
1464      - change del2 calculation.
1465      - use interior masks (instead of maskH, <- to be remove).
1466      - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
1467    o mask & obcs:
1468      - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
1469      - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
1470        (called after packages_init_fixed)
1471    o pkg/obcs:
1472      - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
1473        Fixes bug in obcs+exf with nSx*nSy.GT.1
1474      - fix multi-tile handling in obcs balance code
1475    o nonHydrostatic:
1476      - Implement AB-3 for non-hydrostatic vertical momentum ;
1477        (change ordering of var. stored in pickup file when using NH)
1478      - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
1479      - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
1480        (in prep. for new NH free surface form).
1481    o pkg/obcs:
1482      add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
1483    o model/src:
1484      fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
1485    
1486    checkpoint61z (2009/12/01)
1487    o nonHydrostatic:
1488      Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
1489        a spurious source of energy in simple baroclinic adjusment test case.
1490      Update all non-hydrostatic exp output.
1491    o model/src (3-d solver):
1492      Change again 3-D solver free-surface RHS term when exactConserv=T:
1493        simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
1494        (which was not the case with previous formulation).
1495      To recover previous version, just reset "oldFreeSurfTerm" to previous value.
1496      Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
1497    o nonHydrostatic:
1498      - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
1499        for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
1500      - change 3-D solver to work with r* (for now, only with linear free-surf.)
1501      - add few debug diagnostics (cg3d_x, residual)
1502    o model/src:
1503      fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
1504        update output of exp. global_ocean.cs32x15.viscA4
1505    o update output of exp. global_ocean.cs32x15.icedyn after removing
1506      #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
1507    o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1508    o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
1509      for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
1510    o model: add Christopher Wolfe's implemetation of the single reduction cg2d
1511      (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
1512      runtime flag useSRCGSolver. Modify verification experiment global_with_exf
1513      to test this code
1514    o pkg/cd_code:
1515      Change defaut D-grid time-stepping to get the same for D-grid momentum as for
1516       C-grid momentum. D-grid velocity used to be stepped forward in time with
1517       Adams-Bashforth only on surface pressure term. Tests show that using AB on
1518       D-grid coriolis term improves stability (as expected from CD-scheme paper).
1519      To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
1520      Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
1521       lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
1522       tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
1523      Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
1524           global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
1525    o pkg/obcs:
1526     - fix bug in initialisation (broken since Oct 1rst modification)
1527       for useOBCSprescribe without useEXF.
1528    
1529    checkpoint61y (2009/11/15)
1530    o pkg/seaice
1531     - change (once again) the discretization for the evp solver: rather than
1532       squaring the averages of strain rates, average the squares to give
1533       a better approximation to VP behavior (in simple test); this breaks
1534       verification experiments that use EVP (lab_sea and lab_sea.hb87)
1535        --> update outputs
1536    o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
1537      to improve vectorization of adjoint code on TARGET_NEC_SX
1538    o verification/vermix:
1539      - change vermix to a more "classical" 1d column with high vertical
1540        resolution, seasonal heat flux forcing and constant wind forcing
1541        --> update outputs
1542    o pkg/seaice
1543     - fix diagnostics of principal stress components for EVP
1544     - add optional diagnostics of non-linear convergence for LSOR solver
1545     - make maximum zeta a runtime parameter
1546    o model/src (3-d solver):
1547      Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
1548       which consisted in removing the Surf. Non-Hydrostatic pressure from the
1549       whole column and adding it to Eta (inspired from Casualli, 1999):
1550       Only affects 3-D solver initial guess and only if using ExactConserv,
1551       but tests did show a degradation of solver convergence. For this reason,
1552       decide to disable this piece of code.
1553       to recover previous version, just set zeroPsNH = exactConserv (line 78).
1554      Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
1555    o pkg/ggl90:
1556     - fix previous modif (unfortunatly has not been documented here).
1557    o pkg/seaice/autodiff:
1558     - add CPP flag to include clipping of zeta in EVP code;
1559       although clipping of zeta is not necessary for EVP and not recommended
1560       it was done by default, now clipping is disabled by default
1561     - modify computation and store zetaC/Z in seaice_evp for TAF
1562     - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
1563     - change seaice_calc_viscosities/strainrates for better
1564       vectorization after AD by TAF
1565     - rearrange common blocks in SEAICE.h once again for easier dumps of
1566       adjoint output, adjust adcommon.h and g_common.h
1567     - change flux form of default advection scheme for better vectorization
1568       of adjoint code
1569     - modify lab_sea/input.lsr to test the flux form of default advection
1570       scheme
1571    o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
1572      transition in checkpoint61r)
1573    
1574    checkpoint61x (2009/10/19)
1575    o adjoint: adding two new verification experiments
1576      * tutorial_global_biogeo: an online dic sensitivity experiment
1577        (work with G. Forget)
1578      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
1579        (an update of the Dutkiewicz et al., 2006 paper)
1580      Both use the same CO2FLUX cost function, but different controls
1581      Gradient checks look good, but some recomp. could still be traightened out
1582      Should add xx_dic control variable to test at some point
1583    o model/src:
1584      add run-time parameters to check and/or mask initial Temp & Salt
1585    o pkg/ptracers:
1586      apply zonal filter (if used) to all passive tracers
1587    
1588    checkpoint61w (2009/10/12)
1589    o adjoint:
1590      * update and finish work on adjoint of dic package (G. Forget)
1591      * start adjoint of offline package
1592      * bug fix for cube-sphere TLM code (active_file_g.F)
1593    o tutorial_global_oce_optim:
1594      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
1595      and add SIZE.h_mpi for MPI testing
1596    o pkg autodiff
1597     - fix bug in autodiff_restore
1598     - make genmake2 remove comments and empty lines from ad_input_code.f in
1599       order to reduce file size (new script file remove_comments_sed)
1600    o allows to specify vertical profile of vertical viscosity (viscArNr)
1601    o pkg autodiff
1602      autodiff_ini_model_io: comment out writing of grid information to netcdf
1603      files, because at this time the grid fields are a bunch of zeros
1604      (this is analogous to ini_mnc_vars.F)
1605    o pkg seaice/autodiff:
1606     left-over from removing the 3-time-level fields:
1607     - small rearrangement of common blocks (SEAICE.h)
1608     - fix field declaration in order to get meaningful output in
1609       adseaice.*.nc (adcommon.h)
1610    o pkg obcs:
1611     - go through NH code only if nonHydrostatic=T
1612     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
1613     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
1614       => Update output of experiment seaice_obcs
1615     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
1616     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
1617     - fix restart for useOBCSprescribe + useEXF
1618    o pkg ctrl
1619     - make obcs as control parameter work also with useSingleCPUio
1620     - replace a few sny and snx by Ny and Nx to be consistent with
1621       ctrl_set_globfld_x/yz.F
1622    o pkg seaice
1623     - re-introduce global field frWtrAtm for the case of
1624       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
1625     - catch the case of an empty filename in seaice_cost_init_fixed.F
1626    o pkg ecco:
1627     - small bug fixes in the_main_loop
1628      . fix order of monitor arguments
1629      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
1630      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
1631        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
1632     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
1633       imbalance diagnostics for wmean_h/sflux = 0
1634     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
1635     - catch the case of empty filenames in ecco_cost_init_fixed.F
1636       and ecco_readparms.F
1637     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
1638       to make this statement meaningfull in ecco_cost_weights.F
1639    o pkg zonal_filt:
1640      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
1641      - when using rStar, filter uVel*hFacW instead of uVel
1642       (tested without topography: fix a Pb of growing instability with NLFS)
1643    o pkg/aim/thsice:
1644     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
1645      (works as SST restoring)
1646    o pkg/thsice:
1647     -add specific parameter for salt restoring in slab mixed-layer
1648       (by default equal to the temperature restoring)
1649    
1650    checkpoint61v (2009/09/21)
1651    o pkg/kpp:
1652     -add double diffusive contributions as a hack, turned off by default
1653      for now, and the code can be excluded with a CPP-flag
1654      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
1655     -add a verification experiments to "vermix" to test this code
1656    o pkg/mom_common:
1657      Move computation of length scales to mom_init_fixed.F (avoid recomputation
1658      at each time-steps*levels).
1659    o pkg/layers:
1660      Created a new package for computing volume fluxes in temperature or
1661      [not yet implemented] density layers, e.g. for calculating residual
1662      overturning circulations.
1663    o pkg/diagnostics:
1664      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
1665    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
1666    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
1667      To avoid mixing type (RS/RL) of input/output array argument,
1668      replace single mixed-type array with a pair from each type (RS/RL).
1669    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
1670      is now implemented for all pkgs (previously only done for the main pickup)
1671    
1672    checkpoint61u (2009/08/25)
1673    o pkg/obcs:
1674      - change OB?eta from _RS to _RL and put them into a separate commen block
1675      - add code to read OB?eta from a file via obcs_prescribe_read: the code
1676        compiles and does not destroy any other experiments, the data is read
1677        properly, but the code is not tested in actual applications
1678    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
1679      create a meaningful unit attribute for the time coordinate variable
1680    o pkg/ebm: add plenty of missing "_d 0" ;
1681       update results of experiment global_ocean_ebm (fwd + adjoint tests)
1682      Notes: several pieces of code only works for (very) specific set up
1683       (domain size, lat range, etc ...); should be documented & stop if one
1684       of those assumptions is not meet.
1685    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
1686       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
1687          and offline_exf_seaice (seaicetd + adjoint).
1688    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
1689       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
1690        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
1691    o few changes to pass when compiling with strick checking of arguments
1692       across S/R (allow to find few bugs in S/R calls).
1693    o pkg/seaice:
1694     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
1695       2d-fields, for slightly better performance
1696    
1697    checkpoint61t (2009/07/22)
1698    o pkg/seaice:
1699     - remove unused variables in seaice_evp
1700     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
1701    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
1702       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
1703       each processor opens a different file (a fix from Matt).
1704    o cg2d:
1705       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
1706       this reduces number of EXCH calls by 2 when using exch2.
1707       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
1708       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
1709    o pkg/thsice:
1710       add code for Near Infra-Red albedo (from Jeff)
1711       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
1712    o ini_model_io:
1713       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
1714       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
1715       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
1716    
1717    checkpoint61s (2009/06/30)
1718    o pkg/exch2 (exch2_rxN_cube*):
1719       remove last BARRIER (no need to synchronise after getting data from shared
1720       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
1721    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
1722      and generate new output (for the 2 tests) using default rotationPeriod.
1723    o pkg/exch2:
1724      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
1725        (was already the case with AUTODIFF_EXCH2 defined)
1726      - add bj in exch2 arrays and S/R.
1727      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
1728        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
1729    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
1730      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
1731        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
1732      - verification experiment natl_box.longstep
1733    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
1734      allow different versions of ifort (8 or 9) and different versions
1735       of mpi (mpich or mpich2) to be used with the same optfile.
1736      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
1737       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
1738    o pkg/seaice:
1739      fix previous modif (3-level field removed) for old-pickup reading
1740    
1741    checkpoint61r (2009/06/25)
1742    o pkg/seaice:
1743     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
1744      1. introduce fields for time step (N-1)
1745      2. do not use levels 2 and 3 anymore (but keep them)
1746      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
1747         includes changes to pkg/thsice/thsice_get_velocity.F,
1748         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
1749         pkg/obcs/obcs_apply_uvice.F.
1750     - completely remove code for leap-frog time stepping for second order
1751       advection
1752     - adjusted adjoint accordingly;
1753       gradient checks have improved by an order of magnitude!
1754    
1755    checkpoint61q (2009/06/22)
1756    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
1757     - the boundary conditions along open boundaries are unclear, because the
1758       associated masks are set to zero and are thus treated as closed when
1759       applying the slip-boundary conditions.
1760     - move initialisation of grid variables from seaice_init_varia to _fixed
1761    o adding doc/diags_changes.txt
1762    o model/src:
1763      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
1764       to avoid "_diags" naming if no relation to pkg/diagnostics.
1765      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
1766       file and only call PLOT_FIELD_XYZ if debugMode=T.
1767      remove few PLOT_FIELD_XY calls outside initialisation.
1768      remove few unnecessary BARRIER.
1769    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
1770      of salt_plume package in Southern Ocean
1771    o pkg/thsice:
1772     - fix hOceMxL in overlap (needed for sea-ice advection);
1773       update output of experiment global_ocean.cs32x15.icedyn.
1774    o pkg/seaice:
1775     - make the (placeholder-)tracer IceAge a little more meaningful
1776      by avoiding ridging of age due to convergent ice flow
1777     - add diagnostics for surface temperature, atmospheric and oceanic
1778       heat flux, and atmospheric and oceanic ice growth
1779    
1780    checkpoint61p (2009/06/10)
1781    o eesupp (global_max & global_sum):
1782     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
1783     - remove starting & endding barrier (no longer needed)
1784    o pkg/mdsio, writelocal:
1785       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
1786       (remove the STOP): uses shared buffer IO to store data from all threads
1787       and then let master-thread write nThreads tiles.
1788    o pkg/mdsio (read/write field):
1789     - tiled IO done in 1 piece (all levels at a time);
1790     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
1791     - multi-threaded: allow to read/write local (non-shared) array
1792       (was already working with singleCpuIO ; now works also without);
1793       => no longer needs barrier call after reading a file (added inside
1794       mds_read/write field).
1795     - move barrier calls outside gather/scatter_2d to mds_read/write_field
1796    o pkg/obcs/exf
1797      - exf_getffieldrec.F: add a few ". _d 0" and
1798                            add code to catch the case fldperiod = 0.  
1799      - obcs_precribe_read.F: change if statements so that they match
1800                              the variable type (_RL)
1801      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
1802        exf_iprec) as part of namelist EXF_NML_01
1803    o pkg/mdsio:
1804      - read/write tiled (local) files: read/write 1-level tile chunk at a time
1805        (instead of segment of length sNx); expected to speed up tiled IO.
1806    o pkg/exch2:
1807      - take buffer copy from/to array out of S/R exch2_send/recv into new
1808        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
1809        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
1810      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
1811      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
1812        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
1813        including Topology header file (and common blocks).
1814      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
1815        remove 2nd exch call in exch2_s3d_rx (no longer needed).
1816      - document S/R arg. list (+ update some comments)
1817    o pkg/seaice:
1818      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
1819        temperature and humidity over sea ice based on climatological values.
1820      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
1821        of LSR (this change is expected to change the results slightly because now
1822        it uses slightly difference moduli from the second last LSR solution, but
1823        that is more consistent with the stress computations; this part of the code
1824        is not tested in the verification experiments)
1825      - fix diagnostics for flux of ice in case of B-grid
1826      - turn strain rates eij and press into global fields within global
1827        common block in SEAICE.h for more straighforward diagnostics
1828      - fix diagnostics for principal stress components, press, zeta, eta
1829        to give something meaning full
1830    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
1831      new output (all 4 tests) using default rotationPeriod.
1832    o pkg KPP:
1833      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
1834      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
1835        and normal grid from 1 to Nr)
1836    o Fix computations of L4rdt in mom_calc_visc.F
1837    o eesupp:
1838      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
1839      should be called before a "stop" if we know that all process are going
1840      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
1841    
1842    checkpoint61o (2009/05/26)
1843    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
1844    o model/src/ini_curvilinear_grid.F:
1845       compute angleSin/CosC when they are not read from a file
1846    o pkg/seaice:
1847       add pseudo time stepping for LSOR
1848    o pkg/exch2:
1849       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
1850    o pkg/seaice:
1851       Adding separate sea ice albedo, drag coefficients, and HO in Southern
1852       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
1853    o SingleCpuIO:
1854       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
1855    o pkg/seaice:
1856       put exchanged variable in (local) common block for MPI+Multi-Threads
1857       to work (necessary with exch1, and for now with exch2 too).
1858    o verification: to get more experiments tested with mpi, mth and mpi+mth,
1859      change tiling of:
1860       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
1861       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
1862      update output of exp:
1863       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
1864       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
1865      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
1866                       (note: output.txt generated on faulks using only 1 tile)
1867    o eesupp & mdsio (SingleCpuIO):
1868     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
1869       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
1870       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
1871     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
1872     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
1873       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
1874    o pkg/exch2:
1875     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
1876       read parameter file "data.exch2" if it exists; otherwise try default regular
1877       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
1878     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
1879       with new code (not to be used, just as a backup solution).
1880     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
1881       in utils/exch2/input.
1882    
1883    checkpoint61n (2009/05/12)
1884    o eesupp & mdsio (SingleCpuIO):
1885      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
1886        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
1887        receive real*4 array (instead of real*8) to read/write 32.bit files.
1888        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
1889         and remove new mapping S/R)
1890    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
1891      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
1892        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
1893        when using exch2. Add S/R to map global io-buffer to global model array.
1894      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
1895    
1896    checkpoint61m (2009/04/29)
1897    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
1898      and add 3 other S/R for other types (R4,R8,RS).
1899      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
1900    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
1901     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
1902     - reduce number of macro definitions (keep only those which are used);
1903       can always call directly the corrresponding S/R if needed.
1904     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
1905       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
1906     Fixed wrong type of arg in:
1907       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
1908       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
1909     To fix: global_sum of var in common block is wrong (multi-threaded) in:
1910       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
1911     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
1912    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
1913      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
1914    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
1915    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
1916      edges are closed (zero depth); might happen with "blank tiles";
1917      for now, disabled if using OBCS.
1918    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
1919      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
1920    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
1921      to reduce length of 1.D array print in STDOUT.
1922    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
1923      + use 48 tiles (16x8): this will allow to test "blank tiles".
1924    o start to test MPI + multi-threaded (change testreport to skip tests
1925      where number of tiles do not match).
1926    o genmake2: add option "-omp" to turn on Open-MP ;
1927      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
1928    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
1929      and keep the original tile numbering. Note: compatible with old
1930      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
1931    
1932    checkpoint61l (2009/04/07)
1933    o Overlaps had been forgotten in calculating ijk keys : fixed
1934    o fix cyrus makedepend for gcc 4.4
1935    o experiment fizhi-cs-aqualev20:
1936      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
1937      and generate new output. Note: new output is much closer to the old
1938      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
1939      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
1940    o pkg/fizhi:
1941     - change to avoid indices going deliberately over array-bounds
1942     - remove unnecessary MPI stuff
1943     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
1944     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
1945       does not go over array-bounds and therefore returns reliable output.
1946     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
1947       this S/R has 4 output arguments, which are used inside "get_alarm";
1948       when it is called with the same variable "ndum" in place of several
1949       output arguments, this produces weird side effect inside "get_alarm"
1950      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
1951       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
1952       address) and produces error.
1953    o tools/gemake2: (March 27-29 2009)
1954      with option "-mpi": link *_mpi files from "MODS" dir (this is what
1955      testreport does).
1956    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
1957    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
1958       update lab_sea.lsr & lab_sea.salt_plume results
1959    o pkg/seaice:
1960      Major overhaul of the LSOR solver: change discretization from original
1961      finite differences to finite volume. The old routine is still in the
1962      file seaice_lsr.F and can be turned on with the CPP-flag
1963      SEAICE_OLD_AND_BAD_DISCRETIZATION
1964      Along with this change, the discretization of the strain rates is changed.
1965      The same flag turns on the old discretization in seaice_calc_strainrates.F
1966      All verification experiments with seaice are affected (except for
1967      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
1968      results by setting the above flag.
1969      Further changes involve changes in defaults:
1970      - ALLOW_FLOODING is defined and turned on by default
1971      - SEAICEadvSnow = .true. is now the default
1972      - SEAICEadvSalt = .true. is now the default
1973      - SEAICEadvAge  = .true. is now the default
1974      - SEAICE_clipVelocities  = .false. is now the default
1975                                         (as per J. Zhang's recommendation)
1976      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
1977        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
1978      - seaice_growth: replace computation of UG by a simple copy from wspeed
1979    
1980    checkpoint61k (2009/03/18)
1981    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
1982      seaice_lsr: fixed a few metric terms,
1983                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
1984                  add more debugging diagnostics
1985      seaice_evp: removed superfluous many metric terms of FV discretization
1986                  of stress divergence
1987                  affects lab_sea, lab_sea.hb87
1988      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
1989                  of stress divergence for non-evp solver
1990                  (this part is not tested anywhere)
1991      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
1992                  they were effectively only half slip
1993                  affects lab_sea.hb87
1994      updated all relevant verification experiments (except lab_sea//output_adm.txt
1995        which was left over, but fails at level 7 & 6)
1996    
1997    checkpoint61j (2009/03/17)
1998    o pkg/seaice: turn a few hard wired parameters into run time parameters
1999    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
2000      time in seconds as promised by the usints in seaice_monitor and exf_monitor
2001    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
2002      that are not cubed-sphere grids
2003    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
2004    o pkg/ctrl:
2005      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
2006    o non-hydrostatic (calc_gw.F):
2007      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
2008      update output of exp. global_ocean.cs32x15.viscA4
2009    o remove backward compatibility for thetaMin,phiMin
2010      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
2011    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
2012      interpolated wind field not only for curvilineargrid=.true., but also
2013      for a rotated grid (rotateGrid=.true.)
2014    o pkg/exf: add capability to bypass interpolation for runoff
2015      by setting yet another CPP-flag
2016    o eesupp/src, B-grid exchange:
2017      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
2018    o autodiff
2019      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
2020      allows to switch to single-prec common blocks;
2021      corresponding switch occurs in tamc.h, integer isbyte
2022      TAF store directivs "byte" and "kind" seem equivalent;
2023      Most tamc.h have been updated correspondingly.
2024    
2025    checkpoint61i (2009/02/13)
2026    o autodiff:
2027      fix autodiff_sore/_restore indices for obcs
2028      (spotted by I. Hoteit, M. Mazloff)
2029    o pkg/autodiff, pkg/ctrl:
2030      Add flag to reduce all tapelev I/O to single-prec.
2031      In data.ctrl set
2032        doSinglePrecTapelev = .TRUE.
2033    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
2034      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
2035    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
2036      real fresh water flux (not yet)
2037    o pkg/mdsio & rw:
2038     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
2039     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
2040    o pkg/flt:
2041     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
2042       init_fixed & ini_varia.
2043     - clean-up & simplify linear interpolation S/R:
2044       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
2045     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
2046     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
2047     - add vert. coordinate & horiz. indices to output files.
2048     - change vertical position in initial condition, from index to depth [m].
2049     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
2050       (easier to get to a curvilinear grid) ; delX,delY no longer used.
2051    o pkg/ggl90: a few modifications:
2052     - fix bottom boundary condition, and interpolation of KappaE
2053       near top and bottom
2054     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
2055     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
2056     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
2057    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
2058      (maintain temporary backward compatibility, until next checkpoint)
2059    
2060    checkpoint61h (2009/01/27)
2061    o pkg/diagnostics with "periodic averaging diagnostics":
2062      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
2063    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
2064    o pkg/obcs: fix loop ranges for balancing code
2065    o pkg/flt:
2066     - improve criteria for finding which tile owns a float.
2067     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
2068    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
2069      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
2070      with ocean biogeo)
2071    o pkg/flt:
2072     - do some cleaning and fix the restart ;
2073     - add output.txt in flt_example/results to get this pkg tested.
2074    o genmake2: add an EXTENDED_SRC option and flag.
2075       for now, cannot be turned on on command line (only through genmake_local)
2076    o pkg/mdsio: read/write vector:
2077     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
2078     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
2079       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
2080     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
2081      (drop to 4 digits matching for grad). But this test does not look very
2082      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
2083    
2084    checkpoint61g (2008/12/29)
2085    o pkg/flt:
2086      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
2087       + make OPTIONS file more standard.
2088      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
2089      - fix _BYTESWAPIO CPP-Flag
2090      - standard reading of file-parameter "data.flt"
2091      - fix argument list of S/R FLT_RESTART
2092      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
2093    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
2094    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
2095      a still unfixed compiler/optimization bug
2096    
2097    checkpoint61f (2008/11/21)
2098    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
2099      update results of global_ocean.cs32x15.icedyn test.
2100    o move getcon.F from model/src to pkg/fizhi.
2101    o pkg/exf: add parameter for extrapolation of temp up to the surface
2102       and option to prevent negative evap (in bulk_largeyeager04 only).
2103    o Prather Advection scheme: fix tracer conservation for divergent flow
2104      (e.g., when using NonLin Free-Surface).
2105    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
2106    o gmredi (Visbeck-variable-K):
2107     - add more parameters to Visbeck-variable-K.
2108     - use a 5 points average for dSigmaR in Visbeck-K calculation
2109       (more "homogenous": same stencil and same weights as in dSigmaH)
2110     - update output of ideal_2D_oce experiment.
2111    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
2112      (#undef REAL4_IS_SLOW)
2113     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
2114       coordinate variable
2115     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
2116       (surface forcing fields), removes some of the functionality
2117     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
2118     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
2119       probably not all: copy _RS surface flux fields to RL field before
2120       calling DIAGNOSTICS_FILL
2121     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
2122       real*4 (CALL EXCH_*_RS) versions.
2123     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
2124       (generate new output).
2125    
2126    checkpoint61e (2008/10/23)
2127    o gmredi (Visbeck-variable-K):
2128      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
2129      - change computation of Visbeck-K where Slope > Smax :        
2130        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
2131        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
2132    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
2133      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
2134    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
2135    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
2136      does not become too large (to avoid precision problems in implicit-diffusion
2137      solver); update ideal_2D_oce output.
2138    o pkg ggl90:
2139      - in ggl90_cal.F: compute only one set of visc/diff, used to
2140        step forward TKE/T/S/momentum
2141      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
2142        have Prandlt =1)
2143    o gmredi (fm07):
2144      - add lower limit on Transition layer thickness + lower limit on 1/lambda
2145      - allow to set few more params from data.gmredi
2146    o pkg ggl90:
2147          - add missing sqrt(2) factor in computation of mixing length
2148            scale in ggl90_calc.F
2149            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
2150    
2151    checkpoint61d (2008/09/25)
2152    o adjoint modifs
2153      - adapt to new field rhoInSitu
2154      - allow to revert from StoreDynVars2D, StoreDynVars3D
2155        to individual fields
2156        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
2157    o store 3-D (in-situ) density in commom block (DYNVARS.h)
2158     - save 1 rho computation.
2159     - no longer modify T & S inland when using down_slope pkg.
2160    o gad_som : allow to switch to SOM advection for T & S without corresponding
2161      pickup files (using new S/R: MDS_CHECK4FILE).
2162    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
2163      (for useSingleCpuIO to work in multi-threaded)
2164    o pkg/shelfice:
2165     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
2166       with SHELFICEtopoFile in data.shelfice
2167     - move code for reading ice shelf topography and modifying hFacC into separate
2168       subroutines of the shelfice package
2169     - separate initialisation of "fixed" and "variable" variables
2170     - kTopC is not (yet) replaced by kSurfC, although this is possible
2171    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
2172    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
2173      and rename:
2174      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
2175      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
2176    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
2177    
2178    checkpoint61c (2008/08/30)
2179    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
2180      to add mass source/sink of fluid in the interior (3-D generalisation
2181      of oceanic real-fresh water flux).
2182    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
2183    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
2184    o new pkg: down_slope
2185      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
2186      - presently, modify T & S inland (dwnslp_calc_rho.F).
2187        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
2188      - implementation for ocean in P-coords not tested.
2189      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
2190    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
2191      (to facilitate conversion of oceanic pkg to p-coordinate).
2192    o change FIND_RHO to FIND_RHO_2D :
2193      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
2194    o new pkg: cheapaml
2195    
2196    checkpoint61b (2008/08/05)
2197    o exch2:
2198      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
2199      - no longer depend on the order sequence (N,S,E,W).
2200      - 3rd exchange no longer needed (tested with 24 tiles).
2201      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
2202      - exch_UV_A-grid readily available (but not yet tested).
2203      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
2204      (both are no longer needed) in exch_uv: no effect in forward run; but
2205       get truncation error differences with adjoint exch.
2206    o exch2:
2207     - change index-bounds storage (moved from target to local tile,
2208       more intuitive this way) ; rename/remove some variables.
2209     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
2210    
2211    checkpoint61a (2008/07/29)
2212    o exch2/matlab-topology-generator:
2213      fix bug in index bounds for N-S internal exchange (hard to tell if this
2214      had any effect on the solution).
2215    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
2216      is exceeded
2217    o testreport: modify syntax of awk, so that it works also with
2218      awk, and not only with nawk and gawk
2219    
2220    checkpoint61 (2008/06/24)
2221    o autodiff
2222      Change default for TAF usage by removing argument '-nonew_arg'
2223      This changes TAF subroutine argument list (ordering of active var.)
2224      Omission of this flag leads to incompatibility w.r.t. TAMC
2225      To restore TAMC-compatibility, need following modifs:
2226      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
2227      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
2228      Tested TAF version is 1.9.22
2229      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
2230    
2231    checkpoint60 (2008/06/19)
2232    --->>> This is the last checkpoint for which generating the adjoint
2233    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
2234    --->>> by default.
2235    --->>> Future checkpoints will ommit this flag by default.
2236    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
2237    o pkg/grdchk: Add gradient check to etan0 perturbations.
2238    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
2239    o pkg/autodiff: more flexibility in zeroadj.
2240      model/src: modifying do_oceanic_phys.F accordingly.
2241    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
2242    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
2243      special setup of gmredi for which the adjoint is stable
2244      enough for parameter optimization.
2245    o bridging the gap between eddy stress and GM.
2246      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
2247          along with a change in CPP option (now ALLOW_EDDYPSI).
2248      -> when using GM w/ GM_AdvForm:
2249          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
2250          is applied either in the tracer Eq. or in momentum Eq.
2251          depending on data.gmredi (intro. GM_InMomAsStress).
2252      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
2253      The key modifications are in model/src/taueddy_external_forcing.F
2254      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
2255    
2256    checkpoint59r (2008/05/29)
2257    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
2258      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
2259      fix option to read coriolis(@ cell-corner) from files with CS-grid.
2260    o pkg/mnc: add some attributes to standard 1D-coordinate variables
2261    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
2262      mass points, when using mnc for output
2263      - add runtime parameter (missing_value, missing_value_int) to override
2264        default (which is the value of getcon('UNDEF'))
2265    o pkg/mnc: prepare mnc for the actual use of missing values with the
2266      diagnostics package: small fix in mnc_cw_readwrite.template and more
2267      initialisation of never used fields
2268      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
2269      versions
2270    o pkg/thsice/thsice_ini_vars.F added default initial values so that
2271      thermodynamics sea ice solver does not blow up when some initial fields
2272      are missing.
2273    o move from external_forcing_surf.F to ini_forcing.F
2274      the p-coord. hack consisting in using pLoad to set phi0surf ;
2275      update output of tutorial_global_oce_in_p (affected @ truncation level).
2276    o Freshen up a bit hs94.1x64x5, notably:
2277      remove rotationPeriod and tRef=5*0. (adjoint only), and add
2278      exactConserv=.TRUE.
2279    o pkg/generic_advdiff:
2280      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
2281      applies to files where Temperature & Salinity 2nd Order moments are used.
2282    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
2283      this uses a dynamically allocated internal state data structure
2284      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
2285      and requires a fortran 90 compiler
2286    
2287    checkpoint59q (2008/05/06)
2288    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
2289       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
2290    o Refresh tutorial_global_oce_biogeo, notably:
2291      - change bathymetry (put back seamounts in ACC, use hFacs)
2292      - change EOS (POLY3 --> JMD95Z)
2293      - use Bryan-Lewis vertical diffusivity
2294      - use multidimensional advection
2295      - remove old virtual virtual in dic pkg, now done through ptracer pkg
2296      - change a couple of parameters in dic pkg
2297    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
2298    o pkg/obcs: change default to OBCSfixTopo = .true.,
2299      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
2300      - replace "debugMode" with "debugLevel .GE. debLevB"
2301    o implementation of TAF directives for gchem,cfc,dic
2302    o remove "exp5" (replaced by tutorial_deep_convection).
2303    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
2304      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
2305      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
2306      --> changes results in exp4, seaice_obcs
2307    o tutorial_deep_convection :
2308      update the set-up and increase resolution and domain size ; start
2309      from pseudo initial conditions = output at t=120mn in order to see
2310      something happening when running testreport.
2311    o pkg/seaice: add os7mp as an advection scheme
2312                  add check for advection schemes
2313                  add a flag for restoring T and S underneath sea ice
2314    o pkg/my82: add netcdf-support and diagnostics
2315    o thsice pkg:
2316      - Now hsMax limits snow height by turning it into ice following
2317        flooding scheme (and now conserving energy)
2318      - Slight rewriting of the formula in thsice_calc_thick.F
2319      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
2320      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
2321    
2322    checkpoint59p (2008/04/10)
2323    o gchem / dic / cfc :
2324      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
2325      - add new parameter files: "data.dic" & "data.cfc" ;
2326      - various re-arrangement in initialisation & header file ;
2327      - fix tutorial_global_oce_biogeo for multi-threaded test.
2328    o pkg/dic: test for "pickup_dic" file when restarting ;
2329      if no pickup-file, can restart with a re-initialised pH (same as it did
2330      before) providing pickupStrictlyMatch is set to False.
2331    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
2332      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
2333    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
2334      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
2335    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
2336     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
2337       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
2338    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
2339       scheme to use for vorticty-term ;
2340     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
2341       (with default selectVortScheme, return to original discretisation)
2342     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
2343    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
2344    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
2345      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
2346      also fix diagnostics VISCAHW & VISCA4W.
2347    
2348    checkpoint59o (2008/03/07)
2349    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
2350    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
2351      move a few statemens out the main loop into separate loops
2352    o pkg/shelfice:
2353      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
2354        (kg/m^2/s), does not break tests, because in verification/isomip,
2355        rhoConstFresh=rhoConst (by accident)
2356      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
2357      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
2358        new file model/src/seawater.F, so that they are available for all pkgs.
2359      - convert potential temperature into in-situ temperature. This changes the
2360        isomip tests => update tests
2361    o add a flag writePickupAtEnd (default=true) to be able to suppress
2362      writing a pickup at the last timestep
2363    o tools/mpack-1.6 :
2364      - disable automake (not working) and autoconf (not needed).
2365      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
2366        also cleaner with much less compilation warnings.
2367    o pkg/profiles:
2368      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
2369      (for "less than 32 characters name" compiler requirement)
2370    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
2371      conditions that have a different sampling frequency than S/T/U/V obcs
2372    o pkg/diagnostics (stats-diags):
2373      - fix global Min/Max in case 1 processor get only empty tiles
2374    o genmake2: replace (4 times)
2375         make genmake_tc_1.o >> genmake_warnings 2>&1
2376      with
2377         COMM="$CC $CFLAGS -c genmake_tc_1.c"
2378         echo $COMM >> genmake_warnings
2379         $COMM >> genmake_warnings 2>&1
2380      to make genmake2 always see the value of CC as specified in the optfile.
2381    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
2382      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
2383      - modify verification advect_cs test to test SOM-advection on CS-grid.
2384    o pkg/ctrl:
2385      - Rewrite of ctrl_map_ini_ecco.F,
2386        introducing a generic routine (ctrl_map_ini_gen.F).
2387      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
2388    
2389    checkpoint59n (2008/02/09)
2390    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
2391      number in dedicate array "hdiag":
2392      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
2393        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
2394      - many small changes (integer format) for large number of diagnostics
2395      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
2396        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
2397    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
2398      usingSphericalGrid, this allows to define the rotated grid coordinates
2399      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
2400      geographical coordinates according to the inverse of the rotation defined
2401      by the Euler angles, so that Coriolis parameter and online-interpolation by
2402      exf works with the geographical coordinates on XC/YC/XG/YG.
2403      Naturally, this feature does not work with all packages, so some
2404      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
2405      profiles), because there the coordinates are assumed to be regular
2406      spherical grid coordinates.
2407    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
2408      - introduce isopycnal diffusion coefficient control.
2409    o tools/adjoint_options:
2410      - additional control vector components.
2411    o pkg/mnc: have mnc create marginally meaning full coordinate variables
2412      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
2413    o pkg/mypackage:
2414      - add example of read/write pickup for state-var ;
2415      - add entry points to the main code for state-vars diags & write-pickup.
2416    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
2417      transitions for useExfYearlyFields
2418      - add new subroutine that determines the file to read from for
2419        use*YearlyFields = .TRUE. and .FALSE.
2420      - add a verification experiment to global_with_exf that tests
2421        useExfYearlyFields with USE_EXF_INTERPOLATION defined
2422    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
2423      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
2424      subroutines (which could be generated from a template, because they are
2425      almost identical), for now they are included in obcs_prescribe_read.F for
2426      simplicity
2427    o pkg/exf:
2428      - add a little more diagnostic to exf_interp_read (in analogy to
2429        mds_read_field, can be turned off with debugLevel < debugLevA=1)
2430      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
2431        ugly but fast by unrolling short inner loops, inserting a unroll=8
2432        directive in routine lagran, and splitting a loop and making do while the
2433        outermost loop (the latter requires the intoduction of index arrays)
2434    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
2435    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
2436      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
2437    o verification/seaice_obcs: updated for restart test and latest options
2438    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
2439      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
2440      for now this is only available for the C-grid code and also within
2441      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
2442    
2443    checkpoint59m (2008/01/14)
2444    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
2445      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
2446    o gad_som : fix flux output (& diagnostics) to have same units as other  
2447      advection scheme fluxes (was previously multiplied by deltaT).  
2448    o added verification/seaice_obcs both to test seaice open boundaries
2449      and to provide an example matlab scrpt for generating them
2450    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
2451    o pkg/salt_plume: clean up salt_plume_frac.F to
2452      remove redundancy in PlumeMethod 1 and 4
2453    o pkg/kpp: added saltplume diagnostics
2454    o pkg/obcs and pkg/seaice:
2455      - do not set uice and vice to zero when OB*icefile are unspecified
2456      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
2457      - moved seaice tracer obcs after call to seaice_growth
2458    o pkg/salt_plume: added various options for salt plume depth
2459      criterion and for vertical distribution of the salt
2460    
2461    checkpoint59l (2007/12/18)
2462    o pkg/ptracers: new version of ptracers pickup:
2463      read meta file and write only fields which are needed to restart.
2464      ( same logic as main pickup file ; also using pickupStrictlyMatch )
2465    o pkg/seaice:
2466      - add timescale for melting due to warm mixed layer as a means of
2467        setting SEAICE_availHeatFrac more conveniently
2468      - add a CPP-flag/runtime parameter check for flooding algorithm
2469      - reformulated availHeat in seaice_growth.F to be independent of AREA
2470    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
2471      unit changes
2472    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
2473    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
2474      SX vector computer.
2475    o pkg/seaice:
2476      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
2477        seaice forcing fields can now be read only through pkg/exf
2478      - removed some unused halos
2479    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
2480    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
2481      or U/VICE from U/VWIND before computing U/VSTRESS
2482    
2483    checkpoint59k (2007/11/30)
2484    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
2485      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
2486    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
2487      all experiments pass when compile with un-initialised var. checking option.
2488    o added pkg/salt_plume
2489    o script to test restart (for now, in MITgcm_contrib/jmc_script)
2490    o pkg/seaice: new read/write pickup version.
2491      read meta file and write only fields which are needed to restart.
2492      ( same logic as main pickup file ; also using pickupStrictlyMatch )
2493    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
2494    o lab_sea.hb87: modify the domain & update output.hb87.txt :
2495      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
2496      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
2497      process. Fixed here by closing the domain at the Northern boundary.
2498    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
2499    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
2500      a set of consecutive levels in/from a 3-D array.
2501    o pkg/ptracers:
2502      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
2503      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
2504    
2505    checkpoint59j (2007/11/09)
2506    o in pkgs: dic, obcs, offline, rbcs:
2507      standard way to compute coeff. for time interpolation between 2 time reccords
2508      which retains full precision (& make results less dependent on compiler).
2509      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
2510    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
2511      packages instead of reading ice cover and wind speed separately
2512    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
2513     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
2514      to allow to compile customized code before the update)
2515    o cleaning-up:
2516      - fix CPP instruction syntax in pkg/obcs
2517      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
2518        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
2519      - fix some threads issue in IO parts.
2520    o pkg/dic:
2521      - add tons of "_d 0" (--> much better testreports !)
2522       and then update outputs of tutorial_global_oce_biogeo
2523    o pkg/mom_fluxform:
2524      add a special version of momentum advection intended to conserve momentum
2525      next to a bathymetry step or a coastline edge. (default = off = #undef)
2526    o new read/write pickup version:
2527      - for now, only implemented for main (mdsio) pickup file.
2528      - write out only what is needed to restart; merge pickup_nh , pickup_ph
2529        and main pickup together.
2530      - read meta file; read only what is needed to restart; stop if a field
2531        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
2532        if it make sense (even if the restart is not perfect).
2533      - if no meta file, assume that pickup to read corresponds exactly to
2534        a pickup that would currently be written.
2535      - read pickup written in the old format (until checkpoint59i) if it
2536        recognizes an old meta file (no field-list).
2537      - add a meta file in exp. which starts from a pickup: 2 cases:
2538        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
2539         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
2540        b) a meta file describing the content of the associated pickup file
2541         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
2542    o pkg/mdsio & pkg/rw:
2543      - new routine to read a meta file ; new set of routine to read
2544        Multiple-fields file (with meta file).
2545    o added open boundary conditions capability for seaice
2546        HSNOW, HSALT, UICE, and VICE
2547    
2548    checkpoint59i (2007/10/21)
2549    o adjoint:
2550      * fix multiDimAdvection adjoint
2551        (partial recomputation problem by TAF for fVerT(:,:,kDown)
2552        and comlev1 size definition (maxpass vs. max. number of tracers)
2553      * verification/global_ocean.90x45x15 adjoint now tests
2554        NLFS and multiDimAdvection using DST3 (=30)
2555      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
2556    o pkg/kpp: add "_d 0" to real constant (if missing);
2557      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
2558      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
2559    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
2560      for internal parameters related to restart process (formerly from PARAMS.h)
2561      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
2562    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
2563      as argument. (only atm2d & obcs write_pickup have not yet been updated)
2564    o pkg/monitor:
2565      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
2566      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
2567      - account for deep Atmosphere factor and density factor (anelastic)
2568    o added open boundary conditions capability for seaice HEFF and AREA
2569    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
2570      thermodynamics
2571      - requires a little reorganization, which affects the testreport results
2572        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
2573        so that now the conservative form is tested
2574      - add a few comments
2575    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
2576    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
2577    o add new diagnostics to seaice: advective, diffusive fluxes (only for
2578      multidim-advection, for scheme 2 they are not filled) and transports,
2579      thermodynamic growth rates
2580    o change units of EmPmR (inside the code, + within coupling interface)
2581      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
2582      Affects results @ truncation level (cg2d match) and update output of
2583       experiments: lab_sea(6), global_ocean.90x40x15(10),
2584      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
2585      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
2586      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
2587      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
2588    
2589    checkpoint59h (2007/09/29)
2590    o pkg/exf:
2591      - improve vectorization by moving if-statement out of loops in
2592        exf_mapfields, exf_radiation
2593      - exf_bulkformulae.F: introduce 2D fields and vectorize code
2594    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
2595    o testreport:
2596      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
2597        monitor & update offline_exf_seaice exp. output.
2598      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
2599    o pkg/seaice:
2600      - bug fix in the evp solver: boundary conditions were affected be
2601        masking of zMax/zMin (changes results)
2602      - minor bug fix in boundary conditions in seaice_calc_strainrates
2603        (changes results for no_slip)
2604      - seaice_lsr.F: make interpolation of eta dependent on boundaries
2605      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
2606      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
2607        stress formulation and no-slip boundary conditions
2608    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
2609      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
2610    o pkg/seaice: a first HSALT time stepping equation has been checked in
2611    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
2612      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
2613      without requiring DO-IF statements
2614    o pkg/thsice:
2615      use continuous power-law function for partition of energy between lateral
2616      melting/freezing and thinning/thickening ; old code using step function
2617      still available with #undef THSICE_FRACEN_POWERLAW
2618      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
2619    o testreport: change AD testing : check against results/output_adm.txt
2620      using same scripts as for forward test.
2621    
2622    checkpoint59g (2007/09/17)
2623    o adjoint testing: in preparation for changing testreport:
2624      - output format: cost and grad written on separated lines
2625      - ad output results in directory "results" (instead of "results_ad")
2626    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
2627    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
2628    o pkg/ecco: allow user defined cost function contributions
2629    o testreport:
2630      Allow to choose (per experiment) the list of tested output variables
2631       and the main variable (used to issue a pass/FAIL ) ;
2632      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
2633      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
2634      Also modify printing of summary:
2635       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
2636       b) echo the list of tested variables in the individual summary.txt of
2637          each experiment.
2638    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
2639      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
2640      (but still depend on the tile decompostion of the domain).
2641    o pkg/seaice: change a discretization detail to make the B-grid code
2642      "more symmetric". This change is likely to remove all "ridges/leads" that
2643      where quasi-aligned with the grid in B-grid solutions. It may also be
2644      the solution to the stress coupling issues with the B-grid.
2645    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
2646      remove .cvsignore from input dir. (since testreport no longer run here).
2647    o pkg/thsice:
2648     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
2649     - fix reshaping of sea-ice just after advection:
2650       melt all the ice only if ice-volume is too small.
2651     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
2652       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
2653     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
2654    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
2655      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
2656    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
2657      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
2658      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
2659      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
2660      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
2661      -> update output.txt
2662    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
2663     this affects truncation error: -> update output.txt of exp:
2664      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
2665      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
2666    
2667    checkpoint59f (2007/08/21)
2668    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
2669    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
2670      a bounded range (in forward mode)
2671    o pkg/ecco, ctrl, autodiff and mom_common:
2672     internal parameter controls, completements of implementations
2673    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
2674    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
2675      (not seem any difference in testing results).
2676    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
2677       at face corners.
2678    o pkg/generic_advdiff:
2679     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
2680      loop range indices for computing vertical advection tendency
2681      and do the calculation in the interior only (no overlap) ;
2682      for now, only implemented for SOM advection (to save CPU time).
2683     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
2684    o exch2 adjoint
2685      First set of changes:
2686      - add exch2 hand-written adjoint templates
2687      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
2688        This will require cleanup in pkg/autodiff/*.F
2689        (changed routines currently kept separate in verif. code/)
2690      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
2691        that used to hide exch2 or cubed-sphere specific code
2692        (commented via 'cph-exch2')
2693    o pkg/seaice
2694      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
2695    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
2696       output of global_ocean.cs32x15.thsice .
2697    
2698    checkpoint59e (2007/07/26)
2699    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
2700      for B-grid vector (not yet tested) and C-grid vector (<- only used
2701      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
2702    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
2703      (#ifdef ALLOW_SALT_PLUME)
2704    o gather_2d/scatter_2d: removed halo regions
2705    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
2706      scheme and the corresponding test case (under front_relax dir). For now,
2707      only available with Skew-flux form and not yet tested in realistic set-up.
2708      adjoint: store directives updated, but gradient checks deteriorated,
2709      so maybe GM/Redi adjoint is now broken.
2710    o seaice adjoint
2711      * add AREA, HEFF, HSNOW as control variable
2712        (should not change lab_sea results)
2713      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
2714    o pkg/seaice:
2715      * added computation of saltFlux in seaice_growth;
2716        For time being, sea ice salinity is assumed constant
2717        contribution of snow flooding to freshening of sea ice is neglected.
2718        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
2719        defaults to 0.0 in order to maintain backward compatibility.
2720        Typical values for SEAICE_salinity are 4 to 10 g/kg.
2721      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
2722      * added SEAICE_availHeatFrac, which specifies fraction of surface level
2723        heat content used to melt or grow ice
2724      * commented out cap of HICE: it helps keep ice thinner
2725      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
2726      * applied OBCS T/S mask to HEFFM sea ice mask
2727    
2728    checkpoint59d (2007/06/21)
2729    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
2730     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
2731     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
2732    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
2733     and change default value of parameter "GM_Small_Number";
2734     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
2735       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
2736       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
2737    o pkg/ecco: cost function when applying pkg/smooth to controls
2738    o pkg/ctrl: add forcingPrecond run time parameter
2739    o pkg/seaice:
2740     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
2741     - fix bug in metric terms of u-equation in LSR solver (implicit part),
2742       changes verification/lab_sea
2743     - rearrange implicit part of u-equation in LSR solver to make it easier to
2744       read, understand, and debug. This causes changes at the truncation level.
2745     - fix (serious) bug in the boundary conditions (sign error in the implicit
2746       part) of the LSR solver. Changes all LSR results.
2747     - fixed problem with HSNOW initialization to avoid thick snow when AREA
2748       is initilized with small values - does not change lab_sea results.
2749     - added HsnowFile initialization capability
2750    o pkg/smooth: addition to model/src and pkg/ctrl so allow
2751     initialization of pkg/smooth and application to control vector
2752    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
2753    o dependencies: pkg/profiles requires pkg/cal
2754    o pkg/profiles:
2755     - added option ALLOW_PROFILES_GENERICGRID
2756         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
2757         that interpolation information (grid points and coefficients) is provided
2758         within the netcdf input files.
2759         -> sample matlab scripts can be found in MITgcm_contrib/gael
2760         that allow you to prepare netcdf input files.
2761     - also modified: cleaner include statements, cleaner error print statements,
2762       cleaner stops when error, and more tests of the netcdf input files consistency.
2763    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
2764    o pkg/seaice:
2765     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
2766       requires a new routine: seaice_diagnostics_fill.F
2767     - make sure that seaice does not move if not forced (pressure replacement
2768       method, Hibler and Ip, 1995), changes results
2769     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
2770     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
2771       It is turned off by default (=-1.), because it changes the results.
2772     - make it possible to read AREA from a file, too.
2773    
2774    checkpoint59c (2007/06/04)
2775    o add S/R and diagnostics for oceanic mixed-layer depth
2776    o move GMRedi call after all vertical mixing schemes (including KPP)
2777    o pkg/thsice:
2778     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
2779      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
2780    o pkg/obcs:
2781     - bug fix for balance code
2782    o pkg/seaice:
2783      - allow values of SEAICE_elasticParm > 1
2784      - add new parameter SEAICE_evpTauRelax as an alternative
2785        to SEAICE_elasticParm
2786      - make lsr boundary conditions free slip (by default), changes result
2787      - add code for no slip boundary conditions for lsr
2788      - set minimum of zeta to zero (and not 4e8) (changes results)
2789      - add a cap on AREA after advecting AREA if seaice_growth is not called
2790    o change calculation of Visbeck K:
2791      - no longer depend on tapering scheme; instead, compute slope (limited
2792        by GM_maxSlope). this is equivalent to what was comuted before with
2793        clipping or linear tappering.
2794      - fix vertical averaging (wrong by 1/2 level)
2795      - leave the old version (but will not be maintained) within
2796        #ifdef OLD_VISBECK_CALC / #endif
2797      - update output of exp. ideal_2D_oce
2798    o change error catch in calc_r_star to improve vectorization
2799    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
2800      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
2801    o adjoint:
2802      Re-organized adjoint checkpointing according to Matt Mazloff
2803      (but with modifs/completions/cleanups)
2804      Storing is now bundled into large arrays to optimized I/O
2805      (and second step in cleanup of the_main_loop)
2806    
2807    checkpoint59b (2007/05/16)
2808    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
2809      - export/import (between ocean & coupler) fields needed for ocean DIC.
2810    o pkg/seaice:
2811      - get rid of three more exchanges seaice_calc_viscosities (required
2812        different loop boundaries in seaice_lsr and seaice_ocean_stress)
2813      - bug fix in seaice_ocean_stress (update of lab_sea required)
2814      - reduce loop boundaries to necessary minimum also in seaice_evp
2815      - go back to the old way of computing deltaC/Z as the adjoint likes that
2816        better
2817    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
2818      passive tracer to an Age Tracer) + update output.txt
2819    o pkg/exf:
2820      - implement A-grid / C-grid selection for wind-stress input files.
2821      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
2822      for now, in exf_bulk_largeyeager04.F only :
2823      - change implementation for case where windspeed + 2. components wind-stress
2824        are read-in. AND use rhoConstFresh to convert evap.
2825    o pkg/seaice:
2826      - use correct EXCH_UV for wind-forcing (on A-grid).
2827      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
2828        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
2829    o pkg/exf:
2830      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
2831      EXF_INTERPOLATION:
2832      - merge global_with_exf/code version of exf_interp_read.F
2833        to the main code ;
2834      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
2835        reading the file ; Important: This options needs to be defined to recover
2836        previous code.
2837        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
2838      - no longer loose real*8 precision along the way when using exf_iprec=64.
2839    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
2840      - change discretisation of evp-solver in order to avoid another exchange
2841        (changes lab_sea) and clean up a little
2842      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
2843        help the adjoint (this also changes the results slightly)
2844      - add a few "_d 0" where they had been missing in seaice_evp.F
2845      - cleaning up: remove unused seaice_calc_rhs.F
2846    o pkg/exf: some cleaning-up:
2847      - change various "constants" into runtime parameters
2848      - cleaned-up Large&Yeager04 routine which should eventually
2849        replace exf_bulkformulae.F (changed names of S/R and CPP)
2850        and merged various ALLOW_ATM_WIND options
2851     only used with thsice pkg (in thsice_get_exf.F):
2852      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
2853        which are used when useStabilityFct_overIce=TRUE (= the default)
2854      - change default values of ice & snow emissivity and scale downward LW
2855        by ice & snow emissivity.
2856    o pkg/thsice:
2857     fix few little problems, in thsice_calc_thickn.F:
2858      - growth vertically (and not laterally) if iceFrac == iceMaskMax
2859      - melt only laterally if hIce < hThinIce (as the comments say)
2860      and in thsice_extend.F:
2861      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
2862      - start to form ice as soon as the minimum ice-volume is reachable.
2863     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
2864      and cpl_aim+ocn
2865    o pkg/kpp
2866     - move computation of surface related input fields to KPP into a new
2867       subroutine kpp_forcing_surf.F
2868     - remove wrong (within bi,bj loops) EXCH calls.
2869     - little cleaning (add argument myThid in last position, cvs header ...)
2870     - for now, fix conservation problem by exchanging KPPviscAz (may not
2871       be the best fix)
2872    o pkg/seaice
2873     - check for inconsistent evp parameter/cpp-flag combination
2874     - remove leftover errIO flat for obsolete name list error handling
2875    o OpenAD
2876     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
2877    
2878    checkpoint59a (2007/05/01)
2879    o pkg/seaice: some parameter clarifications and a little bit of clean up
2880    o pkg/thsice: rename run-time parameters:
2881       himin       -> hIceMin
2882       himin0      -> hThinIce
2883       hihig       -> hThickIce
2884       i0          -> i0swFrac
2885       transCoef   -> bMeltCoef
2886       frac_energy -> fracMelting
2887      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
2888       with default values (for now) that do not change the results.
2889      remove old version of thsice vars advection in pkg/seaice.
2890    o in FFIELDS.h:
2891      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
2892      - make pLoad & sIceLoad always available (but still only used if
2893         ATMOSPHERIC_LOADING is #define).
2894    o pkg/kpp: replaced _KPP_RL with _RL
2895    o bug fixes for vertical diffusivity computations when both KPP and
2896        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
2897        are no longer updating the vertical diffusivity array
2898        (passed as argument) but are (re-) setting those arrays.
2899    o pkg/seaice: fix bug in evp solver, while doing that
2900      - change (improve?) discretization of stress computations for both
2901        cgrid-lsr and evp solver
2902      - add a new routine to compute strain rates
2903      - the above changes lab_sea results
2904      - add no slip conditions for evp solver (off by default), lsr-version
2905        may follow
2906      - fix exchange for shear at Z-points (does not change lab_sea)
2907      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
2908        (to force the user to pick a time step since there is not "safe" way
2909        of choosing it)
2910      - add principal stress diagnostics
2911      - rearrange fields for evp a little to avoid having to call a: too many
2912        exchanges and b: exchanges for stress trensor components which we do
2913        not have.
2914      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
2915        of evp, complete rewrite for lsr case (latter is does not yet work
2916        in all cases)
2917    o pkg/kpp: add code to have mixing in shelf ice caverns
2918      - add myThid to all kpp routines (long overdue)
2919    
2920    checkpoint59 (2007/04/19)
2921    o pkg/exf:
2922      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
2923        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
2924      - move exf header files from lower_case.h to UPPER_CASE.h ;
2925        add missing cvs Header & Name
2926      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
2927      - add namelist param. selectStressGridPosition, exf_monFreq
2928      - retire many _CLIM routines, and remove data.exf_clim
2929        + params moved to data.exf
2930        + climsst, climsss now handled by exf_set_gen, i.e.
2931          climss?period=0 refers to constant field,
2932          climss?period=-12 to monthly forcing
2933      - split up namelists in data.exf
2934    o pkg/seaice:
2935      - remove seaice_exch and seaice_exch_uv
2936      - remove superfluous exchange of theta
2937      - add myThid to seaice_budget_ocean/ice
2938      - add new interface for atmospheric wind forcing (C-grid only)
2939        + new routine
2940        + two new field (taux, tauy for stress over ice)
2941        + removed one global field (DAIRN) for C-grid case only
2942    o pkg/thsise
2943      - 2nd set of modifs for thsice adjoint in conjunction with exf
2944    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
2945    
2946    checkpoint58y_post (2007/04/15)
2947    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
2948      vertical diffusivity, similar to that in MOM4; turned on using
2949      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
2950      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
2951    o Added capability for 3D specification of background vertical diffusion
2952      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
2953      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
2954      "data" file that contains the 3D vertical diffusivity coefficients.
2955    o ice dynamics (pkg/seaice) with thsice thermodynamics:
2956      - add code within pkg thsice to advect & diffuse sea-ice fields
2957      similar to (and will replace) what has been added in  seaice_advdiff.F,
2958      but: - conserving Mass, Heat & Salt.
2959           - better when using non-linear advection scheme (not yet fully tested)
2960           - can also be used in atmospheric set-up (for now, only the diffusion).
2961    
2962    checkpoint58x_post (2007/04/04)
2963    o IO option for global-file compact format:
2964      - add options when generating topology (utils/exch2/matlab-topology-generator)
2965      - add I/O capability (pkg/mdsio).
2966      - adapt utils/matlab/rdmds.m to read this format.
2967      for now long-line format not yet supported by pkg/mdsio (& exch2).
2968    o shelfice: add a few diagnostics
2969    
2970    checkpoint58w_post (2007/03/13)
2971    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
2972      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
2973      (and replace horiVertRatio in NH code).
2974      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
2975                         and tutorial_plume_on_slope (sensitive to truncation)
2976    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
2977      directly to drive seaice model (C-grid only)
2978    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
2979     - reintroduce computation of wind from stress,
2980     - compute tau (in exf_bulkformulae.F) from windstress averaged to
2981       mass points to avoid tau = 0
2982     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
2983    o rdmnc.m: make it work with "global" files created with gluemnc
2984    o rdmnc.m : some improvements in dealing with singleton dimension
2985      (tested on all testreport mnc output files).
2986    o genmake2: disable pkg/profiles if netcdf test fails.
2987    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
2988    o move call to cal_readparms up to make calendar parameters/variable available
2989      to all packages
2990    
2991    checkpoint58v_post (2007/02/08)
2992    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
2993      useDynP_inEos_Zc tested.
2994    o pkg/exf: changes to properly interpolate/mask/scale initial fields
2995    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
2996      and portions thereof.  See read_cs.txt for description and examples.
2997    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
2998      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
2999      following the great-circle arc between those 2 points.
3000    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
3001      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
3002    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
3003     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
3004     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
3005     - still needs work (not working with some options ; efficiency to improve)
3006       and serious testing.
3007     - use this scheme for temperature & salinity in 2 advection test exp.:
3008       advect_xy & advect_xz, respectively.
3009    
3010    checkpoint58u_post (2007/01/12)
3011    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
3012    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
3013    o testreport: add option "-skipdir" to skip some test.
3014    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
3015      momentum calculation.
3016    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
3017    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
3018      remove checkpoint.F and the_correction_step.F (no longer used);
3019      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
3020    o add option (linFSConserveTr) to correct for tracer source/sink due to
3021      Linear Free surface
3022    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
3023    o pkg/thsice: fix reading mnc-pickups
3024    
3025    checkpoint58t_post (2006/12/30)
3026    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
3027    o pkg/mdsio:
3028     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
3029       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
3030       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
3031     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
3032     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
3033       either MDS_READ_FIELD or MDS_WRITE_FIELD )
3034     - new S/R (to replace MDSWRITEMETA), which allows to write more
3035       informations (variable names, time ...) to meta files.
3036     - modify rdmds.m to give back the meta file content.
3037    o pkg/diagnostics: change vertical interpolation to be safer, and more
3038       flexible (define p-levels to interpolate to in data.diagnostics);
3039      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
3040       diagnostic pointer.
3041    o pkg/seaice: more cleaning up of seaice_growth, added many comments
3042    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
3043    o fix multi-category seaice:
3044     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
3045       SEAICE_MULTICATEGORY
3046     - fix short wave heat flux
3047    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
3048       and allow to use EVP solver. Change forward lab_sea: test both EVP
3049       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
3050    o Initial check-in of lab_sea adjoint
3051      (very similar to natl_box_adjoint/code_seaice)
3052      * used C-grid and EVP solver
3053      * used KPP, GM/Redi
3054      * uses inAdExact=.TRUE.
3055      * gradient checks fail for both ADM and TLM
3056        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
3057        f.d. gradients actually seem more problematic than ADM, TLM gradients;
3058        issue is related to forward mismatch between g77 an ifort
3059    o pkg/seaice: overhaul of thermodynamics
3060     - growth.F and groatb.F are replaced by new routine seaice_growth.F
3061     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
3062     - move a few global fields out of SEAICE.h into seaice_growth.F and
3063       make them 2D (FICE/QNETO/ ...)
3064     - remove FO (it is the same as QNETO)
3065     - introduce a few local fields to avoid modifying external fields such
3066       as atemp, etc.
3067    
3068    checkpoint58s_post (2006/12/11)
3069    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
3070      changed exf_set_gen.F so that
3071        genperiod=0 means input file is one time-constant field and
3072        genperiod=-12 means input file contains 12 monthly means
3073    o CG2D: use pre-computed solver main-diagonal (stored in common block);
3074      this affects truncation error ; generate new output file for exp. which
3075      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
3076        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
3077        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
3078        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
3079        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
3080        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
3081    o start implementation of deep-atmosphere and anelastic formulation
3082    o verification: remove 2nd copy of input files and use script "prepare_run"
3083      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
3084    o mom_common/vecinv/fluxform: fix a few initialisation isssues
3085    o profiles: fix for multithreaded case
3086    
3087    o diagnostics: rename few diags:
3088      s/'PRESSURE'/'RCENTER '/g
3089      s/'TICE    '/'oceFreez'/g
3090      s/'TAUX    '/'oceTAUX '/g
3091      s/'TAUY    '/'oceTAUY '/g
3092      s/'SWFLUX  '/'oceQsw  '/g
3093      s/DIFx/DFxE/g
3094      s/DIFy/DFyE/g
3095      and add few ocean-forcing diagnostics:
3096      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
3097    o modifications to pkg/seaice/growth.F and budget.F, which change results of
3098      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
3099      as actual snow thickness.  It now refers everywhere to effective snow
3100      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
3101    
3102    checkpoint58r_post (2006/11/17)
3103    o modifications to pkg/seaice/growth.F, which change results of
3104      lab_sea experiment: fixes pertain to melting snow over open water, to
3105      masking EVAP under sea ice, and to using the correct AREA variable for
3106      computations of EVAP, PRECIP, HSNOW, and GHEFF
3107    o add ability to read bathy, salt, and theta using MNC (off by def)
3108    o add flooding algorithm and advection of HSNOW for pkg/seaice;
3109      both are turned off by default and do no change any results
3110    o seaice advection with pkg/thsice: a step toward the use of non-linear
3111      advection scheme, but #ifdef or commented out for now (requires more EXCH).
3112    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
3113      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
3114      in natl_box (affects results @ truncation level: update output.txt)
3115    o multi-threading and IO:
3116      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
3117      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
3118        (needed to work with SingleCpuIO): tested in all verif. exp.
3119    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
3120      affects the results (but none of the verification test uses this scheme).
3121    o Adding some pkg/diagnostics capability to pkg/seaice
3122      (will certainly be subject to changes)
3123    o ctrl: adding new control variables:
3124      lwflux, lwdown, evap, snowprecip, apressure, runoff
3125    
3126    checkpoint58q_post (2006/10/20)
3127    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
3128      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
3129      high_res_cube configuration by 4% on Columbia.
3130    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
3131      add (in global_with_exf/code) a version of EXF_INTERP_READ without
3132      dynamical allocation (seems to work in multi-threaded).
3133    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
3134      single CPU io) so that TAF does not have to see EESUPPORT.h
3135    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
3136    
3137    checkpoint58p_post (2006/09/08)
3138    o obcs: stop if obcs is used with useCDscheme = .true.
3139    o shelfice:
3140     - fix a sign error so that no slip at shelfice interface works
3141     - remove stop for combination non-hydrostatic code and shelfice. That does
3142       not mean, that the results are correct, but at least they are numerically
3143       stable
3144    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
3145    o added adjoint exch routined for all exch*3d* routines
3146      and updated flow directives
3147    
3148    checkpoint58o_post (2006/08/28)
3149    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
3150      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
3151    o change controling S/R for writing pickup file (new S/R do_write_pickup)
3152      and clean-up reading/writing of pickup files.
3153    o fix local version of read/write pickup (NH part) in rotating_tank/code
3154    o simplify EXCH interface:
3155     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
3156     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
3157    o added the regrid package
3158    o shelfice:
3159     - add a simple boundary layer scheme to reduce noise
3160     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
3161    
3162    checkpoint58n_post (2006/08/14)
3163    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
3164       local variable (not in common block).
3165    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
3166      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
3167      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
3168        to work with SingleCpuIO.
3169    o add "_d 0" to real constant of pkg/cfc subroutines ;
3170       update exp. cfc_exemple & tutorial_cfc_offline output files.
3171    o multi-threading and IO:
3172      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
3173        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
3174      - barrier before and after reading.
3175      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
3176      - avoid using MDS_WRITELOCAL for LAND pkg output.
3177      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
3178        common-block variables ; Allows multi-threading with master-thread IO.
3179    o change default MAX_NO_THREADS from 32 to 4 ;
3180      and stop cleanly when MAX_NO_THREADS is too small.
3181    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
3182    
3183    checkpoint58m_post (2006/07/17)
3184    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
3185       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
3186    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
3187       keep global_ocean.90x40x15 (for AD testing) with former secondary test
3188       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
3189    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
3190        add MITgcm_tutorials (= code + all the tutorials)
3191    o ecco, option to compute cost for total ssh (mean+anom)
3192    o consistent with addition of ptracer and ssh in pkg/profiles
3193    o profiles: adding ptracer and ssh
3194    o testreport: change multi-test output-file name
3195      (from output.txt.{name} to output.{name}.txt)
3196    o profiles: now ok for mutli-tiles case
3197    o seaice: add 4 parameters for different advection schemes for area,
3198      (effective) seaice thickness, enthalphy, and snow height. Their default
3199      is the standard parameter SEAICEadvScheme
3200    o calc_gw:
3201     - add cosFacU in zonal viscous flux (harmonic.visc.).
3202     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
3203       of tutorial_plume_on_slope.
3204    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
3205    o calc_gw: true flux-form, account for horizontal grid spacing.
3206      update rotating_tank results, but not plume_on_slope (affected at
3207      truncation level, 11 digits).
3208    
3209    checkpoint58l_post (2006/07/12)
3210    o calc_gw:
3211     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
3212     - remove side-drag for now (need to fix it); update plume_on_slope results.
3213     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
3214    o commit code to make SST/SSS weights spatially variable
3215      (based on either variable in-situ or variable initial T/S weights)
3216    o pkg/ecco:
3217      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
3218        now based on horizontally varying weights wthetaLev, wsaltLev
3219      * cost_averagesflags now returns year indices in addition to day, month
3220      * sflux balance is performed on annual basis
3221        (sflxumm, sfluxmm2, bal_sfluxmm)
3222      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
3223        including separate counting and multipliers
3224    o pkg/rbcs
3225      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
3226    
3227    checkpoint58k_post (2006/07/06)
3228    o testreport:
3229     - always build in dir. "build" (if not there, mkdir build instead of building
3230       & running in input)
3231     - run in dir run (if it exists), in build otherwise.
3232     - call prepare_run (if input/prepare_run exists)
3233     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
3234    o pkg/exf modifications to interpolation and rotation routines for more
3235       reasonable treatment of North Pole singularity: for tracers North Pole
3236       value is set to northernmost zonal-mean value, for zonal velocity it is
3237       set to zero, and for meridional velocity it is set to northernmost value.
3238    o pkg/exf/exf_check_range.F
3239     - add tile index to diagnostics and move stop statement to the very
3240       end of the routine.
3241    o pkg/diagnostics: (diagnostics_main_init.F)
3242      define title of isomorphic variables according to the current config.
3243    o pkg/thsice with pkg/seaice dynamics:
3244    - fix domain of computation (interior only, required for exf) and do exchanges
3245    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
3246    o towards a standard way of dealing with multi-threading in MONITOR
3247      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
3248    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
3249       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
3250    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
3251    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
3252    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
3253       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
3254    o tracer advection:
3255     - clean-up and simplify calc_common_factors.F
3256     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
3257       advection subroutine (but still not used within DST advection S/R)
3258    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
3259    
3260    checkpoint58j_post (2006/06/15)
3261    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
3262      from file (collects calls previously in FORWARD_STEP)
3263    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
3264    o adjoint store dir. adjusted accordingly
3265    o genmake2
3266      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
3267    
3268    checkpoint58i_post (2006/06/14)
3269    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
3270      on wind stress (SEAICEstressFactor defaults to 1.)
3271    o Total number of Timers is finite (<=40): comment out 2 non-essential one
3272      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
3273    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
3274      on CS-grid: no longer loosing mass.
3275    o exf & curvilinear-grid: no longer modify longitude xC & xG.
3276    o pkg/ggl90: fix sloppy output and fix a bug
3277    o pkg/seaice: added SEAICEuseEVPpickup parameter
3278      - Set to false in order to start EVP solver with
3279        non-EVP pickup files when using SEAICEuseEVP
3280      - fix sign error in diffusion in seaice_calc_rhs
3281    
3282    checkpoint58h_post (2006/06/07)
3283    * Modifications for bottom topography control
3284      o replace hFacC by _hFacC at various places
3285      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
3286      o add non-self-adjoint cg2d_nsa
3287      o update autodiff support routines
3288      o re-initialise hfac after ctrl_depth_ini
3289      o works for 5x5 box, doesnt work for global_ocean.90x40x15
3290    * Adding verification for 5x5 box (4-layer) bottom topography control
3291    
3292    checkpoint58g_post (2006/06/07)
3293    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
3294       used for mean seasonal cycle, mean diurnal cycle); add an example
3295       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
3296    o pkg/ggl90:
3297      - add parameter (minimum surface kinetic energy)
3298      - fix bug (avoiding division by zero)
3299    o couple pkg/thsice to pkg/seaice:
3300      - modify advection in seaice to accomodate new scalar fields to be advected
3301      - only muliDimAdection scheme work with seaice/thsice
3302      - mapping of thsice-variables to seaice-variables, back and forth
3303      - does not break the verification experiments, but does not give the
3304        desired results either
3305    o pkg/seaice
3306      - make (default) second order advection a bit less confusing?
3307    
3308    checkpoint58f_post (2006/06/05)
3309    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
3310      to pkg/seaice):
3311      - new routines thsice_map_exf and thsice_get_exf provide the interface
3312      - add an additional formal parameter to thsice_solve4temp
3313    o pkg/exf:
3314      - add new fields wspeed, snowprecip (to be able to couple to thsice)
3315      - correct Stefan-Boltzmann constant
3316      - new parameter for longwave surface emittance
3317      - separate some stuff from exf_bulkformulae into new routines  
3318        exf_radiation, exf_wind
3319      - add new parameters and constants: longwave emissivity for ocean, ice
3320        and snow, evaporation parameters over ice
3321      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
3322        either wind from stress or stress from wind
3323    o pkg/thSIce:
3324    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
3325    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
3326       and THSICE_CALC_THICKN
3327    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
3328    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
3329      to make debugging easier.
3330    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
3331    o pkg/bulk_force:
3332      - clean-up comments and parameters ;
3333      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
3334    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
3335      generate new output for test-experiment: aim.5l_cs.thSI
3336    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
3337      testreport accordingly
3338    
3339    checkpoint58e_post (2006/05/17)
3340    o SEAICE_CGRID adjoint done
3341    o R_STAR adjoint implemented.
3342      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
3343      * need to sort out init. of h0facc, etc.
3344    o Make pkg/profile fully independent of ecco,cost, etc. stuff
3345      to be able to use it in pure forward.
3346    
3347    checkpoint58d_post (2006/04/21)
3348    o upgrade simple test-experiment to tutorial example:
3349     step.1: duplicate the experiment and (step.2) will remove the old copy.
3350      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
3351      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
3352      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
3353      tutorial_global_oce_biogeo    <- copy of dic_example
3354      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
3355      tutorial_plume_on_slope       <- copy of plume_on_slope
3356      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
3357      tutorial_global_oce_optim     <- empty for now (David ?)
3358      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
3359     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
3360    o correct a sign problem in cost_scat.F
3361    o obcs and ptracers: fix boundary conditions for advections schemes
3362      with larger stencil
3363    o thsice adjoint: start
3364    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
3365      completeness
3366    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
3367      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
3368    o ptracers adjoint:
3369      * avoid extensive recomputatations
3370      * fix missing re-init. of gptr (missed by TAF)
3371    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
3372      me to turn off the excessive output to STDOUT that this package produces
3373    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
3374      and add those terms in Vector-Invariant formulation.
3375    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
3376      if the control period (xx_hfluxperiod etc) is 0
3377    o in profiles pkg, clean routines and fix details
3378    o in ecco pkg, reading ssh data:
3379      fix problem in case the model does not start at iter0=0
3380    o fix mnc-pickup/restart for ptracers
3381    o new package prifiles:
3382      code to compute profile-based cost by Gael Forget
3383      (modifs in ecco, ctrl, autodiff)
3384    o Benign bug fix in initialization (spotted by M. Mazloff) of
3385      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
3386    
3387    checkpoint58c_post (2006/03/23)
3388    o adjoint: finish NLFS adjoint and provide reference output in
3389      verification/global_ocean.90x40x15/results_ad_nlfs
3390    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
3391      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
3392      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
3393      with SEAICE_CGRID defined.
3394    o move calendarDumps from "data" to "data.cal" and clean-up the code
3395      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
3396    o add useEXF & useCAL flags (for now, set in hard-coded way)
3397    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
3398      (were missing in NH mode, and wrong in quasihydrostatic mode).
3399      waiting for Chris updated version of calc_gw to add those CALLs.
3400    o fix bug in quasihydrostatic S/R ;
3401      add a test for this option: global_ocean.90x40x15.qshyd
3402    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
3403      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
3404    o add on/off flag useOffLine for package OFFLINE
3405    o seaice:
3406      - modify advection so that it works also on the C-grid
3407      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
3408        problem in multi-tile runs with C-grid
3409      - add flags for clipping ice velocities and/or masking solver forcing
3410      - fix drag (ocean on ice) formulation and a bug that caused noise in the
3411        C-grid solver
3412      - added a few comments to seaice_diffusion.F
3413      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
3414        are now exclusive)
3415      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
3416        required re-ordering the code a little:
3417       + make DAIRN global variable (defined in SEAICE)
3418       + move computation of the viscosities eta and zeta into a new separate
3419         routine (because I need to recompute them in seaice_ocean_stress.F)
3420    
3421    checkpoint58b_post (2006/03/13)
3422    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
3423      update output.txt of exp. aim.5l_cs.thSI
3424    o various mnc cleanups and improvements:
3425      + shrink lookup tables by factor of ~4
3426      + better error reporting when running out of lookup space
3427      + able to handle longer path/file names (up to 500 chars)
3428    o adjoint:
3429      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
3430      - TBD: "hidden" mom_vecinv recomp. in dynamics
3431    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
3432     (allow to differentiate between forcing components using new integer flags:
3433      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
3434     and add new flag to put Dissipation tendency out of Adams-Bashforth.
3435    o ecco
3436      - enable trend removal from SSH anomaly obs.
3437    o adjoint
3438      - a fix for PmEpR when #undef EXACT_CONSERV
3439      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
3440      - try to fix "hidden" recomp. in forward_step for NLFS
3441        (NLFS seems broken sometimes after I checked it in)
3442    o seaice:
3443     - add c-grid version of the dynamic solver:
3444       + three new routines that are the c-grid substitute lsr, dynsolver
3445         and ostres
3446       + put a few fields that were local to dynsolver into global common
3447         blocks, so that I can move the computation of stresses etc into
3448         seaice_lsr (saves coding but may break the adjoint).
3449     - replace more hardwired parameters by runtime parameters
3450     - add ice masks that mask the rhs of the implicit solvers where there
3451       is no ice (commented out in seaice_dynsolver, because i am not sure
3452       if this works properly), eventually this should replace the clipping
3453       of ice velocities in seaice_dynsolver to +/-40cm/s.
3454    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
3455      include it only where its needed
3456    o move balancing of fluxes before the call of external_forcing_surf
3457    o seaice:
3458      - correct units of turning angles (now they are really in degrees)
3459      - move computation of GWATX/Y out of main routine into dynsolver
3460      - initialize GWATX/Y in seaice_init
3461    o Apply mask on Fresh-Water flux (needed for SSH forcing).
3462      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
3463    o seaice: add runtime flags for turning angles (default to zero)
3464    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
3465      and trend from exf forcing and ctrl control adjustments
3466    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
3467      (since checkpoint57x_post)
3468    o change the default rotation period to 86164.s = the Earth rotation
3469    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
3470      and based on a reference stratification. Tested within hs94.cs-32x32x5.
3471    o seaice advection: add code for choosing between the default (2nd order
3472      central differences) and multiDim advection schemes provided by
3473      pkg/generic_advdiff
3474    o seaice:
3475      - removed all references to SEAICE_GRID.h fields from
3476        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
3477        (cubed-sphere configuration will change a little)
3478      - grid computations in seaice_init are obsolete now.
3479      - cleaned up code a little so that is easier to read (hopefully).
3480      - added new (better?) discretizations of default advection and diffusion
3481        (turn on with SEAICEuseFluxForm)
3482      - replace 1 in 3d global fields by kSurface in growth.F
3483      
3484    checkpoint58a_post (2006/02/13)
3485    o seaice:
3486      - bug fix in advect.F
3487    o shelfice:
3488      - separate shelfice load anomaly from pload (breaks with time
3489        dependent forcing), => introduce constant field shelficeLoadAnomaly.
3490        Its default is 0., but it may be computed more cleverly from (unknown)
3491        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
3492        done offline. A good approximation of the pressure load anomaly is
3493        necessary to avoid large initial adjustment processes underneath
3494        deep-reaching shelfice.
3495      - small fix in ISOMIP shelfice_thermodynamics
3496      - add more sophisticated thermodynamics of Hellmer (1989), this is
3497        now the default
3498      - give a few constants more intuitive names
3499    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
3500      if bulk formulae are used in long integration (especially EmPmR). Turn
3501      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
3502      if balancePrintMean, the imbalance that is substracted is printed to
3503      STDOUT.
3504    o fix bug (typo) in obcs_apply_eta.F
3505    o add a new package shelfice which enables us to model the circulation
3506      underneath shelf-ice with draughts of hundreds of meters.
3507     - works
3508     - to do: + include improved thermodynamics
3509              + check whether kSurfC (from model/inc/SURFACE.h) can be used
3510                instead of new field kTopC
3511              + can we use topoFile, Ro_surf and existing code in ini_depth.F
3512                instead of new field R_shelfIce and new code in ini_depth.F
3513                and ini_mask_etc.F?
3514              + adjust vertical mixing schemes?
3515    o seaice pkg:
3516     - add a cpp-flag to include a simple formula for a salinity dependent
3517       freezing point of sea water at the surface
3518     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
3519       meridional stresses are now different (and hopefully correct)
3520    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
3521       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
3522       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
3523    o pkg/diagnostics: add options and parameters for regional-statistics
3524       diagnostics ; define regions by reading a region-mask from a file
3525       (might add other options later)
3526    o pkg/bulk_force:
3527     - add option and parameters to use AIM surface-flux formulae.
3528     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
3529       others forcing fields (defined in PARM05, parameter file "data") are loaded
3530       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
3531     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
3532     - use the right EXCH call for uwind,vwind (to work on CS-grid).
3533     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
3534       and parameters (note: calcWindStress replaces .NOT.readwindstress).
3535     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
3536    
3537    checkpoint58 (2006/01/12)
3538    o add "--embed-source" option to genmake2 which, when the supporting
3539      tools can be compiled (as determined by genmake2) will turn on the
3540      embed_files package which then embeds the entire MITgcm source code
3541      (*.[fFhc] + Makefile) used for the build within the executable
3542      - requested by CNH but off by default
3543      - adds a paltry <9MB to the mitgcmuv executable in most cases
3544      - only writes the output when useEMBEDSRC in eedata is true
3545    o clean up 3-dim. relaxation codes:
3546      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
3547      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
3548      * Thanks to Tom Haine for testing!
3549    
3550    checkpoint57z_post (2005/12/31)
3551    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
3552      affects output (@ truncation level) of exp. plume_on_slope ; updated.
3553    o fix the pickup behavior for obcs in combination with ptracers
3554    o fix a bug in ptracers_external_fields_load
3555    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
3556      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
3557    o transfered surface NH pressure to eta field (if exactConserv).
3558    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
3559         and update lab_sea output.txt file.
3560    o completing 3-dim. relaxation code: additional term
3561         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
3562      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
3563      * At compile time, in "EXF_OPTIONS.h" set
3564          #define  ALLOW_CLIMTEMP_RELAXATION
3565          #define  ALLOW_CLIMSALT_RELAXATION
3566      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
3567          tauThetaClimRelax3Dim = 15552000.0,
3568          tauSaltClimRelax3Dim  = 15552000.0,
3569      * 3 cases:
3570          1) Use a constant-in-time 3-dim. field
3571          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
3572          3) Real-time relax. to time-evolving prescribed field
3573    o Adding Laplacian-type smoothness constraint on
3574      initial and boundary (forcing) controls (ic, bc)
3575      * enable at compile-time via
3576        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
3577      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
3578      * Absolute scale somewhat unclear so far
3579      * no area weighting was included since no other cost term does so far
3580    
3581    checkpoint57y_post (2005/12/08)
3582    First step for a NLFS adjoint
3583    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
3584    o new init. routines for calc_r_star, calc_surf_dr
3585    o still need to deal with ini_masks_etc
3586    o testreport seemed happy
3587    checkpoint57y_pre (2005/12/08)
3588    
3589    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
3590    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
3591    o add new offset feature to offline pkg (plus minor cleanup)
3592    o cfc fixes for final year of integration
3593    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
3594      be in GCHEM_OPTIONS).
3595    
3596    checkpoint57x_post (2005/12/04)
3597    o fix testreport Pb in multiple test experiment.
3598    o cleanup our namelist syntax in verification:
3599      - make it more F95 standards compliant (some work still needed)
3600      - allows the vast majority of our tests to work with gfortran
3601    o Non-Hydrostatic:
3602     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
3603     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
3604    o Allow to apply AB on T,S rather than on AB(gT,gS):
3605     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
3606     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
3607       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
3608     - need a "clever" read_pickup to restart from the other AB formulation
3609    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
3610    o remove some unused variables (reduces number of compiler warnings)
3611    o adjoint
3612      * Disable useVariableViscosity for adjoint for time being
3613        (there are a number of extensive recomputations)
3614      * Initialize certain variables needed for adjoint
3615    
3616    checkpoint57w_post (2005/11/03)
3617    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
3618                 fix the singleCpuIO RS version of MDSWRITEFIELD
3619       and add a WARNING if using globalFiles=T with multi-processors.
3620    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
3621      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
3622    o tracer advection scheme:
3623      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
3624       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
3625       was not very convenient).
3626      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
3627       (further tests needed for the implicit DST & Flux-Limiter schemes).
3628    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
3629      and sRef for convenience, handy, when you want to initialize
3630      ptracers in a large domain with a constant non-zero value. Also,
3631      untangle ptracers_init.F a little.
3632    
3633    checkpoint57v_post (2005/10/13)
3634    o change dome exp. to use variable viscosity in side-drag terms.
3635    o remove all the files from the cfc_offline test since they are now
3636      incorporated into tutorial_cfc_offline which has been producing
3637      identical results for a few days of testing
3638    o add new parameter: sideDragFactor to enable half-slip-side BC
3639      and change side-drag S/R to use viscosity from mom_calc_visc
3640      (can switch back by setting sideDragFactor=0.); affects results at
3641      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
3642       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
3643    o vorticity & strain are now computed without masking, to account for
3644      no-slip-side BC in variable viscosity calculation ; mask is applied
3645      anyway later on, before computing advection/coriolis terms.
3646    o modify exp4 to test new obcs support for reading from external files
3647      and for passive tracers
3648    o fix behavior of ptracers_monitor when monitor output is written to a
3649      netcdf-file; still not independent of monitor.F (writes in the same
3650      file).
3651    o change default value of tRef (put a uniform, meaningful value for ocean
3652      & atmos) and initialize sRef (was missing, as Martin mentioned).
3653    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
3654      to be proportional to enstrophy dissipation length.  Thus,
3655       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
3656      This is now consistent with Smagorinsky and with the manual.
3657    
3658    checkpoint57u_post
3659    o OBCS and PTRACERS: add open boundary support for passive tracers
3660      - either use homogenous (pseudo) v.Neumann conditions or prescribe
3661        OB-values from file; this is not different from the way theta and salinity
3662        are treated
3663      - however, Orlanski-radiation conditions are not supported, and the model
3664        will stop if you use pTracers and Orlanski at the same time.
3665      - beefed up the rountine obcs_external_fields_load: now only those open
3666        boundary values are overwritten with values from files for which there
3667        are really files, otherwise the OB-fields remain untouched. This makes
3668        it possible to use different OBs at different ends of the domain (as
3669        with EXF)
3670    o reduce number of exch calls in shap_filt (s2).
3671    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
3672      truncation level) 4/5 MLAdjust test results (11&12 digits match).
3673    
3674    checkpoint57t_post (2005/10/03)
3675    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
3676    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
3677      same truncation, independent of the face number: affects affects several
3678      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
3679    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
3680      note that biharmonic viscosity + no-slip was not tested in any experiment.
3681    o fix bug in non-linear free-surf side-drag ; generate new output for
3682      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
3683    o make mnc honor the writeBinaryPrec flag for most kinds of output
3684    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
3685    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
3686      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
3687    o add brackets in multi-terms sum to get same truncation, independent of
3688      the face number (manage to get exactly same value of gU,gV at the cs-edge)
3689      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
3690    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
3691      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
3692      a maximum grid-scale Reynolds number.  Also, changes all length calculations
3693      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
3694      Suggested values of viscosity parameters found in mom_calc_visc.
3695      Many new viscosity diagnostics available.
3696    
3697    checkpoint57s_post (2005/09/20)
3698    o Add clearing-house for viscosity calculations, mom_calc_visc and
3699      correct numerous bugs in LeithD and Smagorinsky discretizations.  
3700      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
3701      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
3702      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
3703      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
3704      The Strain-Tension form is now called with useStrainTensonVisc=.true.
3705      ViscAhStrain and viscAhTension are now retired.
3706    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
3707    o In response to JMC's bug report, genmake2 now ignores any soft-links
3708      that it finds in the *current* directory when searching for files.
3709      Soft-links found in any other source directories will still work as
3710      they did before.
3711    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
3712      a C routine to unlimit the stack size
3713    o mnc-ify pkg/aim snapshot vars
3714    o mnc-ify pkg/land as requested by Daniel
3715    o various changes to mnc including:
3716      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
3717      - output can now be grouped so that all files within a group
3718          change the ITER portion of their names in lock-step together
3719      - can now read ("global") PER-FACE (in addition to PER-TILE) files
3720          and works with both EXCH1 and EXCH2 (but needs more testing)
3721      - writing works for all verification test cases w/ g77 on Linux
3722    
3723    checkpoint57r_post (2005/09/07)
3724    o make MNC variable initialization happen earlier
3725    o add diagnostics for (almost) each term of the momentum Eq.
3726    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
3727    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
3728    o remove MINIMAL_TAVE_OUTPUT option ;
3729      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
3730    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
3731      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
3732    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
3733    o add time-dependent SST, SSS control
3734    o cost terms in ecco/ modularized (new cost_generic.F)
3735    o cost_averages routines are modularized (new cost_averagesgeneric.F)
3736    o new infrastructure for seaice model vs. obs misfits in seaice/
3737      * driver from the_main_loop.F is seaice_cost_driver.F
3738      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
3739      * gradient check in Exp. 6a of natl_box_adjoint/
3740    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
3741      (see README file)
3742    
3743    checkpoint57q_post (2005/08/19)
3744    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
3745    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
3746      - bug was reported by Jean-Michel and Ian Fenty
3747    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
3748      update exp. cpl_aim+ocn output.
3749    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
3750      Needed for high-res. runs with large global files
3751      to be able to limit tapelev size
3752    o Changed some tests for adjoint:
3753      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
3754      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
3755      * global_ocean.90x40x15/ back to default 3-level checkpointing
3756    o Modifications to enable scripted COMMON to MODULE conversion
3757      * verification/OpenAD/code/ has necessary scripts and description;
3758      * converts, compiles and runs successfully;
3759    
3760    checkpoint57p_post (2005/08/01)
3761    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
3762    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
3763      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
3764    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
3765    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
3766      (was already the case for dissipation with mom_vecinv,
3767       and also the case for grad.PhiHyd when staggered-timeStep)
3768      This will allow to put dissipation out-off the AB time-stepping.
3769     Unfortunately, affects truncation error. Update output of exp. that "fails"
3770      (cg2d matching number) and leave the others for later: front_relax(10),
3771      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
3772      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
3773    
3774    checkpoint57o_post (2005/07/30)
3775    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
3776      (2) its ready to be documented during the 20050801 DocFest
3777    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
3778      for ideal_2D_oce and lab_sea on linux_ia32_g77
3779    o set to #undef CTRL_SET_OLD_MAXCVARS_30
3780      in global1x1_tot/code_seaice_adj to access indices 32, 33
3781      (worth another tag)
3782    
3783    checkpoint57n_post (2005/07/29)
3784    o adding precip control xx_precip 32
3785    o adding swflux control xx_swflux 33
3786    o Replacing 10 forcing penalty cost routines by 1 generic.
3787    o Implementing partitioning in time-mean and variable adjustment
3788      for atmos. state.
3789    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
3790    o in natl_box_adjoint:
3791      * updated exp 1 to 10
3792        (but does not have time-mean vs. variable split results yet)
3793    o updated global1x1/*_seaice_adj/
3794      to incorporate latest changes
3795    o enable useSingleCpuIO for mdsio vector routines
3796      (applies in particular to tapelev I/O)
3797    o removed inefficient K-loop in all active_file*control*.F
3798    
3799    checkpoint57m_post (2005/07/28)
3800    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
3801      and advect_cs (use EXCH-2 and standard cs-32 grid files).
3802    o pkg/exch2: filling of face-corner halo regions is optional
3803      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
3804    
3805    checkpoint57l_post (2005/07/14)
3806     tag before updating tutorials (pre-release-2)
3807    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
3808       for output and interpolation of input fields onto model grid)
3809    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
3810       Affects results of exp. rotating_tank ; update output.txt.
3811    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
3812          and taking the square quantity and/or using a fraction-weight field.
3813    o fix aim_diagnostics_init.F mate numbers.
3814    o add mnc output capability to diagnostics/diagstat and update
3815      our cvsignore files for the ACSII output generated
3816    
3817    checkpoint57k_post (2005/07/02)
3818    o lab_sea now uses diagnostics package and provides a suite of
3819      new EXF diagnostics output.
3820    
3821    checkpoint57j_post (2005/06/30)
3822    o exf
3823      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
3824        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
3825        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
3826      * extended diagnostics output
3827        - now includes all EXF variables
3828        - hs, hl moved to common block
3829        - separate S/R for diagnostics, called after ctrl vector is added
3830        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
3831        - EXFqnet contains true Qnet (i.e. includes qsw)
3832      * updated verif. lab_sea, global_with_exf
3833      * Rearranging hflux (exf_mapfields -> exf_getforcing)
3834        to ensure that diagnostics sees a true EXFqnet
3835    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
3836    o diagnostics pkg: change pointers so that 1 diagnostic can be used
3837      several times with different frequencies.
3838    o mnc-ify the thsice package as requested by Daniel Enderton
3839      - the monitor--MNC output needs work
3840      - many attributes need to be added (most are currently blank)
3841    o mnc-ify theaim_v23 package as requested by Daniel Enderton
3842      - many attributes need to be added (most are currently blank)
3843    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
3844    o add Sadourny like discretization to the 4th.O vorticity advection scheme
3845    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
3846      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
3847         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
3848    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
3849     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
3850    
3851    checkpoint57i_post (2005/06/19)
3852    o Diagnostics package was changed: diagnostic allocation is now deactivated
3853      by setting an empty file name in the namelist (used to be by setting 0 frequency)
3854    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
3855      add 1rst Order upwind vertical Shear.
3856    o add a quick fix for A/B checkpointing in OFFLINE mode
3857    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
3858      end-run around the C/Fortran linking horror in eesup/src/timers.F
3859    o added pkg/runclock: allows user to terminate run based on wall clock
3860    o added non-hydrostatic scaling parameter: nh_am2
3861    o pkg/my82: futile attempt to make results compiler-independent by adding
3862      some "_d 0", etc. no effect.
3863    o for mnc output, fill the 'T' coordinate var with myTime and create a
3864      separate 'iter' variable for iteration count
3865    o pkg/diagnostics:
3866      add new capability: output of Global/Regional & per-level statistics ;
3867      tested against monitor output (including land & thSIce) on various exp.
3868    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
3869    
3870    checkpoint57h_done (2005/05/19)
3871      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
3872      data.diagnostics, data.gchem, data.ptracers) is done.
3873    
3874    o pkg/diagnostics: prepare for Global/Regional statistics.
3875      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
3876    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
3877      and rename it: DIFFERENT_MULTIPLE
3878    
3879    checkpoint57h_post (2005/05/14)
3880    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
3881    o pkg/diagnostics: change output frequency, now in seconds (instead
3882      of Nb of iterations). This requires to change data.diagnostics.
3883    checkpoint57h_pre (2005/05/12)
3884    
3885    o in mnc, let the user create the output dir if both mnc_outdir_date
3886      and mnc_outdir_num are false
3887    o add fflags() to pkg/diagnostics which allows one to specify, on a
3888      per-file basis, the file precision [default behavior is unchanged]
3889    o added diagnostics to pkg/kpp, including computation of mixed layer
3890      depth based on a temperature/density criterion
3891    o updated verification/natl_box to test the new pkg/kpp diagnostics
3892    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
3893    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
3894    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
3895      not mnc -- this mistake was found by JMC and is now corrected
3896    
3897    checkpoint57g_post (2005/04/15)
3898    o add Adams-Bashforth 3rd Order time stepping:
3899      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
3900      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
3901    checkpoint57g_pre (2005/04/15)
3902    
3903    o make lambda[Theta,Salt]ClimRelax spatially varying
3904      (default remains spatially uniform constant based on tau)
3905    o added new control variables
3906      * init. uVel, vVel, etanN
3907      * lambda[Theta,Salt]ClimRelax
3908    o separate masks used for ctrl_pack/unpack 'from write_grid' output
3909      (suggested by G. Forget)
3910    
3911    checkpoint57f_post (2005/04/06)
3912    o add parameter "baseTime" = model base time = time at iteration zero
3913      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
3914      account for baseTime shift
3915    o move Coriolis arrays from PARAMS.h to GRID.h
3916    checkpoint57f_pre (2005/04/06)
3917    
3918    o mnc-ifying the seaice package
3919    o introduced an alternative length scale calculation for use in the limiting
3920      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
3921    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
3922    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
3923      as well as grad(vort3).  Made it compatible with both approximate form
3924      for the cubed sphere and full form of these gradients.  Added flag
3925      useFullLeith to select between approximate and full form.  
3926    o add "d0" in getcon.F to reduce differences between compilers/platforms
3927      update output.txt of exp. fizhi-gridalt-hs
3928    o change port_rand funtion to allow to set the seed.
3929    o fix obscure MNC bug involving conversion between reals and integers
3930      - it caused no problems with certain (eg. gcc, ifc) compilers but the
3931        new version is now more standards-compliant
3932    o adjoint-related modifications
3933      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
3934      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
3935      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
3936    
3937    checkpoint57e_post (2005/02/28)
3938    o Adding eddy stress controls a la Ferreira et al.
3939    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
3940    
3941    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
3942      update output.txt of exp. fizhi-gridalt-hs
3943    o add more "Z" dimensions and associated coordinate vars to MNC
3944    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
3945    o parameter calendarDumps: when set, approximate months (30-31 days) and years
3946      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
3947      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
3948      months and years.  Requires pkg/cal.
3949    o diagnostics: add pickup functionality
3950      - off by default for backwards compatibility
3951      - current version only uses MDSIO -- MNC will be added
3952    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
3953    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
3954    
3955    checkpoint57d_post (2005/02/11)
3956    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
3957    o modify verification/ideal_2D_oce so that it tests the creation of mnc
3958      output from the diagnostics package
3959    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
3960    o make genmake2 more portable by using ".$FS" instead of ".f" for more
3961      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
3962    o add coordinate variables to the MNC output from the diagnostics package
3963    o change MNC-flags default value: true when useMNC=TRUE
3964    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
3965      the ability (off by default) to read the grid information using MNC
3966    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
3967    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
3968    o do snap-shot diagnostics at the middle of the time-interval (instead of
3969      at the end).
3970    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
3971      new test for AIM with thSIce + slab-ocean
3972    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
3973    o move state variable diagnostics to the beginning of the time step ;
3974      (note: still needs some work specially for snap-shot diagnostics)
3975      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
3976    
3977    checkpoint57c_post (2005/01/27)
3978    o Change testing option (-ieee) to get closer agreement between g77 & ifort
3979    o generate new output.txt files on faulks with g77 & the new -ieee option
3980    checkpoint57c_pre (2005/01/27)
3981    
3982    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
3983      update output.txt of exp. global_ocean.90x40x15
3984    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
3985      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
3986    o add saltFlux(+File) forcing capability with periodicExternalForcing
3987    o allow to use pkg diagnostics for GM-Redi & ThSIce output
3988    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
3989    o improvements for the MNC output from DIAGNOSTICS:
3990      - correct handling of the unlimitied dimension
3991      - all dims now have associated coordinate variables
3992      - variables located at U, V, and Corner ("Z") points are now written
3993        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
3994        *all* data points are output
3995    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
3996    o added pkg/seaice/seaice_monitor.F
3997    o mdsio_readfield.F can now read files visible only to master MPI process.
3998    o pkg/seaice: some test code for ice-modified ocean stress
3999    o exf_getffields interpolation defaults to bilinear for all scalar forcing
4000      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
4001      spurious negative numbers for precipitation and humidity.  Will cause
4002      some small numerical differences for integrations using pkg/exf/exf_interp.F.
4003    o pkg/ctrl/
4004      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
4005        May be enabled via doPackDiag
4006      *  introduce z-scaling of
4007         + gradient (doZscalePack) and
4008         + control (doZscaleUnpack)
4009    o pkg/mdsio/
4010      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
4011      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
4012    
4013    checkpoint57b_post (2004/12/20)
4014    o simplify options in diagnostics_fill arguments (remove weird combinations)
4015    o fix MNC coordinate variables so that they now contain per-face index
4016      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
4017      general, EXCH2 grids are only aligned to a "local" coordinate system
4018    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
4019    o Implement instantaneous output within pkg diagnostics:
4020      setting a negative frequency in data.diagnostics produces
4021     "snap-shot" output (as opposed to time-average if freq > 0)
4022    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
4023      NOTE: change ptracer diagnostics name: use 2 characters to work with
4024            more than 9 tracers. Add also diagnostics of advect & diffus flux.
4025    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
4026      becomes the coordinate variable for the 'T' dimension
4027    o add CF-style coordinate variables to MNC
4028      - just a first cut:  numbers are meaningless on the cubesphere and
4029        missing along the T axis but otherwise it works!
4030    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
4031    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
4032    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
4033      this is based directly on what the model compute, so that the content of
4034      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
4035    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
4036    o clean up build options files for SunOS, in particular
4037      - remove -traditional from xmakedepend
4038      - change -xarch=v9 to -xarch=native for f77
4039      - restore use of make (not gmake)
4040      - add CC=gcc if using g77
4041    o changes per discussion of AM, JMC, & EH3 today:
4042      - move redundant "grid" variables out of "state" -- in preparation of
4043        creating proper CF-style coordinate variables and in recognition
4044        that any/all grid variables can be easily copied (eg. w/NCO) from
4045        the grid files into any of the other NetCDF files
4046      - *always* output grid variables with MDSIO (this will eventually be
4047        changed)
4048      - output MNC grid file if useMNC is true
4049    o every instance of _END_MASTER() has been found and replaced with
4050      _END_MASTER( myThid ) in order to satisfy certain picky Sun
4051      preprocessors
4052    o re-arrange diagnostics pkg initialisation:
4053     - allow each package to extend the available diagnostics list
4054     - add some checking and fix small problems (multi-threaded, ...)
4055     - new S/R diagnostics_fill (replace fill_diagnostics):
4056       look through the short list of active diag. (instead of the long list)
4057       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
4058    
4059    checkpoint57a_post (2004/12/10)
4060    o this set of changes restores TAMC compatibility
4061      tested for global_ocean.90x40x15 adjoint on trough
4062      (what a pain)
4063    
4064    checkpoint57a_pre (2004/12/10)
4065    o some modifs in tools/build_options for sunos
4066    o call ctrl_pack for ctrl at end for optimcycle=0
4067    
4068    checkpoint57 (2004/12/09)
4069    o add horizontal bi-harmonic viscosity for vertical velocity
4070      - new parameter viscA4W (defaults to viscA4)
4071      - affects only non-hydrostatic code
4072      - to be done: no-slip lateral boundary conditions
4073    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
4074    o implement Implicit Vertical advection for pTracers
4075    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
4076      (implemented also for implicit vertical diffusion & advection)
4077    o OBCS: extend application of tracer open boundary conditions
4078      to a strip beyond the boundary of width Olx/Oly
4079    o add call monitor to TAF set of required calls (flow directives)
4080      and include in natl_box_adjoint
4081    o untangle a few ifdefs related to cost, ctrl, autodiff
4082      untangel a few ALLOW_ECCO_OPTIMIZATION
4083    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
4084      (theta2, salt2 in ecco_cost_weights)
4085    
4086    checkpoint56c_post (2004/12/03)
4087    o OBCS as control variables
4088      - update ctrl_ad_diff.list, obcs_ad_diff.list
4089      - remove balance of obcs controls from default
4090      - fix index bug nobcs in ctrl_init
4091      - fix dummy fields filen in ctrl_pack
4092      - add dummy weights for obcs
4093    o lsopt: comment out fort.94 output
4094    o optim:
4095      - remove unnecessary header files
4096      - adjusted namelists
4097      - add xerbla.F to Makefile
4098    o exf:
4099      - multiple modifications of exf_check_range
4100      - unit change in exf_init_runoff from [m/year] to [m/s]
4101    o mdsio:
4102      - i/o-vector change debugLevel from debLevA to debLevB
4103    
4104    checkpoint56b_post (2004/12/01)
4105    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
4106      is called from DO_THE_MODEL_IO
4107      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
4108      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
4109      - clean up PTRACERS_WRITE_TIMEAVE a little
4110    o add another verification experiment that tests both the cfc-pkg and
4111      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
4112      reactive tendencies treated inline with regular timestepping
4113    o testreport previously did a lousy job of comparing small numbers, so
4114      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
4115      implemented in the little c-progam tmp_cmpnum.c which is embedded in
4116      testreport.
4117    o ptracers_monitor: bug fix for MPI
4118    
4119    checkpoint56a_post (2004/11/28)
4120    o GCHEM: finish reorganizating the package
4121      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
4122        (introduces another 3D-array for each passive tracer, but only if
4123        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
4124        gchemTendency is not needed because the timestep is done separately)
4125      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
4126      - GCHEM is now---more or less cleanly---separate from PTRACERS
4127      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
4128        so clear to me how that should be done in a general way.
4129    o CFC: improve formatting of output in CFC_ATMOS
4130    o PTRACERS:
4131      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
4132        that ALL experiments with ptracers enable can be checked. This makes
4133        GCHEM_MONITOR obsolete.
4134      - include a runtime parameter PTRACERS_monitorFreq that defaults to
4135        monitorFreq
4136      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
4137    o add PTRACERS (PTR0[1-5]) to testreport output
4138    o exf_check_range:
4139      * default changed to .TRUE.
4140      * will check values for niter0 if debLevA, every timestep if debLevB
4141      * STOP in exf_check_range if 'out of range'
4142      * range chosen generous to allow for potential extema
4143      TBD: a version with stricter range
4144           permitted range would be runtime parameters
4145    o GMredi:
4146      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
4147      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
4148      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
4149    o GCHEM:
4150      - move call to GCHEM_FORCING_SEP, so that it is now called before
4151        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
4152      - introduced a useGCHEM runtime flag and applied it everywhere.
4153      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
4154        this flag is now only visible within GCHEM-pkg routines.
4155      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
4156        be replaced by a 3D array that is computed before thermodynamics; for
4157        this, the tracer ID iTracer had to be included into the parameter list
4158        of ptracers_forcing
4159      - set up forward_step to call gchem_forcing, that will replace
4160        gchem_forcing_int in ptracers_forcing
4161      - cleaning up
4162    o small cleaning of exch2: remove files that are also in eesupp/src
4163    
4164    checkpoint56 (2004/11/17)
4165    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
4166    o mnc: cleanup "full" files--fixes out-of-memory problem
4167    o ECCO-GODAE
4168      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
4169      * fully merged and updated from SIO code
4170        windstress sign change affects
4171        - exf_inscal_[u/v]stress
4172        - sign of xx_tau[u/v] adjustments
4173        - signs in cost_scat
4174      * ctrl_get_gen: avoid update of tau[u/v] for first few days
4175      * natl_box_adjoint updated and compressed
4176      * 2-level checkpoint switch added
4177        (tested in EXP. 1 of natl_box_adjoint)
4178      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
4179    o SVD
4180      * first complete, non-hacked version for SVD calculations
4181      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
4182        performed via direct access files admtlm_vector.it????
4183        (via ctrl_[un]pack)
4184      * optimcycle is used for ARPACK iteration counter
4185        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
4186      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
4187        and add linear transforms where necessary
4188      * controls are initial/final SST, SSS (can be extended; need to check
4189        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
4190    o mdsio: filename info to both stderr, stdout
4191    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
4192      from sign change
4193    
4194    checkpoint55j_post (2004/11/10)
4195    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
4196      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4197    o add consistent build directories and .cvsignore files to verification
4198    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
4199    o make all subroutines 30 or less characters in length for certain older
4200      compilers to work (a thorough search only turns up two routines in
4201      pkg/ptracers)
4202    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
4203      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4204    
4205    checkpoint55i_post (2004/10/28)
4206    o change arrays for total vertical diffusivity (2.D if explicit,
4207      3.D if implicit) ; each ptracer uses its own background value.
4208    o added mnc/NetCDF output capability to ocn_compon_interf
4209      - added bits to verification/cpl_aim+ocn so that it can run on
4210        ITRDA and other clusters without the mpirun "-wd" option
4211    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
4212      configuration
4213    o give MNC the ability to create additional files rather than
4214      exceeding a specified file size limit "MNC_MAX_FILESIZE"
4215      - the default is just less than 2GB which is a practical limit
4216        on many systems
4217    o Compute the non-local term using either KPP vertical diffusivity (=default)
4218       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
4219    
4220    checkpoint55h_post (2004/10/20)
4221    o add verification test "vermix"
4222    o remove all the *_ioinc flags and replace with the single global
4223      outputTypesInclusive flag
4224    o allow to set a vertical profile of vertical diffusivity for T & S
4225    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
4226    o useMNC moved from data.mnc to data.pkg
4227    
4228    checkpoint55g_post (2004/10/14)
4229    o Renaming carbon AD experiments to comply with testreport conventions
4230    o Updating adjoint of Held-Suarez hs94.1x64x5
4231    o Fixing directives for non-ECCO forward_step, after ECCO directives
4232      have been fixed to avoid recomp. of do_oceanic_phys
4233      Works well for global_ocean.90x40x15,
4234      but recomp. issue remains for carbon
4235    o Updating adjoint output for natl_box_adjoint after
4236      pkg/ecco has been modified (see taga c55d_post)
4237    
4238    checkpoint55f_post (2004/10/13)
4239    o rename to timeave_init_fixed
4240    
4241    checkpoint55e_post (2004/10/13)
4242    o some delicate re-shuffle of store directives to avoid one
4243      extra call of do_oceanic_physics
4244      affects ecco_the_main_loop.F, do_oceanic_physics.F
4245      checkpoint_lev1_directives.h
4246    o NB: this may break global_ocean adjoint temporarily,
4247      but it is clear how to fix it. Will do later, need this now.
4248    
4249    checkpoint55d_post (2004/10/11)
4250    o ECCO specific cost function terms (up-to-date with 1x1 runs)
4251    o ecco_cost_weights is modified to 1x1 runs
4252    o modifs to allow observations to be read in as
4253      single file or yearly files
4254    o enable to read exf forcing fields as either
4255      single file or yearly files (flag useExfYearlyFields)
4256    checkpoint55d_pre (2004/10/08)
4257    
4258    o switch between 2-level and 3-level checkpointing
4259    o add ability of MNC to write local and "partial" (eg. 2D slices where
4260      the full 3D field is never actually stored) arrays to NetCDF files
4261      with the correct (that is, the complete multi-dimensional) set of
4262      array indicies
4263      - used in mom_vecinv() to write the diagFreq output
4264      - tested (demonstrated) in verification/aim.5l_cs
4265    o further mnc-ification
4266      - add verification/lab_sea to the list with mnc setups
4267      - fix undefined mnc v-names in cd_code
4268      - add kpp to mnc output (both snapshot and timeave)
4269    o non-hydrostatic code
4270      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
4271        in calc_gw.F
4272      - defaults to viscAh
4273      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
4274        friction or Leith) in non-hydrostatic mode, as long as there is
4275        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
4276    o pkg/cost
4277      extend simple cost functions to treat time mean quantities
4278      (T,U,V) via cost_accumulate_state from cost_tile
4279    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
4280        be 2 times larger than the minimum size the advection scheme requires.
4281        now get a perfect conservation of salt in advect_cs test-exp (updated)
4282    o GGL90 (Gaspar's TKE mixed layer)
4283      - add horizontal diffusion of TKE, requires exchanges in
4284        do_fields_blocking_exchanges, horizontal diffusivity is zero by
4285        default. In OPA there is no horizontal diffusion of TKE but the
4286        mixing coefficients are computed from a horizontal average of TKE of
4287        6 points or so. I think that diffusion has a little more physical
4288        justification.
4289      - clean up ggl90_calc in the hope of reducing memory usage (this hope
4290        was in vain)
4291      - mask tke-variable in ggl90_init
4292    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
4293    o fix biharmonic diffusion on CS-grid.
4294    o more obcs stuff
4295      - added obcs_external_fields_load as an alternative to the EXF-pkg option
4296        for reading boundary values. This routine is called from
4297        obcs_prescribe_read
4298      - updated obcs_check
4299      - changed sponge layer relaxation parameter units for days to seconds
4300      - turned off sponge layer by default
4301      - changed argument list of OBCS_CALC to myTime+deltaTclock
4302      - fixed about 35 bugs in obcs_external_fields_load
4303    
4304    checkpoint55c_post (2004/09/23)
4305    o obcs stuff
4306      - new runtime flags useOBCSprescribe, useOBCSbalance
4307      - re-arranged obcs_calc
4308      - moved exf_getobcs to obcs_prescibe_read
4309        obcs_prescibe_read is called after ORLANSKI stuff
4310        and independent of it (executable can contain all).
4311      - updated obcs_check
4312      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
4313        These may be necessary only if tangential velocities are
4314        prescribed at OB, not sure, needs testing.
4315    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
4316      which simplifies the calls and passes the ifc check-bounds test
4317    
4318    checkpoint55b_post (2004/09/22)
4319    o add a 2D scalar, Z location, exchange_2 routine.
4320    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
4321      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
4322      affects advect_cs results (for the wrong reason): update output.txt
4323    o use a more standard discretization for biharmonic viscosity ;
4324     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
4325      affects results of dome set-up: update output.txt
4326    o fix gad_advection.F (CubedSphere part), back to version 1.23
4327    o fix bug in mom_vi_del2uv.F (CubedSphere part).
4328    
4329    checkpoint55a_post (2004/09/20)
4330    o merged code to
4331      * prescribe/read time-dependent open boundaries
4332        (works in conjunction with exf, cal)
4333      * sponge layer code for open boundaries
4334      * each boundary N/S/E/W now has its own CPP option
4335        (healthy for the adjoint)
4336    
4337    checkpoint55 (2004/09/17)
4338    o up-to-date adjoint of previous breaks
4339      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
4340      - global_ocean_ebm: adjoint still needs fix (TLM ok)
4341      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
4342      - carbon: * remove tr1-related adjoint verification
4343                * add ptracer as control variable
4344    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
4345      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
4346    
4347    checkpoint54f_post (2004/09/16)
4348    o in verification/carbin/ remove experiment related to
4349      ALLOW_PASSIVE_TRACER (array tr1 etc)
4350      code_ad/ input_ad/ results_ad
4351    
4352    o add two new packages
4353      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
4354        + subject to optimization (memory)
4355      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
4356        + subject to reordering (many GOTOs in the original code)
4357        + so far opps is called for every (i,j) point, and then operates in
4358          the vertical; one may want to reorder the scheme in order operate in
4359          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
4360          fields)
4361    o overhaul of IO so that we now have flags for MDSIO and/or MNC
4362      - all verification tests compile and run with linux_ia32_g77
4363      - defaults are compatible with current input files--nothing
4364        should change if you were not previously using MNC
4365      - MNC output has been added in numerous places (eg. timeave)
4366        but there are still a few writes not yet do-able with MNC
4367        (this is in progress)
4368      - flags now allow for either/or/both use of MDSIO and MNC and
4369        documentation will soon follow
4370      - numerous small formatting cleanups for ProTeX
4371    o add version info (via BUILD_INFO.h) to MNC and stdout
4372    
4373    checkpoint54e_post (2004/09/02)
4374    o add two new packages
4375      - pp81 (Packanowski and Philander, 1981), Richardson number and
4376        stratification dependent mixing
4377      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
4378      - these scheme operate in a similar manner as KPP (without ghat, of
4379        course), however there is only one diffusivity that is used for both
4380        temperature and salinity (and passive tracers)
4381    o add offline package
4382    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
4383      provided by Stephanie Dutkiewicz
4384    o genmake2: add ability to search for C compilers and cleanup test output
4385      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
4386    
4387    checkpoint54d_post (2004/07/27)
4388    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
4389    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
4390      leading to additional shift by 5 days each year of integration
4391       (i.e. leading to considerable offset over the years)
4392    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
4393    o start with no AB and no initial filtering (staggerTimeStep):
4394      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
4395    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
4396      (external loading & cpl import/export stay in forward_step.F)
4397    o update coupling interface to work with new staggerTimeStep
4398    o change MDSIO ptracers_pickup.
4399    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
4400    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
4401    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
4402    
4403    checkpoint54c_post (2004/07/18)
4404    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
4405      this affects (truncation error) output.txt of test-exp:
4406       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
4407    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
4408    o change Qnet to always be the net heat flux, (+upward).
4409      affects (truncation error) output of natl_box exp.: updated
4410    o define the max number of passive tracers in PTRACERS_SIZE.h
4411    o start to test mnc routinely in exp0
4412    o add sea-ice loading (sIceLoad) as a new forcing field.
4413    
4414    checkpoint54b_post (2004/07/08)
4415    o add testreport "-j JOBS" option for parallel builds (tested and pretty
4416       impressive on Altix and Opteron systems)
4417    o diagnostics can now write NetCDF files through the mnc package
4418    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
4419    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
4420    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
4421      affects (truncation error) output of lab_sea & natl_box exp.: updated
4422    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
4423    
4424    checkpoint54a_post (2004/07/06)
4425    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
4426    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
4427    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
4428    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
4429      + internal_wave (shift in writing cg2d_ini_res)
4430    checkpoint54a_pre (2004/07/05)
4431    
4432    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
4433      - modified verification/lab_sea and natl_box_adjoint accordingly
4434    
4435    checkpoint54 (2004/07/02)
4436    checkpoint53g_post (2004/07/02)
4437    o prepare splitting of thermodynamics: store convect.counter in common block
4438    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
4439      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
4440    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
4441    o new parameter "nShapS": allow to treat differently S from T (nShapT)
4442    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
4443    o restore adjointability
4444    
4445    checkpoint53f_post (2004/06/25)
4446    o modifications that affect AIM experiment results (update output.txt):
4447      - no advection of S at top interface Nr (pkg/generic_advdiff)
4448      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
4449    o AIM pkg:
4450      - include stability function into surf.Flux derivative relative to Tsurf
4451      - calculate clear-sky radiation & surface temp. change (for diagnostics)
4452    
4453    checkpoint53e_post
4454    o merged cylindrical coord configuration
4455    o added rotating_tank experiment
4456    checkpoint53e_pre
4457    
4458    checkpoint53d_post (2004/06/14)
4459    o faulks upgraded: re-generate output.txt that have changed:
4460       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
4461    o Added Bryan and Lewis, 1979, vertical diffusivity profile
4462    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
4463    o added Sadourny discretization of Coriolis
4464      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
4465      - re-enabled use of omega3 (useAbsVorticity)
4466    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
4467      vector-invariant equations
4468      - note: does *NOT* yet use same variable visc. for no-slip BC's.
4469    o recoded the lateral boundary conditions for non-hydrostatic w, this time
4470      hopefully without new bugs
4471      - still to do: biharmonic friction for non-hydrostatic w
4472    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
4473    o regenerated output for global_ocean_ebm (using -ieee)
4474    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
4475      of mom_common/
4476      - simple re-arrangement of instructions within computing loop
4477    checkpoint53d_pre (2004/05/21)
4478    
4479    checkpoint53c_post (2004/05/21)
4480    o new version of coupler for AIM+thSIce and Ocean models
4481     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
4482     - land: change Evaporation of snow
4483     - aim with thSIce: fix bug in snow-precip.
4484    o changes to calc_gw.F
4485     - bug fix for w^2 term near the bottom boundary
4486     - (hopefully) improve the lateral slip boundary condtions for use with
4487        partial/looped cells
4488      - because the bug fix changes two verification experiments anyway (exp5
4489        and plume on slope), change the lateral boundary condition from half slip
4490        to the value of no_slip_sides
4491    o ebm package wasnt quite up to the parallel task. Fixed that.
4492    o Adjoint of EBM package + verification
4493      * TLM OK
4494      * ADM not sufficient accuracy yet (needs further testing)
4495    
4496    checkpoint53b_post (2004/05/14)
4497    o Commiting new energy balance model to repository
4498      * package is pkg/ebm
4499      * verif. is verification/global_ocean_ebm
4500      * references are in ebm_driver.F
4501    C      * X. Wang, P. Stone and J. Marotzke, 1999:
4502    C        Global thermohaline circulation. Part I:
4503    C        Sensitivity to atmospheric moisture transport.
4504    C        J. Climate 12(1), 71-82
4505    C      * X. Wang, P. Stone and J. Marotzke, 1999:
4506    C        Global thermohaline circulation. Part II:
4507    C        Sensitivity with interactive transport.
4508    C        J. Climate 12(1), 83-91
4509    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
4510    C        Destabilization of the thermohaline circulation
4511    C        by atmospheric eddy transports.
4512    C        J. Climate 7(12), 1870-1882
4513    o Will need long integration testing.
4514    checkpoint53b_pre (2004/05/14)
4515    
4516    o created pkg/mom_common in preparation for variable viscosity code
4517    o renamed and split ini_mnc_io
4518    o pkg/land: only liquid water can diffuse or run-off
4519    o AIM using land: soil wetness availability account for snow
4520    o added printMapIncludesZeros to EEPARMS namelist
4521    
4522    checkpoint53a_post (2004/05/11)
4523    o restore TAMC compatiility for exf_constants.h
4524      (no usage of _d in .h)
4525    o Additional storing in KPP in an attempt to fix
4526      TAMC problem with adjoint of KPP code.
4527      (no success...)
4528      Identical code works fine with TAF.
4529    o Fixed verification/natl_box_adjoint experiments.
4530      Initial conditions for Experiments 4 and 5 are now
4531      set to "SEAICE_initialHEFF=0", which is more reasonable,
4532      and hence gives results closer to that of Experiment 2.
4533      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
4534    
4535    checkpoint53 (2004/05/06)
4536    o stable checkpoint with up to date adjoint
4537      TLM tests only run for 1st grdchk at the moment. Its unclear if
4538      this is a code problem or a problem with resetting code for g_
4539      variables that is being autogenerated wrong.
4540      Otherwise:
4541       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
4542       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
4543         are both still in chaos following their security messes.
4544    
4545    checkpoint52n_post (2004/05/06)
4546    o various build (mostly genmake2) changes including:
4547      - ability to build/run more easily within Cygwin and MacOS X
4548      - more complicated Makefiles with a stronger dependence on Gnu Make
4549    o pkg/seaice modifications
4550      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
4551        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
4552        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
4553      - changed proxy for geostrophic velocity and updated
4554        verification/lab_sea/results/* accordingly
4555      - removed ADI dynamic solver from pkg/seaice
4556      - replaced all occurrences of 1/CSTICE or 1/CSUICE
4557        they caused a segmentation fault under certain circumstances
4558      - removed unused field WATR
4559    o bug fix in exf-package:
4560      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
4561         now reflect that.
4562    o small fixes in the cal-package:
4563      - set reference date to first of January for the 'model'-calendar
4564      - failing of cal_CheckDate in cal_FullDate now actually results in a
4565        warning
4566    o small modifications in exf-package to increase flexibility:
4567      - change climtempfreeze from a constant to a runtime parameter that
4568        is specified in data.exf_clim (default = -1.9)
4569      - introduce runtime parameter windstressmax (default = 2.0) that is
4570        specified in data.exf
4571    o fix in pkg/thsice:
4572      - update Evap (Tsf changes) to be consistent with Latent heat flux
4573      - maintain snow precipitation unchanged (even if Tsf >=0).
4574     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
4575    
4576    checkpoint52m_post (2004/04/18)
4577    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
4578      this does not change any of the results, because myIter=0 in swfrac always
4579      lead to jwtype=2 (the default anyway), but the call makes little sense
4580      as a default
4581    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
4582    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
4583      atmospheric model (AIM) to use it ; add a "slab ocean" component.
4584    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
4585    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
4586    o extending useSingleCpuIO option to work with new exch2 I/O format
4587      - old-style, missing-tile I/O is still accessible by defining CPP
4588        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
4589    o monitor package can write to NetCDF files and/or STDOUT
4590    o fix re-definition bug in MNC_GRID_INIT_ALL()
4591    o doc/api_reference added
4592      - a framework for building an API Reference Manual using all
4593        the "protex" comments embedded in the code
4594      - see pkg/generic_advdiff, pkg/mnc for examples
4595    o MNC:
4596      - make myThid the last argument for all subroutines
4597      - new default for the grid files: NO halos
4598      - add useMNC and other run-time flags
4599      - separate per-file-group handling of the unlimited dimension
4600      - early initialization of MNC w/ flags read at the eeboot stage
4601        and lookup tables set in initialize_fixed
4602      - write all MNC output to a freshly-created directory
4603    o thermodynamics sea-ice (thsice) is now tested with testreport.
4604    o test exp. advect_cs: use the standard cs32 grid ; update output.
4605    o Added functionality to grdchk:
4606      pick global i,j,k position (or nearest wet) where to perform check.
4607    
4608    checkpoint52l_post (2004/03/11)
4609    o new land formulation:
4610      a) use ground enthalpy as prognostic variable to ensure exact
4611         energy conservation.
4612      b) account for water temperature and for latent heat of freezing
4613         in all processes (rain, run-off, ground storage)
4614      c) compute surface and ground temperature implicitly.
4615    o aim_v23 modification for new land model:
4616      a) Treat separately land / ocean / sea-ice surface fluxes
4617         to allow implicit computation of land & sea-ice surface temp.
4618      b) add snow precipitation.
4619    checkpoint52l_pre (2004/03/11)
4620    
4621    o fix problem (when 1 tile is empty) in min/max monitor.
4622    o fix bug in timeAve (u,vZetatave in common block)
4623    o no restoring terms under ice for pkg/seaice
4624    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
4625    o bug fix for pkg/seaice pickups
4626    o change MNC call locations and add coordinate attributes
4627    o mask vorticity at the corner ; affects global_ocean.cs output
4628    o fix ini_curvilinear_grid ; test CS experiments with mpi
4629    o aim.5l_cs: modify sea-ice fraction input file ; update output
4630    o exf: Adding simple range check routine for exf fields after read
4631    
4632    checkpoint52k_post (2004/02/23)
4633    o removed top-level directory "diags"
4634      - we migrated these functions to pkg/timeave a long time ago
4635    o fixed bug introduced in pkg/monitor
4636    o accuracy ctrlprec = 32 insuffient for gradient checks using
4637      averaged fields (I/O via cost_averages)
4638      -> use ctrl.h in active_file*.F to control I/O precision.
4639    o paramter list of CALL ADTHE_MAIN_LOOP
4640    o added initial do_the_model_io to ecco
4641    o set all ...Freq to zero after cost_final
4642      taveFreq, dumpFreq, pChkptFreq
4643    o MAIN and ECCO differentiability restored
4644    
4645    checkpoint52j_post (2004/02/18)
4646  o fix nchklev in tamc.h for global_ocean...  o fix nchklev in tamc.h for global_ocean...
4647  o Bringing flow and store directives up-to-date  o Bringing flow and store directives up-to-date
4648  o Really weird thing!  o Really weird thing!
# Line 11  o Really weird thing! Line 4650  o Really weird thing!
4650    starttime, niter0, instead of mytime, myiter, screws up the adjoint:    starttime, niter0, instead of mytime, myiter, screws up the adjoint:
4651    TAF places a faulty re-call of initialise_varia    TAF places a faulty re-call of initialise_varia
4652    after cost_final call which should not be there!    after cost_final call which should not be there!
4653  checkpoint52j_pre  checkpoint52j_pre (2004/02/03)
4654    
4655  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and  o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
4656    error messages    error messages
# Line 28  o merged mom_vi_calc_relvort3.F, mom_vi_ Line 4667  o merged mom_vi_calc_relvort3.F, mom_vi_
4667    mon_vort3.F to make exch2 friendly with >1 tile per cube face    mon_vort3.F to make exch2 friendly with >1 tile per cube face
4668  o limit timeave output for hi-res integrations  o limit timeave output for hi-res integrations
4669    
4670  checkpoint52i_post  checkpoint52i_post (2004/01/21)
4671  o removed CPP_EEOPTIONS.h from verification/*/code  o removed CPP_EEOPTIONS.h from verification/*/code
4672  o updated the tiling for global_ocean_pressure  o updated the tiling for global_ocean_pressure
4673  checkpoint52i_pre  checkpoint52i_pre (2004/01/20)
4674    
4675  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of  o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
4676    the old pkg/aim).    the old pkg/aim).
4677    
4678  checkpoint52h_pre  checkpoint52h_pre (2004/01/20)
4679  o shortened offending lines in exch2_send_rx?.template  o shortened offending lines in exch2_send_rx?.template
4680  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator  o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
4681  o genmake2: add build & execute test for NetCDF code  o genmake2: add build & execute test for NetCDF code
# Line 47  o added temporary hack for sea-ice dynam Line 4686  o added temporary hack for sea-ice dynam
4686    metric terms are ignored and it is assumed that    metric terms are ignored and it is assumed that
4687    there is no sea-ice on cube faces 1, 2, 4, and 5.    there is no sea-ice on cube faces 1, 2, 4, and 5.
4688    
4689  checkpoint52f_post  checkpoint52f_post (2004/01/09)
4690  o added exch2 cube routines to pkg/exch2  o added exch2 cube routines to pkg/exch2
4691  o modified hs94.cs-32x32x5 to use it  o modified hs94.cs-32x32x5 to use it
4692  o added new grid files to hs94.cs-32x32x5  o added new grid files to hs94.cs-32x32x5
4693  checkpoint52f_pre  checkpoint52f_pre (2004/01/07)
4694    
4695  checkpoint52e_post  checkpoint52e_post (2004/01/07)
4696  o first attempt to solve vertical advection (momemtum & T,S) Implicitly  o first attempt to solve vertical advection (momemtum & T,S) Implicitly
4697    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)    for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
4698  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)  o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
# Line 61  o step.1 : rewrite (as in MultiDimAdvec) Line 4700  o step.1 : rewrite (as in MultiDimAdvec)
4700  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.  o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
4701  o update output (gad_calc_rhs.F changes affect truncation error) of exp:  o update output (gad_calc_rhs.F changes affect truncation error) of exp:
4702   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box   front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
4703  checkpoint52e_pre  checkpoint52e_pre (2004/01/02)
4704    
4705  o fix bug in impldiff when Nr=1 or Nr=2.  o fix bug in impldiff when Nr=1 or Nr=2.
4706  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt  o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
# Line 72  o added exf_offset_atemp for Celsius to Line 4711  o added exf_offset_atemp for Celsius to
4711  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024  o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
4712  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations  o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
4713    
4714  checkpoint52d_post  checkpoint52d_post (2003/12/16)
4715  o re-tiled many expts to allow comparison in multi-processor mode  o re-tiled many expts to allow comparison in multi-processor mode
4716    - updated output accordingly    - updated output accordingly
4717    - changed hs94.128x64x5 to use intial T from file rather than use the    - changed hs94.128x64x5 to use intial T from file rather than use the
# Line 101  o check-in the first version of the coup Line 4740  o check-in the first version of the coup
4740  o new verification experiment, cpl_aim+ocn:  o new verification experiment, cpl_aim+ocn:
4741     coupled ocean - AIM atmosphere on cs32 grid.     coupled ocean - AIM atmosphere on cs32 grid.
4742    
4743  checkpoint52d_pre  checkpoint52d_pre (2003/12/06)
4744  o surface flux time-av diagnostic modified for NLFS & RealFreshWater  o surface flux time-av diagnostic modified for NLFS & RealFreshWater
4745  o add call to AIM pendant S/R in external_forcing & external_fields_load.F  o add call to AIM pendant S/R in external_forcing & external_fields_load.F
4746    
4747  checkpoint52c_post  checkpoint52c_post (2003/11/25)
4748  o Fixing OPTIONS files for use of exf:  o Fixing OPTIONS files for use of exf:
4749    - ALLOW_ECCO not needed    - ALLOW_ECCO not needed
4750    - ECCO_CPPOPTIONS.h should not be included from    - ECCO_CPPOPTIONS.h should not be included from
# Line 119  o Removed all CPP options for cal packag Line 4758  o Removed all CPP options for cal packag
4758  o modified STOREs in GAD_ADVECTION  o modified STOREs in GAD_ADVECTION
4759  o corrected key comp. for passkey  o corrected key comp. for passkey
4760    
4761  checkpoint52b_post  checkpoint52b_post (2003/11/23)
4762  o new version: "thsice" of thermodynamic sea-ice pkg:  o new version: "thsice" of thermodynamic sea-ice pkg:
4763   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.   - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
4764   - modify fluxes but do not change theta directly;   - modify fluxes but do not change theta directly;
# Line 127  o new version: "thsice" of thermodynamic Line 4766  o new version: "thsice" of thermodynamic
4766   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice   - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
4767     + output_thsice.txt to test thsice & bulk_force pkgs.     + output_thsice.txt to test thsice & bulk_force pkgs.
4768  o put back grid & coriolis monitor output.  o put back grid & coriolis monitor output.
4769  checkpoint52b_pre  checkpoint52b_pre (2003/11/23)
4770    
4771  o call "do_the_model_io" at the beginning (=> dump initial state)  o call "do_the_model_io" at the beginning (=> dump initial state)
4772  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)  o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
# Line 137  o missing PTRACERS headers in some routi Line 4776  o missing PTRACERS headers in some routi
4776  o default tamc.h in pkg/autodiff supposed to crash  o default tamc.h in pkg/autodiff supposed to crash
4777    to ensure proper customization    to ensure proper customization
4778    
4779  checkpoint52a_post  checkpoint52a_post (2003/11/17)
4780  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp  o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
4781    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
4782    - subroutine FREEZE_SURFACE now limits only surface temperature    - subroutine FREEZE_SURFACE now limits only surface temperature
# Line 152  o fix problem with ECCO-related divided Line 4791  o fix problem with ECCO-related divided
4791    snapshot file was missing some ad-variables,    snapshot file was missing some ad-variables,
4792    but no warning issued by TAF    but no warning issued by TAF
4793    
4794  checkpoint52a_pre  checkpoint52a_pre (2003/11/12)
4795  o some bug fixes for #undef REAL4_IS_SLOW  o some bug fixes for #undef REAL4_IS_SLOW
4796    
4797  checkpoint52 = ecco_c52_e35  checkpoint52 = ecco_c52_e35
4798  o after testing adjoints of checkpoint51u_post  o after testing adjoints of checkpoint51u_post
4799    
4800  checkpoint51u_post  checkpoint51u_post (2003/11/06)
4801  o this is the post-merge tag of the ecco-branch  o this is the post-merge tag of the ecco-branch
4802    (needs another clean checkout and re-testing)    (needs another clean checkout and re-testing)
4803  o various natl_box_adjoint configs and results  o various natl_box_adjoint configs and results
# Line 173  o top level routines the_main_loop, forw Line 4812  o top level routines the_main_loop, forw
4812    (new namelist ecco_cost_nml)    (new namelist ecco_cost_nml)
4813  o in ctrl/ cleaned some cross-dependencies and updated CPP options  o in ctrl/ cleaned some cross-dependencies and updated CPP options
4814    
4815  checkpoint51t_post  checkpoint51t_post (2003/11/04)
4816  o this is the pre-merge tag of the ecco-branch  o this is the pre-merge tag of the ecco-branch
4817    
4818  checkpoint51s_post  checkpoint51s_post (2003/11/04)
4819  o cleanup: removed various obsolete #define-s  o cleanup: removed various obsolete #define-s
4820  o pkg/grdchk  o pkg/grdchk
4821    - renamed 'ph-grd 3' to 'grad-res'    - renamed 'ph-grd 3' to 'grad-res'
# Line 185  o pkg/grdchk Line 4824  o pkg/grdchk
4824    - additional high-precision output for testreport    - additional high-precision output for testreport
4825      (grep for 'precision_grdchk_result')      (grep for 'precision_grdchk_result')
4826    
4827  checkpoint51r_post  checkpoint51r_post (2003/11/03)
4828  o cleaned up or removed CPP_OPTIONS.h files  o cleaned up or removed CPP_OPTIONS.h files
4829  o updated results for some of the tests to reflect the new  o updated results for some of the tests to reflect the new
4830    optfiles (-ieee: -O0 instead of -O3)    optfiles (-ieee: -O0 instead of -O3)
4831    
4832  checkpoint51q_post  checkpoint51q_post (2003/10/30)
4833  o cd_code:  o cd_code:
4834    - moved cd_scheme.F -> cd_code_scheme.F    - moved cd_scheme.F -> cd_code_scheme.F
4835    - separate read_checkpoint from cd_code_ini_vars.F    - separate read_checkpoint from cd_code_ini_vars.F
# Line 206  o ctrl package totally restructured Line 4845  o ctrl package totally restructured
4845    - confined inclusion of AD_CONFIG.h to where necessary.    - confined inclusion of AD_CONFIG.h to where necessary.
4846  o genmake2: changed AD dependencies from SRCFILES to AD_FILES  o genmake2: changed AD dependencies from SRCFILES to AD_FILES
4847    
4848  checkpoint51p_post  checkpoint51p_post (2003/10/30)
4849  o create initial cd_code package  o create initial cd_code package
4850    - WARNING: the initialization of fields within packages    - WARNING: the initialization of fields within packages
4851      is broken because INI_FIELDS (where READ_CHECKPOINT is      is broken because INI_FIELDS (where READ_CHECKPOINT is
# Line 221  o create initial cd_code package Line 4860  o create initial cd_code package
4860  o cleanup verification/*/code/GMREDI_OPTIONS.h  o cleanup verification/*/code/GMREDI_OPTIONS.h
4861  o cleanup testreport  o cleanup testreport
4862    
4863  checkpoint51o_post  checkpoint51o_post (2003/10/27)
4864  o bringing AD-related verif's up to date with genmake2  o bringing AD-related verif's up to date with genmake2
4865    - carbon/    - carbon/
4866    - global_ocean.90x40x15/    - global_ocean.90x40x15/
# Line 242  o Correcting initialisations for fVerU, Line 4881  o Correcting initialisations for fVerU,
4881  o helping TAF to recognize dependency on kUp for  o helping TAF to recognize dependency on kUp for
4882    fVerU, fVerV    fVerU, fVerV
4883  o Replacing delZ by delR in pkg/ctrl/  o Replacing delZ by delR in pkg/ctrl/
4884  checkpoint51o_pre  checkpoint51o_pre (2003/10/24)
4885    
4886  o undid all of cp51 pending some cleanups and discussion  o undid all of cp51 pending some cleanups and discussion
4887  o added the [#include "AD_CONFIG.h"] statement to all files that need  o added the [#include "AD_CONFIG.h"] statement to all files that need
# Line 250  o added the [#include "AD_CONFIG.h"] sta Line 4889  o added the [#include "AD_CONFIG.h"] sta
4889   o re-worked the build logic in genmake2 to support AD_CONFIG.h   o re-worked the build logic in genmake2 to support AD_CONFIG.h
4890   o removed tools/genmake since it no longer works   o removed tools/genmake since it no longer works
4891    
4892  checkpoint51n_post  checkpoint51n_post (2003/10/23)
4893  o modifications to make FREEZE flux visible to pkg/kpp  o modifications to make FREEZE flux visible to pkg/kpp
4894    - moved surfaceTendencyTice from pkg/seaice to main code    - moved surfaceTendencyTice from pkg/seaice to main code
4895    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP    - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
# Line 259  o modifications to make FREEZE flux visi Line 4898  o modifications to make FREEZE flux visi
4898       global_ocean.cs32x15, and global_with_exf)       global_ocean.cs32x15, and global_with_exf)
4899  o added surface flux output variables to TIMEAVE_STATVARS  o added surface flux output variables to TIMEAVE_STATVARS
4900    
4901  checkpoint51n_pre  checkpoint51n_pre (2003/10/23)
4902  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F  o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
4903  o added [#include "AD_CONFIG.h"] to all files that use the following  o added [#include "AD_CONFIG.h"] to all files that use the following
4904    defines:    defines:
# Line 267  o added [#include "AD_CONFIG.h"] to all Line 4906  o added [#include "AD_CONFIG.h"] to all
4906    - ALLOW_TANGENTLINEAR_RUN    - ALLOW_TANGENTLINEAR_RUN
4907    - ALLOW_ECCO_OPTIMIZATION    - ALLOW_ECCO_OPTIMIZATION
4908    
4909  checkpoint51m_post  checkpoint51m_post (2003/10/21)
4910  o incorporating changes to get TAMC/TAF working in genmake2  o incorporating changes to get TAMC/TAF working in genmake2
4911    - added new TAMC/TAF targets to the Makefile    - added new TAMC/TAF targets to the Makefile
4912    - various cleanups related to package handling    - various cleanups related to package handling
4913    - these changes should have no impact on the forward model    - these changes should have no impact on the forward model
4914    
4915  checkpoint51l_post  checkpoint51l_post (2003/10/20)
4916  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations  o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
4917   - faster algorithm for cal_addtime.F   - faster algorithm for cal_addtime.F
4918   - higher precision arithmetic, where needed   - higher precision arithmetic, where needed
4919   - pkg/exf *startdate variables changed from calendar date to   - pkg/exf *startdate variables changed from calendar date to
4920     model integration time     model integration time
4921    
4922  checkpoint51l_pre  checkpoint51l_pre (2003/10/17)
4923  o add salt flux to forcing fields (used when salty sea-ice forms or melts)  o add salt flux to forcing fields (used when salty sea-ice forms or melts)
4924  o enable to apply restoring on S & T only in a latitude band.  o enable to apply restoring on S & T only in a latitude band.
4925  o update output (external_forcing_surf modif. change truncation errors)  o update output (external_forcing_surf modif. change truncation errors)
4926     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
4927    
4928  checkpoint51k_post  checkpoint51k_post (2003/10/16)
4929  o change default to: useNHMTerms=.FALSE.  o change default to: useNHMTerms=.FALSE.
4930   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):   - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
4931     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
# Line 300  o added an include barrier to the defaul Line 4939  o added an include barrier to the defaul
4939    removed the #include "PACKAGES_CONFIG.h" from it    removed the #include "PACKAGES_CONFIG.h" from it
4940  o fix a bug in mom_fluxform (from chk51j_post)  o fix a bug in mom_fluxform (from chk51j_post)
4941    
4942  checkpoint51j_post  checkpoint51j_post (2003/10/10)
4943  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/  o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
4944  o adjusted some flow directives (dynamics, thermodynamics)  o adjusted some flow directives (dynamics, thermodynamics)
4945  o added cubed-sphere case to test cost function  o added cubed-sphere case to test cost function
# Line 314  o Moving pkg-specific flow directives to Line 4953  o Moving pkg-specific flow directives to
4953         - pkg_ad_diff.list         - pkg_ad_diff.list
4954         - pkg_ad_check_lev?_dir.h         - pkg_ad_check_lev?_dir.h
4955    
4956  checkpoint51i_post  checkpoint51i_post (2003/10/09)
4957  o merge of the branch-genmake2  o merge of the branch-genmake2
4958    - knowingly breaks the older genmake    - knowingly breaks the older genmake
4959    - automatic generation of all ALLOW_${PKG_NAME} defines    - automatic generation of all ALLOW_${PKG_NAME} defines
4960    - new testreport supersedes older testscript    - new testreport supersedes older testscript
4961  o large number of package inclusion and header cleanups  o large number of package inclusion and header cleanups
4962  checkpoint51i_pre  checkpoint51i_pre (2003/10/08)
4963    
4964  o new output for adjoin of global ocean vector invariant  o new output for adjoin of global ocean vector invariant
4965  o fix for checkpoint of thermodynamic seaice and bulk_force  o fix for checkpoint of thermodynamic seaice and bulk_force
# Line 332  o modify gchem pkg to be more versatile Line 4971  o modify gchem pkg to be more versatile
4971  o modifications to clean up dic pkg  o modifications to clean up dic pkg
4972  o add pkg/cfc  o add pkg/cfc
4973    
4974  checkpoint51g_post  checkpoint51g_post (2003/10/02)
4975  o provide links for ARPACK and ADM*TLM  o provide links for ARPACK and ADM*TLM
4976  o start removing verification/vero/  o start removing verification/vero/
4977  o update AD-related stuff  o update AD-related stuff
# Line 340  o update AD-related stuff Line 4979  o update AD-related stuff
4979  o adding to verification/global_ocean.90x40x15/ adjoint of  o adding to verification/global_ocean.90x40x15/ adjoint of
4980    vector invariant setup    vector invariant setup
4981    
4982  checkpoint51f_post  checkpoint51f_post (2003/10/02)
4983  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)  o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
4984  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation  o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
4985    of tracer Green's fucntions for ocean inversion project.    of tracer Green's fucntions for ocean inversion project.
4986    
4987  checkpoint51f_pre  checkpoint51f_pre (2003/08/07)
4988  o Added on-the-fly spatial interpolation capability  o Added on-the-fly spatial interpolation capability
4989      "USE_EXF_INTERPOLATION" to pkg/exf.      "USE_EXF_INTERPOLATION" to pkg/exf.
4990    - This is a temporary Cartesian-grid hack until    - This is a temporary Cartesian-grid hack until
# Line 357  o Bug fix to pkg/ptracers, pkg/generic_a Line 4996  o Bug fix to pkg/ptracers, pkg/generic_a
4996      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer      and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
4997      non-local transport term.      non-local transport term.
4998    
4999  checkpoint51e_post  checkpoint51e_post (2003/08/03)
5000  o pkg/mom_vecinv:  o pkg/mom_vecinv:
5001    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)    - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
5002    - add time-ave diagnostic of vorticity advection.    - add time-ave diagnostic of vorticity advection.
# Line 367  o atmospheric geopotential: - include wa Line 5006  o atmospheric geopotential: - include wa
5006  o land pkg: read initial state from files.  o land pkg: read initial state from files.
5007  o AIM : add stratospheric drag in the upper level  o AIM : add stratospheric drag in the upper level
5008    
5009  checkpoint51d_post  checkpoint51d_post (2003/07/18)
5010  o change function ILNBLNK (=> last non-blank char.) to return zero  o change function ILNBLNK (=> last non-blank char.) to return zero
5011    (instead of the string length) when the string. char is empty    (instead of the string length) when the string. char is empty
5012  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)  o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
# Line 380  o Use cluster local disks for purely loc Line 5019  o Use cluster local disks for purely loc
5019    - new active_file_loc... and mdsio_..._loc routines    - new active_file_loc... and mdsio_..._loc routines
5020    - affected packages: autodiff, ctrl, grdchk, mdsio    - affected packages: autodiff, ctrl, grdchk, mdsio
5021    
5022  checkpoint51c_post  checkpoint51c_post (2003/07/08)
5023  o introducing integer flag debugLevel  o introducing integer flag debugLevel
5024    - debLevZero: suppress all output    - debLevZero: suppress all output
5025    - debLevA: standard    - debLevA: standard
# Line 403  o added verification for adjoint with pt Line 5042  o added verification for adjoint with pt
5042    - checked tapelev/comlev recomputations: OK    - checked tapelev/comlev recomputations: OK
5043  <<<checkpoint51b_pre  <<<checkpoint51b_pre
5044    
5045  checkpoint51a_post  checkpoint51a_post (2003/06/25)
5046  o added code for biogeochemistry package  o added code for biogeochemistry package
5047    - new pkgs: dic, gchem    - new pkgs: dic, gchem
5048    - new subroutine in ptracers    - new subroutine in ptracers
5049  o modify code for biogeo packages  o modify code for biogeo packages
5050    - in model/src and pkg/ptracers    - in model/src and pkg/ptracers
5051    
5052  checkpoint51  checkpoint51 (2003/06/24)
5053  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN  o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
5054    - autodiff, ctrl, exf, grdchk, seaice    - autodiff, ctrl, exf, grdchk, seaice
5055    kept separate packages    kept separate packages
# Line 418  o merged improved packages from ecco-bra Line 5057  o merged improved packages from ecco-bra
5057  o updating verification/internal_wave, verification/lab_sea  o updating verification/internal_wave, verification/lab_sea
5058    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)    (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
5059    
5060  checkpoint50i_post  checkpoint50i_post (2003/06/23)
5061  o Preparing next differentiable checkpoint and sync  o Preparing next differentiable checkpoint and sync
5062    of MAIN vs. ecco-branch    of MAIN vs. ecco-branch
5063    - 1st step: this one is differentiable    - 1st step: this one is differentiable
5064    - 2nd step: next(! not this) checkpoint will have updated packages    - 2nd step: next(! not this) checkpoint will have updated packages
5065                from ecco-branch)                from ecco-branch)
5066    
5067  checkpoint50h_post  checkpoint50h_post (2003/06/20)
5068  o new package "land": provide surface BC for AIM.  o new package "land": provide surface BC for AIM.
5069  o pkg/ptracers: apply exchange to all tracers after reading a pickup.  o pkg/ptracers: apply exchange to all tracers after reading a pickup.
5070  o AIM: use true log-P extrapolation for near surface temp (= as in  o AIM: use true log-P extrapolation for near surface temp (= as in
# Line 434  o New variable in PARM03 for more flexib Line 5073  o New variable in PARM03 for more flexib
5073  o somewhat cleaned package initialisation sequence for  o somewhat cleaned package initialisation sequence for
5074    ctrl/ cost/ ecco/ in packages_... routines    ctrl/ cost/ ecco/ in packages_... routines
5075    
5076  checkpoint50g_post  checkpoint50g_post (2003/05/23)
5077  o merged with release1_p17 (pkg/seaice and verification/lab_sea)  o merged with release1_p17 (pkg/seaice and verification/lab_sea)
5078    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics    - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
5079    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and    - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
5080      made the default because of faster convergence than ADI      made the default because of faster convergence than ADI
5081    
5082  checkpoint50f_post  checkpoint50f_post (2003/05/23)
5083  o exf totally restructured  o exf totally restructured
5084    - replaced all exf_set_ routines by one generic exf_set_gen.F    - replaced all exf_set_ routines by one generic exf_set_gen.F
5085      and made sure it's still differentiable      and made sure it's still differentiable
# Line 448  o exf totally restructured Line 5087  o exf totally restructured
5087    - exf_inscal_/exf_outscal_ suffixes consistent with field names    - exf_inscal_/exf_outscal_ suffixes consistent with field names
5088    - updated adjoint/makefile and relevant verif. accordingly    - updated adjoint/makefile and relevant verif. accordingly
5089    
5090  checkpoint50f_pre  checkpoint50f_pre (2003/05/23)
5091   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;   o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
5092        + change Evap over land. (update aim.5l_cs output)        + change Evap over land. (update aim.5l_cs output)
5093   o added missing .cvsignores and made uniform across expts   o added missing .cvsignores and made uniform across expts
# Line 458  checkpoint50f_pre Line 5097  checkpoint50f_pre
5097   o new fn in pkg/monitor to stop model if solution grows too big   o new fn in pkg/monitor to stop model if solution grows too big
5098   o removed lots of single quotes from comments   o removed lots of single quotes from comments
5099    
5100  checkpoint50e_post  checkpoint50e_post (2003/05/14)
5101  o make KPP work with PTRACERS  o make KPP work with PTRACERS
5102   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
5103     nearly a copy of kpp_transport_s     nearly a copy of kpp_transport_s
5104   - there is no analogue to SurfaceTendencyS, so I have to use   - there is no analogue to SurfaceTendencyS, so I have to use
5105     gPtr(of the surface layer) instead     gPtr(of the surface layer) instead
5106  o add a new platform SunFire+mpi (SunFire 15000) to genmake  o add a new platform SunFire+mpi (SunFire 15000) to genmake
5107  checkpoint50e_pre  checkpoint50e_pre (2003/05/13)
5108    
5109  checkpoint50d_post  checkpoint50d_post (2003/05/13)
5110  o change kpp output from multiple-record state files to single-record state  o change kpp output from multiple-record state files to single-record state
5111    files analogous to write_state.F    files analogous to write_state.F
5112  o reduce the output frequency of cg3d-related stuff to the monitor frequency,  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
5113    analogous to the cg2d-related output.    analogous to the cg2d-related output.
5114  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
5115    so that writing to internal file fn (with length 512) fails.    so that writing to internal file fn (with length 512) fails.
5116  checkpoint50d_pre  checkpoint50d_pre (2003/05/12)
5117    
5118  checkpoint50c_post  checkpoint50c_post (2003/05/12)
5119  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)  o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
5120  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.  o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
5121  o add time-average diagnostic of U*V and vertical diffusive flux for theta.  o add time-average diagnostic of U*V and vertical diffusive flux for theta.
5122  o bug fixed in convective adjustment diagnostic (multi-tile set-up).  o bug fixed in convective adjustment diagnostic (multi-tile set-up).
5123  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.  o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
5124    
5125  checkpoint50c_pre  checkpoint50c_pre (2003/04/30)
5126  Merging from release1_p13:  Merging from release1_p13:
5127  o bug fix for pkg/seaice dynamic solver  o bug fix for pkg/seaice dynamic solver
5128  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
5129    
5130  checkpoint50b_post  checkpoint50b_post (2003/04/17)
5131  o store u*,v* in gU,V instead of in guNm1,gvNm1  o store u*,v* in gU,V instead of in guNm1,gvNm1
5132  o in order to put the momForcing out of the Adams-Bashforth:  o in order to put the momForcing out of the Adams-Bashforth:
5133    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv    move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
# Line 497  o new flag "useCDscheme" (default=F); re Line 5136  o new flag "useCDscheme" (default=F); re
5136  o re-generate output for highly sensitive test-exp:  o re-generate output for highly sensitive test-exp:
5137     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
5138    
5139  checkpoint50b_pre  checkpoint50b_pre (2003/04/17)
5140  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)  o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
5141  o corrected CPP option mismatch in exf_Bulk... functions for case  o corrected CPP option mismatch in exf_Bulk... functions for case
5142    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP    #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
5143    
5144  checkpoint50a_post  checkpoint50a_post (2003/03/21)
5145  o Bug fix for merging between c50 and KPP.  o Bug fix for merging between c50 and KPP.
5146    ikey was passed from thermodynamics to kpp_calc via    ikey was passed from thermodynamics to kpp_calc via
5147    common block rather than being recomputed in kpp_calc,    common block rather than being recomputed in kpp_calc,
5148    in contradiction with new key itdkey.    in contradiction with new key itdkey.
5149    New key ikppkey created, and tamc.h headers updated.    New key ikppkey created, and tamc.h headers updated.
5150    
5151  checkpoint50  checkpoint50 (2003/03/08)
5152  - 2nd step of merge with ecco-branch:  - 2nd step of merge with ecco-branch:
5153    merge changes in ecco-branch back into main trunk    merge changes in ecco-branch back into main trunk
5154  - bug fix in find_alpha  - bug fix in find_alpha
# Line 517  checkpoint50 Line 5156  checkpoint50
5156  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC  - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
5157  - merged some sliced AD support routines  - merged some sliced AD support routines
5158    
5159  checkpoint49  checkpoint49 (2003/03/06)
5160  merged from ecco-branch:  merged from ecco-branch:
5161  o exf:  o exf:
5162    - Enable initialisation of forcing fields to constant    - Enable initialisation of forcing fields to constant
# Line 555  o DIVA: Line 5194  o DIVA:
5194    (see MITgcm manual).    (see MITgcm manual).
5195  o cal: synchronized between MAIN and ecco-branch  o cal: synchronized between MAIN and ecco-branch
5196    
5197  checkpoint48i_post  checkpoint48i_post (2003/03/05)
5198  o Changes to restore differentiability of code w.r.t. previous tag  o Changes to restore differentiability of code w.r.t. previous tag
5199    (mostly adding new routines to make list and replacing    (mostly adding new routines to make list and replacing
5200    pressure by totPhiHyd).    pressure by totPhiHyd).
# Line 573  o Modif. for DIVA: Line 5212  o Modif. for DIVA:
5212    tbar, sbar, psbar, which should not be reinitialised;    tbar, sbar, psbar, which should not be reinitialised;
5213    only relevant for ecco-branch)    only relevant for ecco-branch)
5214    
5215  checkpoint48h_post  checkpoint48h_post (2003/02/28)
5216  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd  o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
5217  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F  o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
5218  o Added SEAICE_initialHEFF to pkg/seaice  o Added SEAICE_initialHEFF to pkg/seaice
5219  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT  o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
5220    
5221  checkpoint48g_post  checkpoint48g_post (2003/02/18)
5222  --- EOS:  --- EOS:
5223  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF  o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
5224    store total Potential in totPhyHyd for diagnostics & EOS.    store total Potential in totPhyHyd for diagnostics & EOS.
# Line 593  o accurate phiHyd when using interface-W Line 5232  o accurate phiHyd when using interface-W
5232   ( changes results of ideal_2D_oce )   ( changes results of ideal_2D_oce )
5233  o includes r* 2nd term in potential gradient.  o includes r* 2nd term in potential gradient.
5234    
5235  checkpoint48f_post  checkpoint48f_post (2003/02/18)
5236  Merging from release1_p12:  Merging from release1_p12:
5237  o Modifications for using pkg/exf with pkg/seaice  o Modifications for using pkg/exf with pkg/seaice
5238    - improved description of the various forcing configurations    - improved description of the various forcing configurations
# Line 621  o pkg/seaice: Line 5260  o pkg/seaice:
5260    - adjoint-friendly modifications    - adjoint-friendly modifications
5261    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F    - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
5262    
5263  checkpoint48e_post  checkpoint48e_post (2003/02/12)
5264  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)  o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
5265  o dynamics: change definition of computational domain & adapt mom_fluxform  o dynamics: change definition of computational domain & adapt mom_fluxform
5266    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.    accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
# Line 632  o following exp works with Olx=Oly=2 (an Line 5271  o following exp works with Olx=Oly=2 (an
5271      inverted_barometer solid-body.cs-32x32x1      inverted_barometer solid-body.cs-32x32x1
5272    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)    (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
5273    
5274  checkpoint48d_post  checkpoint48d_post (2003/02/09)
5275  o in preparation for r*:  o in preparation for r*:
5276   a) use pre-computed gradient of hydrostatic potential:   a) use pre-computed gradient of hydrostatic potential:
5277      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce      changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
# Line 640  o in preparation for r*: Line 5279  o in preparation for r*:
5279      => affects results of glob_oce_pressure (different truncation error)        => affects results of glob_oce_pressure (different truncation error)  
5280    update output.txt of ideal_2D_oce & global_ocean_pressure    update output.txt of ideal_2D_oce & global_ocean_pressure
5281    
5282  checkpoint48d_pre  checkpoint48d_pre (2003/02/08)
5283  o in preparation for r*:  o in preparation for r*:
5284    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.    new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
5285    pass the 2 comp. of the grad. as arguments to momentum S/R.    pass the 2 comp. of the grad. as arguments to momentum S/R.
5286    but for the moment, only used if it does not change the results.    but for the moment, only used if it does not change the results.
5287  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP  o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
5288    
5289  checkpoint48c_post  checkpoint48c_post (2003/02/06)
5290  Modifications in treatment of initial flux forcing controls  Modifications in treatment of initial flux forcing controls
5291  to avoid extra storing of flux fields.  to avoid extra storing of flux fields.
5292    
5293  checkpoint48c_pre  checkpoint48c_pre (2003/01/21)
5294  o Added tidal_basin_2d experiment (currently 1D!)  o Added tidal_basin_2d experiment (currently 1D!)
5295  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)  o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
5296    
5297  checkpoint48b_post  checkpoint48b_post (2003/01/27)
5298  o r* coordinate added in #ifdef NONLIN_FRSURF block.  o r* coordinate added in #ifdef NONLIN_FRSURF block.
5299   (modification to pressure gradient not yet implemented)   (modification to pressure gradient not yet implemented)
5300  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports  o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
5301    (for U & V) that are used for vertical advection of momentum.    (for U & V) that are used for vertical advection of momentum.
5302    
5303  checkpoint48a_post  checkpoint48a_post (2003/01/24)
5304  o In preparation for r*, use temp. array to compute vertical transport  o In preparation for r*, use temp. array to compute vertical transport
5305     in flux-form momentum pkg. => change results of few test-exp.     in flux-form momentum pkg. => change results of few test-exp.
5306    Update output of: exp4, exp5, front_relax, global_ocean_pressure,    Update output of: exp4, exp5, front_relax, global_ocean_pressure,
5307                      lab_sea, natl_box & plume_on_slope                      lab_sea, natl_box & plume_on_slope
5308    
5309  checkpoint48  checkpoint48 (2003/01/23)
5310  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
5311    
5312  checkpoint47j_post  checkpoint47j_post (2003/01/21)
5313  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.  o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
5314  o moved adexch from forward_step to addummy_in_stepping  o moved adexch from forward_step to addummy_in_stepping
5315  o added exch in ctrl_map_...  o added exch in ctrl_map_...
# Line 689  o Yet more changes in gmredi: Line 5328  o Yet more changes in gmredi:
5328      re-activated full calculation of taperfct for case 'ac02'      re-activated full calculation of taperfct for case 'ac02'
5329  o updating verification/ adjoints of carbon, global_ocean.90x40x15  o updating verification/ adjoints of carbon, global_ocean.90x40x15
5330    
5331  checkpoint47i_post  checkpoint47i_post (2003/01/13)
5332  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.  o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
5333  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)  o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
5334    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)    default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
# Line 705  o case GM_BOLUS_ADVEC should be cleaned Line 5344  o case GM_BOLUS_ADVEC should be cleaned
5344    S/R gmredi_slope_psi should be cleaned    S/R gmredi_slope_psi should be cleaned
5345  o verification/carbon now has exactConserv=.TRUE.  o verification/carbon now has exactConserv=.TRUE.
5346    
5347  checkpoint47g_post  checkpoint47g_post (2003/01/10)
5348  o time-average AIM output: becomes independent from statvars time-average  o time-average AIM output: becomes independent from statvars time-average
5349    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)    (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
5350  o After TAF bug fix:  o After TAF bug fix:
# Line 731  Gradient checks OK for Line 5370  Gradient checks OK for
5370  in conjunction with data.gmredi parameters to be checked in  in conjunction with data.gmredi parameters to be checked in
5371  in a few minutes under verification/carbon/code/  in a few minutes under verification/carbon/code/
5372    
5373  checkpoint47f_post  checkpoint47f_post (2002/12/28)
5374  Merging from release1_p10:  Merging from release1_p10:
5375  o modifications for using pkg/exf with pkg/seaice  o modifications for using pkg/exf with pkg/seaice
5376    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING    - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
# Line 743  o modifications for using pkg/exf with p Line 5382  o modifications for using pkg/exf with p
5382    - verification/lab_sea default experiment now uses    - verification/lab_sea default experiment now uses
5383      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf      pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
5384    
5385  checkpoint47e_post  checkpoint47e_post (2002/12/27)
5386  o created a tag prior to creating a branch  o created a tag prior to creating a branch
5387    
5388  checkpoint47d_post  checkpoint47d_post (2002/12/16)
5389  o fixed bug in the oceanic pressure coordinates code: vertical viscosity  o fixed bug in the oceanic pressure coordinates code: vertical viscosity
5390    at the bottom boundary had an erroneous half slip boundary condition    at the bottom boundary had an erroneous half slip boundary condition
5391  o added bottom drag and no slip boundary condition capabilities to  o added bottom drag and no slip boundary condition capabilities to
5392    oceanic pressure coordinates code    oceanic pressure coordinates code
5393  o added new verification experiment global_ocean_pressure, this experiment is  o added new verification experiment global_ocean_pressure, this experiment is
5394    also described in the tutorial section of the manual    also described in the tutorial section of the manual
5395  checkpoint47d_pre  checkpoint47d_pre (2002/12/16)
5396    
5397  checkpoint47c_post  checkpoint47c_post (2002/12/16)
5398  o Added a verification experiment for a global cubed-sphere ocean run  o Added a verification experiment for a global cubed-sphere ocean run
5399    -  verification/global_ocean.cubed32x32x30    -  verification/global_ocean.cubed32x32x30
5400    -  uses pkg/therm_seaice and pkg/bulk_forcing    -  uses pkg/therm_seaice and pkg/bulk_forcing
# Line 767  o OCEANICP & realFreshWater: include P-E Line 5406  o OCEANICP & realFreshWater: include P-E
5406    NOTES: requires option NONLIN_FRSURF to be "#define".    NOTES: requires option NONLIN_FRSURF to be "#define".
5407  o update advect_xz/results/output.txt (left from checkpoint44g_post)  o update advect_xz/results/output.txt (left from checkpoint44g_post)
5408    
5409  checkpoint47b_post  checkpoint47b_post (2002/12/05)
5410  Merging from release1_p9:  Merging from release1_p9:
5411  o pkg/seaice  o pkg/seaice
5412    - removed GOTO's and added taf directives    - removed GOTO's and added taf directives
# Line 784  o verification/lab_sea Line 5423  o verification/lab_sea
5423    - added missing matlab routines    - added missing matlab routines
5424    - added test of thermodynamics parallelization    - added test of thermodynamics parallelization
5425    
5426  checkpoint47a_post  checkpoint47a_post (2002/11/23)
5427  o new pkg: aim_v23  o new pkg: aim_v23
5428   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.   = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
5429     for now, keep the same surface forcing as before.     for now, keep the same surface forcing as before.
# Line 801  o bulk_force and therm_seaice Line 5440  o bulk_force and therm_seaice
5440  - Two ifdef statements for compile time,  - Two ifdef statements for compile time,
5441     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
5442    
5443  checkpoint47  checkpoint47 (2002/11/15)
5444  differentiable version of checkpoint46n_post  differentiable version of checkpoint46n_post
5445  o bug fix in quasihydrostaticterms  o bug fix in quasihydrostaticterms
5446  o * "clean" adjoint code (in terms of extensive recomputations)  o * "clean" adjoint code (in terms of extensive recomputations)
# Line 830  o Updated verification/carbon/ Line 5469  o Updated verification/carbon/
5469    - #define GM_VISBECK_VARIABLE_K    - #define GM_VISBECK_VARIABLE_K
5470    - GM_taper_scheme    = 'ldd97'        - GM_taper_scheme    = 'ldd97'    
5471    
5472  checkpoint46n_post  checkpoint46n_post (2002/11/12)
5473  Merging from release1_p8:  Merging from release1_p8:
5474  o verification/natl_box:  o verification/natl_box:
5475    updating new external_fields_load routine    updating new external_fields_load routine
# Line 884  o Adding new verification experiment glo Line 5523  o Adding new verification experiment glo
5523    the exf (and cal) package instead of the    the exf (and cal) package instead of the
5524    external_fields_load routine (cf README file).    external_fields_load routine (cf README file).
5525    
5526  checkpoint46m_post  checkpoint46m_post (2002/11/07)
5527  o modified testscript to return -- when there are no lines of "%MON" output  o modified testscript to return -- when there are no lines of "%MON" output
5528  o added new flag "quasiHydrostatic" for QH mode  o added new flag "quasiHydrostatic" for QH mode
5529    and new routine quasihydrostaticterms()    and new routine quasihydrostaticterms()
# Line 897  o introduced flag for controllin non-hyd Line 5536  o introduced flag for controllin non-hyd
5536  o removed gravitySign from PARM04  o removed gravitySign from PARM04
5537  o switched to g77/ifc from pgf77 in aim experiments  o switched to g77/ifc from pgf77 in aim experiments
5538    
5539  checkpoint46l_post  checkpoint46l_post (2002/11/01)
5540  o made convective adjustment work with pressure coordinates:  o made convective adjustment work with pressure coordinates:
5541   - changed the direction of k-loop in convective_adjustment.F for the   - changed the direction of k-loop in convective_adjustment.F for the
5542     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
# Line 910  o made convective adjustment work with p Line 5549  o made convective adjustment work with p
5549     at the beginning of find_rho, find_alpha, and find_beta, does a     at the beginning of find_rho, find_alpha, and find_beta, does a
5550     check of the entire slice, if CPP-option     check of the entire slice, if CPP-option
5551     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
5552  checkpoint46l_pre  checkpoint46l_pre (2002/10/23)
5553    
5554  checkpoint46k_post  checkpoint46k_post (2002/10/23)
5555  o fixed the verification/global_ocean.90x40x15 experiment:  o fixed the verification/global_ocean.90x40x15 experiment:
5556   - new bathymetry (the world according to A., JMC, and M.)   - new bathymetry (the world according to A., JMC, and M.)
5557   - new initial fields and forcing fields (*.bin files)   - new initial fields and forcing fields (*.bin files)
# Line 926  o S/R aim_initialise.F replace S/R aim_i Line 5565  o S/R aim_initialise.F replace S/R aim_i
5565   - read AIM physics parameters from a file (data.aimphys)   - read AIM physics parameters from a file (data.aimphys)
5566   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)   - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
5567    
5568  checkpoint46j_post  checkpoint46j_post (2002/10/07)
5569  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH  o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
5570  o move wVel computation at the end of the time step, in S/R integr_continuity  o move wVel computation at the end of the time step, in S/R integr_continuity
5571  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)  o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
5572  o update timeave pkg for wVel diagnostic.  o update timeave pkg for wVel diagnostic.
5573  checkpoint46j_pre  checkpoint46j_pre (2002/09/27)
5574    
5575  checkpoint46i_post  checkpoint46i_post (2002/09/25)
5576  o Clean up AIM package (and keep the results unchanged):  o Clean up AIM package (and keep the results unchanged):
5577    include CPP_OPTION and use IMPLICT NONE in all routines ;    include CPP_OPTION and use IMPLICT NONE in all routines ;
5578    declare all the variables _RL ; use _d 0 for all numerical constants.    declare all the variables _RL ; use _d 0 for all numerical constants.
5579    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !    use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
5580    
5581  checkpoint46h_post  checkpoint46h_post (2002/09/25)
5582  o cleaned up the use of rhoNil and rhoConst.  o cleaned up the use of rhoNil and rhoConst.
5583    - rhoNil should only appear in the LINEAR equation of state, everywhere    - rhoNil should only appear in the LINEAR equation of state, everywhere
5584      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst      else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
# Line 949  o introduced new parameter rhoConstFresh Line 5588  o introduced new parameter rhoConstFresh
5588    value is 999.8 kg/m^3    value is 999.8 kg/m^3
5589  o cleanup up external_forcing.F and external_forcing_surf.F  o cleanup up external_forcing.F and external_forcing_surf.F
5590    - can now be used by both OCEANIC and OCEANICP    - can now be used by both OCEANIC and OCEANICP
5591  checkpoint46h_pre  checkpoint46h_pre (2002/09/18)
5592    
5593   Added code to convert surface volume flux (fresh water) into   Added code to convert surface volume flux (fresh water) into
5594   a mass flux when using P coordinates in the ocean (OCEANICP).   a mass flux when using P coordinates in the ocean (OCEANICP).
5595   Note: It assumes you have set rho0=rhoConst=density of fresh water.   Note: It assumes you have set rho0=rhoConst=density of fresh water.
5596    
5597  checkpoint46g_post  checkpoint46g_post (2002/09/18)
5598  o Include a new diagnostic variable phiHydLow for the ocean model  o Include a new diagnostic variable phiHydLow for the ocean model
5599    - in z-coordinates, it is the bottom pressure anomaly    - in z-coordinates, it is the bottom pressure anomaly
5600    - in p-coordinates, it is the sea surface elevation    - in p-coordinates, it is the sea surface elevation
# Line 973  o cleaned up find_rho Line 5612  o cleaned up find_rho
5612    - removed obsolete 'eqn' from the parameter list.    - removed obsolete 'eqn' from the parameter list.
5613  o added two new verification experiments: gop and goz  o added two new verification experiments: gop and goz
5614    (4x4 degree global ocean, 15 layers in pressure and height coordinates)    (4x4 degree global ocean, 15 layers in pressure and height coordinates)
5615  checkpoint46g_pre  checkpoint46g_pre (2002/09/16)
5616    
5617  checkpoint46f_post  checkpoint46f_post (2002/09/16)
5618  o Enable tangent linear (forward mode) gradient checks:  o Enable tangent linear (forward mode) gradient checks:
5619    - extended active file handling to g_... files    - extended active file handling to g_... files
5620    - added TANGENT_SIMULATION to theSimulationMode    - added TANGENT_SIMULATION to theSimulationMode
# Line 983  o Enable tangent linear (forward mode) g Line 5622  o Enable tangent linear (forward mode) g
5622  o added tangent linear setup in verification/carbon/code_ftl  o added tangent linear setup in verification/carbon/code_ftl
5623  o added adjoint setup in verification/front_relax/code_ad  o added adjoint setup in verification/front_relax/code_ad
5624    
5625  checkpoint46e_post  checkpoint46e_post (2002/09/05)
5626  o Added new equation of state -> MDJWF  o Added new equation of state -> MDJWF
5627    - EOS of McDougall et al., 2002, JAOT, submitted    - EOS of McDougall et al., 2002, JAOT, submitted
5628    - caveat: the equation of state is only valid for a smaller (more    - caveat: the equation of state is only valid for a smaller (more
# Line 992  o Added new equation of state -> MDJWF Line 5631  o Added new equation of state -> MDJWF
5631    - added more check values for density in check_eos (ini_eos.F), some of    - added more check values for density in check_eos (ini_eos.F), some of
5632      the old check values are out of the range of the MDJWF-eos, so don't      the old check values are out of the range of the MDJWF-eos, so don't
5633      expect perfect matches for those      expect perfect matches for those
5634  checkpoint46e_pre  checkpoint46e_pre (2002/08/19)
5635    
5636  checkpoint46d_post  checkpoint46d_post (2002/08/19)
5637  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and  o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
5638    'OCEANICP', also initialised field pressure correctly in ini_eos in the    'OCEANICP', also initialised field pressure correctly in ini_eos in the
5639    case of pressure coordinates. eosType='JMD95Z' in    case of pressure coordinates. eosType='JMD95Z' in
5640    combination with buoyancyRelation='OCEANICP' now causes an error.    combination with buoyancyRelation='OCEANICP' now causes an error.
5641  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
5642    in find_alpha/beta.    in find_alpha/beta.
5643  checkpoint46d_pre  checkpoint46d_pre (2002/08/15)
5644    
5645  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)  o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
5646    so that JMD95Z and JMD95P give approptiate static stability in find_rho.    so that JMD95Z and JMD95P give approptiate static stability in find_rho.
5647    
5648  checkpoint46c_post  checkpoint46c_post (2002/08/15)
5649  o Changes necessary for ocean in p-coordinates  o Changes necessary for ocean in p-coordinates
5650   -  Added new buoyancy relation = 'OCEANICP'   -  Added new buoyancy relation = 'OCEANICP'
5651   -  Added new parameters = gravitySign (this used to be contained inside   -  Added new parameters = gravitySign (this used to be contained inside
5652      the factor dRdZ which I added when we first switched to R coordinates).      the factor dRdZ which I added when we first switched to R coordinates).
5653   X GM/Redi is not compatible (yet)   X GM/Redi is not compatible (yet)
5654   X bottom drag and no-slip need to be debugged.   X bottom drag and no-slip need to be debugged.
5655  checkpoint46c_pre  checkpoint46c_pre (2002/08/07)
5656    
5657  checkpoint46b_post  checkpoint46b_post (2002/08/07)
5658  o Added new equation of state -> JMD95Z and JMD95P  o Added new equation of state -> JMD95Z and JMD95P
5659    - EOS of Jackett and McDougall, 1995, JAOT    - EOS of Jackett and McDougall, 1995, JAOT
5660    - moved all EOS parameters into EOS.h    - moved all EOS parameters into EOS.h
# Line 1024  o Added UNESCO EOS, but not recommended Line 5663  o Added UNESCO EOS, but not recommended
5663    in-situ temperature (see JMD95)    in-situ temperature (see JMD95)
5664  o Modified formatting for knudsen2.f in utils/knudsen2 and added  o Modified formatting for knudsen2.f in utils/knudsen2 and added
5665    unesco.f to be used with POLY3    unesco.f to be used with POLY3
5666  checkpoint46b_pre  checkpoint46b_pre (2002/07/31)
5667    
5668  checkpoint46a_post  checkpoint46a_post (2002/07/31)
5669  o Added (atmospheric) pressure loading  o Added (atmospheric) pressure loading
5670    - new field in FFIELDS.h, etc...    - new field in FFIELDS.h, etc...
5671    - new cpp flag ATMOSPHERIC_LOADING    - new cpp flag ATMOSPHERIC_LOADING
5672  o Changed hFacC to _hFacC in calc_phi_hyd.F  o Changed hFacC to _hFacC in calc_phi_hyd.F
5673  o Added SHORTWAVE_HEATING to some files for consistency  o Added SHORTWAVE_HEATING to some files for consistency
5674  checkpoint46a_pre  checkpoint46a_pre (2002/07/13)
5675    
5676  checkpoint46  checkpoint46 (2002/07/13)
5677  further merges from release1_p5  further merges from release1_p5
5678  o new ctrl package  o new ctrl package
5679    - adopted from ECCO environment to enable optimization    - adopted from ECCO environment to enable optimization
# Line 1061  o added hooks for Eliassen Palm fluxes ( Line 5700  o added hooks for Eliassen Palm fluxes (
5700  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)  o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
5701  o incorporated hooks for sponge layer code (external_forcing.F)  o incorporated hooks for sponge layer code (external_forcing.F)
5702    
5703  checkpoint45d_post  checkpoint45d_post (2002/07/12)
5704  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)  o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
5705  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S  o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
5706    (affects plume_on_slope "cg2d" output)    (affects plume_on_slope "cg2d" output)
# Line 1075  o add new flags: Line 5714  o add new flags:
5714   - for each tracer, define internal flag for multiDimAdvection & A-B   - for each tracer, define internal flag for multiDimAdvection & A-B
5715  o monitor: change definition of KE to check conservation of Energy  o monitor: change definition of KE to check conservation of Energy
5716    
5717  checkpoint45c_post  checkpoint45c_post (2002/05/30)
5718  o Removed f90 comments ("!")  o Removed f90 comments ("!")
5719  o Modified initialisations to enable exf package for MITgcm  o Modified initialisations to enable exf package for MITgcm
5720    (without invoking ECCO_PACKAGE).    (without invoking ECCO_PACKAGE).
# Line 1083  o modifications to gradient check packag Line 5722  o modifications to gradient check packag
5722    - enable centered differences    - enable centered differences
5723    - modified format of standard output    - modified format of standard output
5724    
5725  checkpoint45b_post  checkpoint45b_post (2002/05/30)
5726  o cleaned exchange calls in cg2d  o cleaned exchange calls in cg2d
5727  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step  o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
5728  o included CPP option SINGLE_LAYER_MODE in thermodynamics  o included CPP option SINGLE_LAYER_MODE in thermodynamics
# Line 1095  o in initialise_varia, moved call packag Line 5734  o in initialise_varia, moved call packag
5734    (corresponding adjustment of TAF tape initialisation).    (corresponding adjustment of TAF tape initialisation).
5735  o in calc_diffusivity/calc_viscosity extended domain to full overlap.  o in calc_diffusivity/calc_viscosity extended domain to full overlap.
5736    
5737  checkpoint45a_post  checkpoint45a_post (2002/05/01)
5738  o compute Rho over the whole domain (extend iMin,jMin indices)  o compute Rho over the whole domain (extend iMin,jMin indices)
5739  o specific exchange for X-slice domain (case Ny=1)  o specific exchange for X-slice domain (case Ny=1)
5740  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code  o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
# Line 1115  o errorMessageUnit set non-equal zero in Line 5754  o errorMessageUnit set non-equal zero in
5754    (conflict on some platforms, e.g. IBM SP3)    (conflict on some platforms, e.g. IBM SP3)
5755  o modified carbon verif.  o modified carbon verif.
5756    
5757  checkpoint44h_pre  checkpoint44h_pre (2002/03/14)
5758  o vertical grid option: allow to put the Interface at the middle between  o vertical grid option: allow to put the Interface at the middle between
5759    2 cell-centers ; replace delZ in pkg/kpp by drF.    2 cell-centers ; replace delZ in pkg/kpp by drF.
5760  o GM Advective form: Tracers are advected using the residual transport (=  o GM Advective form: Tracers are advected using the residual transport (=
5761    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.    Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
5762    
5763  checkpoint44g_post  checkpoint44g_post (2002/03/05)
5764  o fix surface correction term in multiDimAdvection (affects plume_on_slope  o fix surface correction term in multiDimAdvection (affects plume_on_slope
5765    results) ; ifdef missing in thermodynamics.F    results) ; ifdef missing in thermodynamics.F
5766    
# Line 1186  o merge of relevant stuff from the ecco- Line 5825  o merge of relevant stuff from the ecco-
5825  o check parameters & config (chkpt44a_pre,post)  o check parameters & config (chkpt44a_pre,post)
5826  o OBC and NonLin_FrSurf.  o OBC and NonLin_FrSurf.
5827    
5828  checkpoint44  checkpoint44 (2002/01/18)
5829  o fix bug in mom_vi_del2uv  o fix bug in mom_vi_del2uv
5830  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)
5831  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 1194  o update AIM experiments (NCEP input fil Line 5833  o update AIM experiments (NCEP input fil
5833  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)  o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
5834  o added some stuff for AD  o added some stuff for AD
5835    
5836  checkpoint43  checkpoint43 (2001/09/28)
5837  o added two new advection tests  o added two new advection tests
5838  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test
5839  o added test of H&S94 with free surface on cube  o added test of H&S94 with free surface on cube
5840  o some final mods for gradient check, adjoint,...  o some final mods for gradient check, adjoint,...
5841    
5842  checkpoint42  checkpoint42 (2001/09/27)
5843    Fixed AD-related problems:    Fixed AD-related problems:
5844  o Store directives up-to-date with re-arranged Adams-Bashforth  o Store directives up-to-date with re-arranged Adams-Bashforth
5845    (mainly thermodynamics.F)    (mainly thermodynamics.F)
# Line 1212  o Modified store directives for split of Line 5851  o Modified store directives for split of
5851    for the case ALLOW_KPP    for the case ALLOW_KPP
5852  o Cleaned argument list for timestep_tracer.F  o Cleaned argument list for timestep_tracer.F
5853    
5854  checkpoint41  checkpoint41 (2001/09/27)
5855  o re-formatted/added comments in prologues of key subroutines  o re-formatted/added comments in prologues of key subroutines
5856    to work with protex    to work with protex
5857    
5858  checkpoint40  checkpoint40 (2001/09/27)
5859  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
5860  o added FLT (floats) package from Arne along with demo. experiment  o added FLT (floats) package from Arne along with demo. experiment
5861  o re-arranged Adams-Bashforth scheme for tracers to allow easier  o re-arranged Adams-Bashforth scheme for tracers to allow easier
# Line 1225  o more mods for non-linear free-surface Line 5864  o more mods for non-linear free-surface
5864  o modified multi-dim method to work on cube  o modified multi-dim method to work on cube
5865  o bug fix in KPP (from DM)  o bug fix in KPP (from DM)
5866    
5867  checkpoint40pre9  checkpoint40pre9 (2001/09/27)
5868  o added DST advection schemes  o added DST advection schemes
5869  o fix MPI bug on SGI's  o fix MPI bug on SGI's
5870  o modifications for non-linear free-surface  o modifications for non-linear free-surface
# Line 1235  o changes to commenting of arguments for Line 5874  o changes to commenting of arguments for
5874  o added/updated many matlab scripts  o added/updated many matlab scripts
5875  o added multi-dimensional advection method for tracers  o added multi-dimensional advection method for tracers
5876        
5877  checkpoint40pre8  checkpoint40pre8 (2001/09/05)
5878  o new package rw/  o new package rw/
5879    Added method for dumping intermediate local arrays:    Added method for dumping intermediate local arrays:
5880    mdsio_writetile - same as mdsio_writefield except works from inside    mdsio_writetile - same as mdsio_writefield except works from inside
# Line 1254  o TAMC-related update to cope with mom_f Line 5893  o TAMC-related update to cope with mom_f
5893    currently nothing implemented to switch this storing off    currently nothing implemented to switch this storing off
5894    in case fluxform is used since no CPP flag available).    in case fluxform is used since no CPP flag available).
5895    
5896  checkpoint40pre7  checkpoint40pre7 (2001/08/14)
5897  o bug fix in dynamics.F  o bug fix in dynamics.F
5898    calc_viscosity called before k=1,Nr loop.    calc_viscosity called before k=1,Nr loop.
5899  o added some #ifdef's ALLOW_PASSIVE_TRACER  o added some #ifdef's ALLOW_PASSIVE_TRACER
5900  o cleaned initialisations in ctrl_map_ini  o cleaned initialisations in ctrl_map_ini
5901    related to TAF    related to TAF
5902    
5903  checkpoint40pre6  checkpoint40pre6 (2001/08/13)
5904  o split dynamics into thermodynamics & dynamics  o split dynamics into thermodynamics & dynamics
5905  o corresponding split of calc_diffusivity into  o corresponding split of calc_diffusivity into
5906    calc_diffusivity, calc_viscosity    calc_diffusivity, calc_viscosity
# Line 1269  o corresponding split of calc_diffusivit Line 5908  o corresponding split of calc_diffusivit
5908  o Added diffkr, kapgm to control variables  o Added diffkr, kapgm to control variables
5909  o bug fix in gmredi_slope_limit for ldd97  o bug fix in gmredi_slope_limit for ldd97
5910    
5911  checkpoint40pre5  checkpoint40pre5 (2001/07/31)
5912  o proper initialization of Adams-Bashforth time stepping  o proper initialization of Adams-Bashforth time stepping
5913    + uses forward step for very first step of model (iter=0)    + uses forward step for very first step of model (iter=0)
5914  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 1283  o added new expt "solid-body.cs-32x32x1" Line 5922  o added new expt "solid-body.cs-32x32x1"
5922    + this uses an alternative form of ini_curvilinear_grid.F which    + this uses an alternative form of ini_curvilinear_grid.F which
5923      is not necessarily any better than the current one...      is not necessarily any better than the current one...
5924    
5925  checkpoint40pre4  checkpoint40pre4 (2001/07/30)
5926  o added re-initialisations of utrans,vtrans,rtrans in  o added re-initialisations of utrans,vtrans,rtrans in
5927    calc_common_factors which are crucial for TAF.    calc_common_factors which are crucial for TAF.
5928  o extended iMin,jMin range for calc_common_factors,  o extended iMin,jMin range for calc_common_factors,
# Line 1291  o extended iMin,jMin range for calc_comm Line 5930  o extended iMin,jMin range for calc_comm
5930  o added option ALLOW_PASSIVE_TRACER  o added option ALLOW_PASSIVE_TRACER
5931  o a few minor updates and fixes  o a few minor updates and fixes
5932    
5933  checkpoint40pre3  checkpoint40pre3 (2001/07/13)
5934  o created calc_gtr1.F for gad package  o created calc_gtr1.F for gad package
5935  o split the_main_loop and re-introduced forward_step  o split the_main_loop and re-introduced forward_step
5936  o some recomputations of nIter0 for TAMC  o some recomputations of nIter0 for TAMC
5937    
5938  checkpoint40pre2  checkpoint40pre2 (2001/07/13)
5939  o Updated to latest branch of AJA, JMC  o Updated to latest branch of AJA, JMC
5940  o Added gradient check package  o Added gradient check package
5941  o Added routines for passive tracer handling  o Added routines for passive tracer handling
5942  o Added carbon sequestration sensitivity experiment  o Added carbon sequestration sensitivity experiment
5943    
5944  checkpoint39  checkpoint39 (2001/05/14)
5945   o Modifications and fixes to support TAMC   o Modifications and fixes to support TAMC
5946     (mainly missing or wrong directives)     (mainly missing or wrong directives)
5947   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 1316  checkpoint39 Line 5955  checkpoint39
5955           (NB: this is not the full ECCO environment)           (NB: this is not the full ECCO environment)
5956   o disabled some packages by default in genmake   o disabled some packages by default in genmake
5957    
5958  checkpoint38  checkpoint38 (2001/04/10)
5959   o see notes_c37_adj.txt   o see notes_c37_adj.txt
5960   o corrected wrong layer index in external_forcing_t   o corrected wrong layer index in external_forcing_t
5961   o replaced the_main_loop/forward_step by the_main_loop   o replaced the_main_loop/forward_step by the_main_loop
# Line 1324  checkpoint38 Line 5963  checkpoint38
5963     (replaced criteria for initial/final state)     (replaced criteria for initial/final state)
5964   o added runtime flag for pre-C35 pickups: usePickupBeforeC35   o added runtime flag for pre-C35 pickups: usePickupBeforeC35
5965    
5966  checkpoint37  checkpoint37 (2001/03/13)
5967   o mdsio.F routine split and packaged in pkg/mdsio   o mdsio.F routine split and packaged in pkg/mdsio
5968     (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
5969      used unless genmake -disable=mdsio)      used unless genmake -disable=mdsio)
# Line 1341  checkpoint37 Line 5980  checkpoint37
5980   o Non-Hydrostatic pickup file Pb fixed.   o Non-Hydrostatic pickup file Pb fixed.
5981   o bug with Rigid-lid version (since c35) fixed.     o bug with Rigid-lid version (since c35) fixed.  
5982    
5983  checkpoint36  checkpoint36 (2001/02/20)
5984   o implement Crank-Nickelson barotropic time-stepping   o implement Crank-Nickelson barotropic time-stepping
5985   o recover Time-Average diagnostics   o recover Time-Average diagnostics
5986   o fix Pb in checkpoint (PR#19)   o fix Pb in checkpoint (PR#19)
5987   o AIM become a standard package ; clean unused CPP_kees   o AIM become a standard package ; clean unused CPP_kees
5988    
5989  checkpoint35  checkpoint35 (2001/02/08)
5990   o subtantial rewrite of dynamics.f   o subtantial rewrite of dynamics.f
5991   o allows staggered time-stepping   o allows staggered time-stepping
5992   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt   o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
5993   o added bottom drag (linear + quadratic)   o added bottom drag (linear + quadratic)
5994    
5995  checkpoint34  checkpoint34 (2001/01/30)
5996   o Modified exchange routines for correct reverse simulation.   o Modified exchange routines for correct reverse simulation.
5997   o Added verification output to comply with bug fix in impldiff.F   o Added verification output to comply with bug fix in impldiff.F
5998     as of c33 (exp2, natl_box).     as of c33 (exp2, natl_box).
# Line 1364  checkpoint34 Line 6003  checkpoint34
6003   o Added routine GLOBAL_SUM_INT to global_sum.F   o Added routine GLOBAL_SUM_INT to global_sum.F
6004   o Added mdsio_gl.F for ECCO purposes.   o Added mdsio_gl.F for ECCO purposes.
6005    
6006  checkpoint33  checkpoint33 (2000/11/30)
6007   o Fixed bug in lower BC in impldiff.F   o Fixed bug in lower BC in impldiff.F
6008   o Fixed confusion about units of forcing arrays in FFIELDS.h   o Fixed confusion about units of forcing arrays in FFIELDS.h
6009     namely Fu,Fv,Qnet,Qsw,EmPmR:     namely Fu,Fv,Qnet,Qsw,EmPmR:
# Line 1382  checkpoint33 Line 6021  checkpoint33
6021       possibly use them.       possibly use them.
6022   o Corrected genmake to delete a temporary file during configuration   o Corrected genmake to delete a temporary file during configuration
6023    
6024  checkpoint32  checkpoint32 (2000/11/13)
6025   o Scaling of forcing fields moved from external_forcing.F to   o Scaling of forcing fields moved from external_forcing.F to
6026     external_fields_scale.F, called directly after loading fields.     external_fields_scale.F, called directly after loading fields.
6027   o Surface relaxation terms added to surface tendency fields in   o Surface relaxation terms added to surface tendency fields in
# Line 1393  checkpoint32 Line 6032  checkpoint32
6032   o Modifications and bug fixes in KPP package.   o Modifications and bug fixes in KPP package.
6033   o Verification experiment for KPP added (verification/nat_box/)   o Verification experiment for KPP added (verification/nat_box/)
6034    
6035  checkpoint31  checkpoint31 (2000/09/11)
6036   o Packages interface brought in line with defined standard   o Packages interface brought in line with defined standard
6037     -> new routines packages_...F     -> new routines packages_...F
6038     -> changes in initialise_fixed.F, initialise_varia.F     -> changes in initialise_fixed.F, initialise_varia.F
# Line 1410  checkpoint31 Line 6049  checkpoint31
6049     - not yet tested for GMRedi.     - not yet tested for GMRedi.
6050     - not yet tested for KPP.     - not yet tested for KPP.
6051    
6052  checkpoint30  checkpoint30 (2000/07/13)
6053   o Updates for OBCs   o Updates for OBCs
6054   o New experiment for test OBCs (internal_wave)   o New experiment for test OBCs (internal_wave)
6055   o New output.txt in verification/exp4/results/   o New output.txt in verification/exp4/results/
# Line 1419  checkpoint30 Line 6058  checkpoint30
6058   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.)
6059     and entry for T90 in genmake     and entry for T90 in genmake
6060    
6061  checkpoint29  checkpoint29 (2000/06/21)
6062   o packaged KPP and GM/Redi   o packaged KPP and GM/Redi
6063    
6064  checkpoint28  checkpoint28 (2000/06/09)
6065   o Corrected initialization of hFacMin for difference vertical coordinates   o Corrected initialization of hFacMin for difference vertical coordinates
6066   o Modified calculation of partial cell thickness to more robust algorithm   o Modified calculation of partial cell thickness to more robust algorithm
6067   o config_summary.F: replaced write_1D_... by write_0D_...   o config_summary.F: replaced write_1D_... by write_0D_...
# Line 1435  checkpoint28 Line 6074  checkpoint28
6074     included store directives and tape key computations required for TAMC.     included store directives and tape key computations required for TAMC.
6075   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC   o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
6076    
6077  checkpoint27  checkpoint27 (2000/04/10)
6078   o fixed calc_isoslopes() to so that cancellation of terms in tensor   o fixed calc_isoslopes() to so that cancellation of terms in tensor
6079     formulation works properly with variable resolution.     formulation works properly with variable resolution.
6080   o restructured the calling tree between the_model_main() and dynamics()   o restructured the calling tree between the_model_main() and dynamics()
# Line 1443  checkpoint27 Line 6082  checkpoint27
6082   o introduced initialization file pSurfInitFile for free surface (cg2d_x)   o introduced initialization file pSurfInitFile for free surface (cg2d_x)
6083     in new routine ini_psurf()     in new routine ini_psurf()
6084    
6085  checkpoint26  checkpoint26 (2000/04/05)
6086   o moved some #ifdef in optional routines to encompass everything   o moved some #ifdef in optional routines to encompass everything
6087     except the argument declarations. This was using up some memory.     except the argument declarations. This was using up some memory.
6088   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 1453  checkpoint26 Line 6092  checkpoint26
6092     (macros are now in eesupp/inc/CPP_EEMACROS.h)     (macros are now in eesupp/inc/CPP_EEMACROS.h)
6093   o patch for 2 processor JAM mode   o patch for 2 processor JAM mode
6094    
6095  checkpoint25  checkpoint25 (2000/03/15)
6096   o updates for OBCs and NH   o updates for OBCs and NH
6097   o dramatically reduced memory usage   o dramatically reduced memory usage
6098   o added "JAM" routines for use on Artic network   o added "JAM" routines for use on Artic network
# Line 1464  checkpoint25 Line 6103  checkpoint25
6103      an explicit free-surface option)      an explicit free-surface option)
6104   o initial state input files for U and V   o initial state input files for U and V
6105    
6106  checkpoint24  checkpoint24 (1999/08/02)
6107   o Removed some spurious "REAL"s   o Removed some spurious "REAL"s
6108   o Updated KPP to latest version from JPL   o Updated KPP to latest version from JPL
6109   o Added a COS(latitude) in horizontal viscosity   o Added a COS(latitude) in horizontal viscosity
6110    
6111  checkpoint23  checkpoint23 (1999/05/26)
6112   o Added del^4 diffusion for salt and temperature   o Added del^4 diffusion for salt and temperature
6113   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)   o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
6114    
6115  checkpoint22  checkpoint22 (1999/05/18)
6116   o Made many small changes: implicit none, format(i5), etc...   o Made many small changes: implicit none, format(i5), etc...
6117   o Introduced KPP mixing scheme (compiles and runs but *not* tested)   o Introduced KPP mixing scheme (compiles and runs but *not* tested)
6118    
6119  checkpoint21  checkpoint21 (1999/05/18)
6120   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)
6121   o Split-up mid-level I/O routines   o Split-up mid-level I/O routines
6122   o Updated input data for experiments 0,1,2,4 and 5   o Updated input data for experiments 0,1,2,4 and 5
6123   o Finally removed the genmake.* scripts (everyone seems happy with genmake)   o Finally removed the genmake.* scripts (everyone seems happy with genmake)
6124    
6125  checkpoint20  checkpoint20 (1999/03/22)
6126   o Tidied up open-boundaries some more   o Tidied up open-boundaries some more
6127   o Added non-hydrostatic code   o Added non-hydrostatic code
6128   o Fixed some input data   o Fixed some input data
6129   o Modified MPI start-up to work in "coupled" context.   o Modified MPI start-up to work in "coupled" context.
6130    
6131  checkpoint19  checkpoint19 (1998/12/15)
6132   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
6133   o Added new code for open boundaries.   o Added new code for open boundaries.
6134   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
# Line 1497  checkpoint19 Line 6136  checkpoint19
6136   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
6137   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.
6138    
6139  checkpoint18  checkpoint18 (1998/11/30)
6140   o Further changes for optional code generation with   o Further changes for optional code generation with
6141     CPP - ugh!     CPP - ugh!
6142    
6143  checkpoint17  checkpoint17 (1998/11/03)
6144   o Beginning to incorporating modularity   o Beginning to incorporating modularity
6145     for supporting atmos. and ocean configs.     for supporting atmos. and ocean configs.
6146   o Small changes for TAMC complinace   o Small changes for TAMC complinace
6147   o New ultra simple test case. Barotropic box   o New ultra simple test case. Barotropic box
6148     configuration "exp0".     configuration "exp0".
6149    
6150  checkpoint16  checkpoint16 (1998/10/28)
6151   o Minor changes to exchange routines to support   o Minor changes to exchange routines to support
6152     accumulation in reverse mode. Adjoint of an     accumulation in reverse mode. Adjoint of an
6153     assignment is an addition.     assignment is an addition.
# Line 1516  checkpoint16 Line 6155  checkpoint16
6155     syntax) and by g77 under Linux ( 72 character     syntax) and by g77 under Linux ( 72 character
6156     limit ).     limit ).
6157    
6158  checkpoint15  checkpoint15 (1998/09/29)
6159   Rewrote exchange routines to allow   Rewrote exchange routines to allow
6160   o General tile <-> tile connectivity.   o General tile <-> tile connectivity.
6161   o TAMC reverse mode flag ( is this really needed? )   o TAMC reverse mode flag ( is this really needed? )
# Line 1525  checkpoint15 Line 6164  checkpoint15
6164     shmput/shmget, VIA, SYSV shmem and every other cool     shmput/shmget, VIA, SYSV shmem and every other cool
6165     communication method.     communication method.
6166    
6167  checkpoint14  checkpoint14 (1998/09/09)
6168   Consistent isomorphism chages made. These allow dynamical core   Consistent isomorphism chages made. These allow dynamical core
6169   to support both pressure and meters as a vertical coordinate.   to support both pressure and meters as a vertical coordinate.
6170    
6171  checkpoint13  checkpoint13 (1998/07/17)
6172   Release which corrects global_max problem and a couple   Release which corrects global_max problem and a couple
6173   of KGM time-averaging diagnostic errors. Also contains   of KGM time-averaging diagnostic errors. Also contains
6174   a double-gyre experiment setup as well as the baseline   a double-gyre experiment setup as well as the baseline
# Line 1544  branch-point-rdot Line 6183  branch-point-rdot
6183   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
6184   we've actually tested it...   we've actually tested it...
6185    
6186  checkpoint12  checkpoint12 (1998/07/08)
6187   Tidy up and added generic genmake script (formerly   Tidy up and added generic genmake script (formerly
6188   configure script).   configure script).
6189   Released to testers.   Released to testers.
6190    
6191  checkpoint11  checkpoint11 (1998/07/02)
6192   Re-arranged initialise() and introduced ini_vertical_grid()   Re-arranged initialise() and introduced ini_vertical_grid()
6193   and ini_masks_etc().   and ini_masks_etc().
6194    
6195  checkpoint10  checkpoint10 (1998/07/01)
6196   Introduced the configure script.   Introduced the configure script.
6197   Separated out the diags package.   Separated out the diags package.
6198   Added template for writing time-averages of tile/intermediate quantities.   Added template for writing time-averages of tile/intermediate quantities.
6199   Updated SIZE.h in exp2 and made the data big-endian.   Updated SIZE.h in exp2 and made the data big-endian.
6200    
6201  checkpoint9  checkpoint9 (1998/06/22)
6202   MPI fix. Filename changes (meta/data). salbin*y stuff.   MPI fix. Filename changes (meta/data). salbin*y stuff.
6203   General tidy-up.   General tidy-up.
6204   SST.bin SSS.bin added to verification/exp2   SST.bin SSS.bin added to verification/exp2
6205    
6206  checkpoint8  checkpoint8 (1998/06/22)
6207   Inludes time-dependant forcing and time-averaging.   Inludes time-dependant forcing and time-averaging.
6208   Works at 4x4 and 2.8125x2.8125 global   Works at 4x4 and 2.8125x2.8125 global
6209    
# Line 1574  checkpoint7-4degree-ref Line 6213  checkpoint7-4degree-ref
6213   model etc..   model etc..
6214   Configured for verification/exp2 - 4 degree global, two process.   Configured for verification/exp2 - 4 degree global, two process.
6215    
6216  checkpoint7  checkpoint7 (1998/06/15)
6217   Created by cnh   Created by cnh
6218   Simple 4 degree global simulation   Simple 4 degree global simulation
6219   configuration.   configuration.
# Line 1582  checkpoint7 Line 6221  checkpoint7
6221   hydrography, bathymetry etc   hydrography, bathymetry etc
6222   Does not include Heat Flux and E-P   Does not include Heat Flux and E-P
6223    
6224  checkpoint6  checkpoint6 (1998/06/08)
6225   Created by cnh   Created by cnh
6226   merged checkpoint5 with CD and   merged checkpoint5 with CD and
6227   spherical polar code.   spherical polar code.
6228   Still some problems with GM Redi   Still some problems with GM Redi
6229   abd full topography.   abd full topography.
6230    
6231  checkpoint5  checkpoint5 (1998/06/08)
6232   Created by AJA   Created by AJA
6233   contains updates to GM Redi   contains updates to GM Redi
6234   and reordered timestepping loop   and reordered timestepping loop
6235   for Implicit Diffusion.   for Implicit Diffusion.
6236    
6237  checkpoint4  checkpoint4 (1998/05/30)
6238   Created by cnh   Created by cnh
6239   Contains memory saving macros ( _rdxc etc..) for when   Contains memory saving macros ( _rdxc etc..) for when
6240   grid variations are limited.   grid variations are limited.
6241   Contains polynomial coeffs for EOS and knudsen program   Contains polynomial coeffs for EOS and knudsen program
6242   for generation.   for generation.
6243    
6244  checkpoint3  checkpoint3 (1998/05/26)
6245   Created by cnh   Created by cnh
6246   Added extra flags for runtime options   Added extra flags for runtime options
6247   Added this file   Added this file

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