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Revision 1.1497 - (hide annotations) (download)
Mon Aug 29 17:23:24 2011 UTC (12 years, 8 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint63b
Changes since 1.1496: +2 -1 lines
tag checkpoint63b

1 jmc 1.1497 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1496 2011/08/29 03:00:09 jmc Exp $
2 jmc 1.475 $Name: $
3 cnh 1.1
4     Notes on tags used in MITgcmUV
5     ==============================
6 dfer 1.1157
7 jmc 1.1497 checkpoint63b (2011/08/29)
8 jmc 1.1496 o pkg/ebm:
9     - fix sign of runoff;
10     - update directly forcing fields (Qnet,EmPmR) to use standard
11     external_forcing_surf.F (remove ebm_forcing_surf.F);
12     - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
13     - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
14     and apply relaxation towards corresponding SST field (2-D map or ZonAver).
15     - update global_ocean_ebm parameters file data and update output (fwd+ad).
16 jmc 1.1494 o verification/matrix_example:
17 jmc 1.1495 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
18     MPI and mutlti-threaded testing.
19     o pkg/matrix:
20     - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
21     - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
22     - fix for multi-threaded (remove DATA statement);
23     - use standard DIFFERENT_MULTIPLE function;
24     - add MATRIX_OPTIONS.h
25     o verification/matrix_example:
26 jmc 1.1494 To allow to split the domain in several tiles, change the domain size
27     from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
28     Western side) of land points.
29     o (*_)write_pickup:
30     - fix few bugs in mypackage_read/write_pickup.F
31     - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
32     array of length 1 (was caught by compiler syntax-check).
33 jmc 1.1493 o pkg/diagnostics (velocity potential solver):
34     - fix initialisation of main diagonal matrix (for overlap values)
35 jmc 1.1492 o tools/build_options:
36     - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
37     into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
38     - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
39     * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
40     * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
41     and use "-devel" testreport option for standard testing on baudelaire.
42 jmc 1.1491 o pkg/grdchk:
43     - Assume that all gradient-check position are within the same tile
44     corresponding to global indices (iGloTile,jGloTile) and that
45     positions (i,j indices or nbeg) are local to this tile;
46     - set tile local-indices and proc. number according to tile global-indices;
47     - remove grdchkwhichproc from namelist (retired param);
48     - send adjoint gradient to all procs so that all procs print it to STDOUT;
49     - switch on MPI test for global_ocean.90x40x15 AD test experiment.
50 dimitri 1.1489 o adding package bbl (Bottom Boundary Layer)
51     description in MITgcm/pkg/bbl/bbl_description.tex
52     example/test experiment in MITgcm_contrib/bbl
53 heimbach 1.1488 o adjoint verifications
54 jmc 1.1490 - changed 5 experiments to multi-tiles
55 heimbach 1.1488 * global_ocean.90x40x15
56     * obcs_ctrl
57     * offline_exf_seaice
58     * tutorial_dic_adjoffline
59     * tutorial_tracer_adjsens
60     changed reference output for those that crossed tile boundaries
61     (changed choices of gradient check positions)
62 jmc 1.1490 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
63 heimbach 1.1488 - temporary bug fix in grdchk_loc.F for obcs
64 jmc 1.1487 o genmake2 & testreport
65     - add target "obj" (just for OBJFILES files) to Makefile;
66     - add option to specify FEXTRAFLAGS on command line.
67 jmc 1.1486 o pkg/mypackage:
68     - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
69    
70 jmc 1.1485 checkpoint63a (2011/08/02)
71 jmc 1.1484 o pkg/diagnostics (velocity potential):
72     - fix velocity-potential calculation when using OBCS: balance net inflow
73     at each level (new S/R OBCS_DIAG_BALANCE).
74     - fix some of the problems with OBCS in stream-function calculation.
75 mlosch 1.1483 o pkg/exf/exf_readparms.F
76 jmc 1.1484 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
77 mlosch 1.1483 EXF_NML_OBCS) more consistent, so that you need not have these lists
78     in data.exf when they are not used.
79 mlosch 1.1481 o optim/optim_readdata.F:
80     - add some output about obcs variables that might help debugging
81 mlosch 1.1482 - add a check about nvarlength
82 mlosch 1.1480 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
83 jmc 1.1479 o pkg/diagnostics (velocity potential):
84     - fix mask for OBCS (still problems in stream-function with OBCS);
85     - add specific parameter (default = main code CG2D params) for solver;
86     - in case of poor convergence, use solution corresponding to lowest residual.
87 mlosch 1.1478 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
88     adjoint code. In general statements like tmpscal=fld(i,j) are problematic
89     and should be avoided where possible.
90 jmc 1.1477 o model/src (rStar):
91     - include r* effect on reference-state (PhiRef) in totPhiHyd
92     (so that it's really the potential anomaly at the cell center);
93     affect solution only if z* with full pressure in EOS.
94     - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
95     update output (because of z* in totPhiHyd and viscA4 changes);
96     - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
97     @ constant r) until interpolation at constant r is implemented.
98     o pkg/diagnostics
99     - fix RCENTER diagnostics in case cell center is not at interface middle
100 mlosch 1.1476 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
101     this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
102     that THETA and SALT are "conservative temperature" and "absolute
103     salinity"
104     o pkg/ctrl
105     - fix computation of endrec in s/r ctrl_init_rec
106     - ctrl_pack/unpack_*: remove unused variables and some obsolete code
107 mlosch 1.1475 o pkg/seaice/seaice_growth.F
108     - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
109     remove then obsolete STORE directives
110     - fix STORE directives for tice and tices, so that only the
111     appropriate part of the fields are stored (and not the entire
112 jmc 1.1477 field); update global_ocean.cs32x15.seaice AD output.
113 mlosch 1.1475 - cosmetic changes: adjust CPP flags and indentation for better
114     legibilty
115     o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
116     Chris Wilson)
117 jmc 1.1474 o pkg/gmredi:
118     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
119     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
120    
121 jmc 1.1485 checkpoint63 (2011/07/11)
122 jmc 1.1472 o pkg/exch2:
123     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
124     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
125     (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
126     increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
127 jmc 1.1470 o pkg/diagnostics:
128     - deal with pairs of post-processed diags which are computed together; in
129     particular, re-order list of diags within 1 file to save 2nd computation.
130     - add S/R to compute velocity stream-function (called after velocity-potential
131     calculation) from divergence free transport -> new diagnostics "PsiVEL".
132 jmc 1.1471 - add parameter to select grid-point location where PsiVEL == 0.
133 jmc 1.1470 o eesupp/src:
134     new S/R to calculate cumulated sum on tiled array, corner grid-cell location
135     (specific S/R needed with exch2 topology - for now, just print an error msg)
136 heimbach 1.1468 o pkg/shelfice
137     - Implement friction velocity-dependent transfer coefficients following
138     Holland and Jenkins, JPO, 1999
139     Original code by M. Losch with small modifs.
140     Enable with CPP option SHI_ALLOW_GAMMAFRICT
141     and runtime flag SHELFICEuseGammaFrict
142 jmc 1.1467 o verification lab_sea & global_ocean.cs32x15:
143     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
144     does not miss some dependencies (but is slower) and also works with many files
145     (default makedepend limitation for AD built).
146     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
147 jmc 1.1466 o pkg/diagnostics:
148     - add run-time parameter "useMissingValue" (def=False) to fill land-point
149     (i.e., where mask=0) with MissingValue ; used only in MNC output file.
150     This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
151     - Extend the use of "missing_value" setting from data.diagnostics for the case
152     of counter-diagnostics (where fraction-weight is zero). This applies both to
153     MNC and MDS output files.
154 gforget 1.1465 o pkg/seaice/seaice_growth.F:
155 ifenty 1.1469 - add 'a priori' cap of latent heat flux based on actual mass considerations
156     when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
157     non-legacy seaice_solve4temp.
158     - add diagnostic of the residual sublimation freshwater flux (the freshwater
159 jmc 1.1470 flux taken from the ocean if the total actual latent heat fluxes exceed
160 ifenty 1.1469 the maximum)
161 gforget 1.1465 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
162     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
163     - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
164     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
165     - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
166     - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
167 ifenty 1.1464 o verification 1D_ocean_ice_column:
168     made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
169     update results
170 jmc 1.1461 o pkg/diagnostics:
171     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
172     which are not filled-up but computed from other diags ; In this case, the mate
173     diag points to the primary (filled-up) diag to used for post processing.
174     - Update Velocity-potential computation using post-processed diag framework.
175 jmc 1.1463 ==> Change the ordering of fields and time-periods in MDS output file
176 jmc 1.1462 when using periodic averaging: now writes one time record with the full set
177     of fields for this time period, then the next time reccord (it used to be
178     one field with the full set of time records then the next field).
179 jmc 1.1463 Note: this is now similar to NetCDF (MNC) output file. <==
180 jmc 1.1461
181 jmc 1.1460 checkpoint62z (2011/06/21)
182 heimbach 1.1456 o adjoint monitor:
183     - Add adjoint monitor output for packages exf, seaice
184 heimbach 1.1457 and update relevant testreport output
185 gforget 1.1455 o pkg/seaice:
186     - re-order diags inits so that they appear in order in available_diagnostics.log
187     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
188     area/heff/hsnow preceeding thermodynamic growth/melt.
189     - modified diag: SIdA; output actual effect, as the description states.
190     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
191     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
192 jmc 1.1459 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
193 gforget 1.1455 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
194     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
195 jmc 1.1459 - added diagnostics for seaice generic tracers (SItr*).
196 gforget 1.1455 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
197     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
198 heimbach 1.1458 I. Fenty: 18-Jun-2011:
199     Minor changes to seaice package:
200     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
201     added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
202 jmc 1.1459 - Differentiated "regularization variables" from "floor variables"
203 heimbach 1.1458 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
204     * hiceMin became SEAICE_hice_reg (old hiceMin)
205     (with _reg meaning regularization variable)
206     - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
207     so as to ensure energy conservation when going between phases
208 jmc 1.1459 - A22 was not used anywhere
209 heimbach 1.1458 2) Changed regularization procedure for heffActual and hsnowActual to ensure
210     well-boundedness and smooth adjoint in seaice_growth.F
211     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
212     because the old regularization always set heffActual >= 0.05 cm
213     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
214 jmc 1.1459 on AREA when HEFF > 0.
215     - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
216     requiring that DISABLE_AREA_FLOOR *not* be defined
217 heimbach 1.1458 Affected verifications:
218     - 1D_ocean_ice_column (output.txt output_adm.txt)
219     - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
220 jmc 1.1453 o pkg/diagnostics:
221     - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
222     - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
223     (was _RL, now integer) with option = 0 to retrieve all levels.
224 jmc 1.1454 - add pieces of code to compute velocity potential at each level (new diagnostics
225     PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
226     for now, using same params as CG2D (target-resisual, max Nb of iter ...).
227 jmc 1.1459 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
228     diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
229     and in diagnostics_fract_fill.F (do not need a valid pointer for the
230     diagnostics counter-mate); check that definition of counter-diagnostic
231     includes a valid counter-mate (in diagnostics_set_levels.F).
232 jmc 1.1452 o model/src (rStar):
233     - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
234     affect solution only if z* with full pressure in EOS;
235     update output of test-exp global_ocean.90x40x15.
236     o pkg/seaice:
237 gforget 1.1451 - introduce siEps=1e-5 parameter
238     - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
239     - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
240 jmc 1.1452 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
241 gforget 1.1451 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
242     as well as ice cover age and ridging index (attached to AREA).
243 jmc 1.1452 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
244     SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
245 gforget 1.1451 Up to SItrMaxNum=3 tracers can be used simultaneously.
246     o pkg/salt_plume:
247 jmc 1.1452 -introduce SPsalFRAC run time parameter that sets the fraction of the
248     salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
249     that gets vertically redistributed (fluxed down) by pkg/salt_plume.
250 jmc 1.1450 o model debug options:
251     - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
252     in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
253     - Refine debug-msg printing selection (3 new levels):
254     debugMode : controls printing of debug messages (sequence of S/R calls).
255     debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
256     debLevZero = 0 ; /* level of disabled aux. msg printing */
257     debLevA = 1 ; /* level of minimum aux. msg printing */
258     debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
259     debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
260     debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
261     debLevE = 5 ; /* level of extensive debug printing */
262     New debugLevel default: with default debugMode value (=F),
263     = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
264     and if debugMode=T, default debugLevel = 4 (debLevD).
265     Relation with previous settings:
266     debLevB (=2) corresponds to former debLevA (=1)
267     debLevD (=4) corresponds to former debLevB (=2)
268     Note:
269     a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
270     b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
271     to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
272     - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
273     detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
274 jmc 1.1449 o pkg/obcs:
275     - change OBCSfixTopo default from True to False (should not change the results);
276     keep OBCSfixTopo=T in verification-exp. seaice_obcs.
277 jmc 1.1448 o pkg/thsice:
278     - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
279     2nd layer seaice sublimation (unlikely to happen)
280     - use Interior mask for OBCS in thsice_advection.F (similar to what is
281     done in gad_advection & seaice_advection).
282 heimbach 1.1447 o adjoint:
283     bug fix spotted by Gael Forget:
284     seaice_advection and thsice_advection still had
285     legacy CPP options to avoid CS corner updates for adjoint
286 jmc 1.1446 o pkg/seaice:
287     => Change some of the defaults (2011/05/29):
288     - change SEAICEuseFluxForm default (from False to True)
289     - change DIFF1 default (from 0.004 m/s to 0. m/s)
290     And print warnings if DIFF1 is not set in data.seaice and centered
291     avection scheme is used without any diffusion.
292     also:
293     - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
294     - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
295     - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
296     other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
297     #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
298     update results of test exp.:
299     lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
300     output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
301     output_adm.noseaicedyn (SEAICEuseFluxForm=T)
302     offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
303     seaice_obcs: output (SEAICEuseFluxForm=T)
304     and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
305     for standard fwd & AD lab_sea tests (to keep the same output).
306 gforget 1.1445 o pkg/seaice/seaice_growth.F:
307 jmc 1.1446 - use Ian Fenty's capping formulas for actual ice
308 gforget 1.1445 thickness thoughout EVOLUTION branch.
309     - put treatment pathological case #2) in CPP brackets
310     (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
311 jmc 1.1446 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
312 gforget 1.1445 o pkg/seaice:
313     - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
314 jmc 1.1446 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
315     also pass fac as a param, which can be 1. (to update the tendency
316 gforget 1.1445 field) or the time step (to update the field itself).
317 jmc 1.1446 - seaice_advdiff.F: for multidim, call seaice_diffusion with
318 gforget 1.1445 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
319     seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
320 jmc 1.1446 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
321 gforget 1.1445 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
322 jmc 1.1444 o pkg/seaice:
323     diffusion with centered advection scheme (diffus.F & advect.F):
324     - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
325     to just compute the laplacian of input-field.
326     - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
327     - fix flux-form version in diffus.F to conserve tracer.
328     update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
329     machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
330    
331 jmc 1.1443 checkpoint62y (2011/05/26)
332 gforget 1.1442 o pkg/seaice:
333 jmc 1.1443 - seaice_growth.F : in EVOLUTION branch, always include
334 gforget 1.1442 a_QSWbyATM_cover in qnet (as it should be).
335     - verification/global_ocean.cs32x15 : update results accordingly
336 jmc 1.1443 (output.seaice.txt output_adm.seaice.txt).
337 jmc 1.1441 o pkg/seaice + obcs:
338     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
339     equivalent of assuming no tracer gradient outside the OB region.
340     update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
341     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
342     after changes above);
343     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
344     only at OB location (instead of over a band of OLx width).
345     o pkg/seaice:
346     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
347     (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
348 jmc 1.1438 o pkg/obcs:
349 jmc 1.1439 - split header file "OBCS.h" into 4 separated files:
350     OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
351     Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
352 jmc 1.1440 (contain no conditional statement which depends on OBCS options).
353     - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
354     to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
355 jmc 1.1439 o ctrl, cost, grdchk & autodiff pkgs:
356     - make options file more standard (like other {PKG}_OPTIONS.h file but
357     with AD_CONFIG.h); clean-up some of the included header files.
358     o pkg/obcs:
359 jmc 1.1438 - do not mask tracer when applying OB (tracer == 0 could generate problems)
360     - apply tracer OB values to tracer field only at OB location (instead of
361     over a band of OLx width)
362     - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
363     - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
364     obcs_apply_tloc.F & obcs_apply_sloc.F
365     o obcs in model/src:
366     - call OBCS_APPLY_W only if NonHydrostatic.
367     - call OBCS_APPLY_ETA only if NonLinFreeSurf.
368     - reset dEtaHdt and wVel to zero outside OB interior region ;
369     - leave tracer unchanged outside OB interior region: This has no effect
370     on the solution but just to prevent unrealistic tracer value outside OB.
371     - zero out velocity outside OB interior region: This has no effect on
372     the solution but just to prevent unrealistic velocity outside OB.
373 jmc 1.1437 o obcs and non-lin free-surf:
374     move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
375     and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
376     + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
377     this fixes missing EXCH + get consistent eta OB value (+ fix restart).
378     update results of test-exp. exp4(nlfs).
379 jmc 1.1436 o exp4 (nlfs) test-exp:
380     use OBC for Eta at Western & Eastern OB (to test prescribing Eta
381     with NonLin-FreeSurf); update output.nlfs.txt
382 jmc 1.1435 o obcs and 2d/3d solver norm:
383 jmc 1.1436 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
384     and outside OB interior region (will allow to place OB further inside the
385     domain). Depending on the domain, can affects cg2d-Norm (previous
386 jmc 1.1438 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
387 jmc 1.1435 and cg3d-Norm (previous Norm was computed before canceling OB terms),
388     e.g. in tutorial_plume_on_slope.
389     - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
390 jmc 1.1433 o pkg rbcs:
391     - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
392     - add capability to apply relaxation to horizontal velocity uVel & vVel.
393 mlosch 1.1432 o pkg/grdchk: add gradient check for control variable xx_shifwflx
394     o pkg/shelfice/shelfice_init_fixed.F
395     fix CPP-flag combinations
396 heimbach 1.1434 o pkg/seaice: Merge iceage code of Pierre Rampal
397     * update/change/correct ice age calculations
398 jmc 1.1436 * add age updates for pathological cases
399 heimbach 1.1434 Probably needs more testing...
400 mlosch 1.1432
401 jmc 1.1431 checkpoint62x (2011/05/13)
402     o pkg/mom_vecinv:
403 jmc 1.1433 high-order vorticity scheme: use interior masks (maskInW & S)
404 jmc 1.1431 to zero-out (outside OB) gradient of vorticity.
405 jmc 1.1430 o verification exp.:
406     turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
407     hs94.128x64x5 and seaice_obcs ; update results.
408 jahn 1.1429 o pkg/obcs:
409     fix bug in OBeta for YZ sections in obcs_exf_load.F
410 jmc 1.1430 o pkg/ctrl, pkg/shelfice, and optim:
411     - add new control variable xx_shifwflx (fresh water flux underneath ice
412     shelves). This is almost as tedious as obcs-ctrl, because the
413 mlosch 1.1427 variables needs its own mask.
414 jmc 1.1430 - add a cost function term that penalizes the deviation of xx_shifwflx
415 mlosch 1.1427 from the first guess (zero) in analogy to other control variables
416 heimbach 1.1426 o pkg/shelfice:
417     - start basic adjoint
418 jmc 1.1430 o pkg/ctrl:
419 mlosch 1.1425 - remove extra 2D field "for good measure" when initializing in
420     ctrl_set_globfld_[xy/xz/yz].F
421 mlosch 1.1424 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
422     - improve error messages in ctrl_set_unpack_*
423 jmc 1.1423 o OBC implementation in momentum:
424     use interior masks (maskInC,W & S) in momentum S/R:
425     - multiply divergence, tension and some del^i.u or del^j.v by maskInC
426     - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
427     - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
428     - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
429     Motivation: fix/clean implementation of OBC with biharmonic-viscosity
430     (and also with Leith/Smagorinsky harmonic-viscosity).
431     Update output of experiment dome and exp4 (+nlfs).
432 jmc 1.1421 o exp4 test-exp:
433 jmc 1.1422 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
434     and prescribe time-varying OB (without pkg/exf) for zonal-velocity
435     at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
436     time-varying OB at Western-side for wVel (NonHyd); update output.
437 jmc 1.1421 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
438 jmc 1.1422 and biharmonic-viscosity ; also use prescribed time varying OB.
439 jmc 1.1421 o pkg/obcs:
440     fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
441 jmc 1.1420 o model/src:
442     - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
443     - initialise startTime & nIter0 with unlikely values: allows to set one
444     from the other without ambiguity.
445 jmc 1.1419 o seaice_obcs test-exp.:
446     add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
447 jmc 1.1418 o pkg/obcs:
448     - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
449     no longer needed with maskInC,W,S in pkg/generic_advdiff.
450 ifenty 1.1417 o pkg/seaice:
451 jmc 1.1418 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
452 ifenty 1.1417 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
453 jmc 1.1418 - fixed bug in the initialization of sea ice salinity variable HSALT
454 ifenty 1.1417 in seaice_init_varia.F (removed dependence on ICE2WATR)
455 jmc 1.1416 o fizhi-cs test exp.:
456     switch reference output convention for these 2 non-standard test-exp,
457 jmc 1.1418 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
458 jmc 1.1416 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
459     reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
460 jmc 1.1415 o model/inc:
461     - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
462     of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
463 ifenty 1.1414 o pkg/seaice:
464     - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
465     o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
466 ifenty 1.1417 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
467     and initial HSALT
468 ifenty 1.1414
469 jmc 1.1413 checkpoint62w (2011/04/26)
470 jmc 1.1412 o pkg/mom_fluxform:
471     - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
472     - use parameter "sideDragFactor" in no-slip BC side-drag part.
473     - update output of exp. global_ocean.90x40x15
474 jmc 1.1411 o pkg/mom_vecinv:
475     mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
476 jmc 1.1413 o update seaice exp.:
477     use more consistent parameter values (remove "backward compatability only":
478     ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
479     related to thermodynamics seaice. Update output (fwd+AD) of exp.:
480     1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
481 jmc 1.1411 o update test-exp global_ocean.90x40x15:
482     o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
483     o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
484     o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
485     o turn on zStar & viscA4 in standard set-up (dir input/)
486     and update output files: output.txt & output.dwnslp.txt
487 jmc 1.1409 o new AD-test experiment: obcs_ctrl
488     (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
489     o pkg/dic:
490     fix two bugs in handling water vapour pressure in carbonate chemistry
491     and air-sea fluxes. Found by Val Bennington and Galen McKinley
492     (add DIC Option = WATERVAP_BUG to recover old results)
493     update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
494 dimitri 1.1408 o adding allowInteriorFreezing option to check for water below freezing point
495     at depth and bring the negative heat anomaly to the surface level
496 jmc 1.1409 o pkgs _fields_load:
497     - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
498     - use new S/R GET_PERIODIC_INTERVAL in pkgs:
499 jmc 1.1410 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
500     rbcs to get interpolation weights and time reccord number.
501 jmc 1.1409 - fix multi-threading in aim_fields_load.F
502     - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
503 jmc 1.1407 o external_fields_load:
504     new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
505     interpolation weights) to use in a periodic time-series ; do not divide by
506     time-step to convert to integer:
507     - this fixes case where externForcingPeriod is not multiple of time-step
508     (Thanks to Christopher L. Wolfe)
509     - this fixes case where externForcingPeriod is an odd multiple of time-step
510     (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
511     store index of time-record which is currently loaded:
512     - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
513     - needed for the adjoint but not yet used because of extensive recomputations;
514     (to be fixed soon)
515    
516 jmc 1.1405 checkpoint62v (2011/04/02)
517 ifenty 1.1406 o verification/1D_ocean_ice_column added to test Ian Fenty's
518     pkg/seaice_growth.F modifications for improving sea ice code differentiability
519 jmc 1.1405 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
520     (new velocity statistics after changing maskInW & maskInS definition)
521 jmc 1.1404 o pkg/generic_advdiff with OBCS:
522     use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
523     equivalent to assumption of no tracer gradient outside the OB region.
524     This will affect the results if using obcs+biharmonic diffusion.
525     update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
526 jmc 1.1403 o pkg/obcs:
527     change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
528     (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
529     in Interior region. No impact on solution but affects Velocity monitor stats.
530 heimbach 1.1402 o pkg/ptracers (adjoint)
531 jmc 1.1403 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
532 heimbach 1.1402 tape file for each tracer
533 jmc 1.1403 o model/inc/src and pkg/autodiff: add parameters that allow to turn
534     of parts of the adjoint code at run time. For now, there are only
535     useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
536     parameters are set in data.pkg.
537     This is the lazy coward's version of doing this, but still useful for
538     debugging. In order to do it right, everything needs to be moved to
539 mlosch 1.1401 pkg/autodiff.
540 jmc 1.1403 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
541 mlosch 1.1401 the end; this fixes the adjoint balancing code for open boundaries.
542 mlosch 1.1399 o pkg/ctrl:
543     - change behavior of xx_${varname}period to be analogous to exf-conventions:
544     xx_${varname}period = 0., means time-independent control part
545 jmc 1.1403 xx_${varname}period = -12., means one-year-periodic monthly control part
546 mlosch 1.1399 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
547     clean up ctrl_init a little, remove unused variables
548 mlosch 1.1400 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
549 mlosch 1.1399 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
550    
551 mlosch 1.1398 checkpoint62u (2011/03/15)
552 jmc 1.1397 o model/src:
553     - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
554     h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
555     - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
556     INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
557     o pkg/ctrl/obcs/ecco:
558 mlosch 1.1396 - remove obsolete, unused, and partially broken code:
559 jmc 1.1397 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
560 mlosch 1.1396 ALLOW_CTRL_OBCS_BALANCE
561 jmc 1.1397 - put a stop statement into ecco/cost_obcsvol.F, but also add
562 mlosch 1.1396 cost_obcsvol to ecco_ad_diff.list
563 mlosch 1.1395 o pkg/ecco: fix counting cost function contributions for obcs (code
564     by Matt M.) and diffkr for diagnostics
565 heimbach 1.1394 o pkg/ecco, pkg/ctrl, pkg/grdchk:
566     add cost penalty terms for initial uvel, vvel, eta controls
567     and I/O for prior error files
568 jmc 1.1393 o pkg/mdsio:
569     move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
570     (new argument) to check for tiled file in mdsioLocalDir : this fix the
571     restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
572 mlosch 1.1392 o pkg/ctrl:
573     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
574     ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
575     unused and superfluous variables
576     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
577 mlosch 1.1391 o pkg/ecco
578     - enable adjoint of Stevens OB
579 jmc 1.1393 o pkg/ctrl/ecco/grdchk:
580 mlosch 1.1390 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
581 mlosch 1.1391 Fortunately, we do not have any tests for the numerous cpp-flagged
582 mlosch 1.1390 option of "obcs as control parameters" so we will never know
583     if this is an improvement (but at least now things compile).
584     - remove an obsolete initialization from ecco_cost_init_barfiles.F
585 jmc 1.1393 - fix some problems within never used ifdefs to make the code compile
586 jmc 1.1388 o pkg/obcs:
587     - Refine Interior mask definition to work with more complex OB (e.g.
588     if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
589     read in Interior mask from file. Check if Interior mask is consistent
590     with OB list of indices.
591 heimbach 1.1387 o pkg/seaice
592     - beginning code for a seaice tracer package,
593     but currently only used for seaice age: SEAICE_AGE
594     SEAICE_num = 4
595     iTracer = 1: area-weighted ice age
596     = 2: volume-weighted ice age
597     = 3, 4: template for one-year vs. multi-year ice
598     data.seaice has new namelist SEAICE_PARM03 for arrays related to
599     SEAICE_num
600    
601 heimbach 1.1386 checkpoint62t (2011/03/05)
602 jmc 1.1383 o pkg/obcs:
603 jmc 1.1384 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
604     then normal component. This ensures that the normal component is set
605     correctly even when it conficts with tangential setting from an other OB.
606     Affects results of test-experiment seaice_obcs: update the output.txt
607     o pkg/obcs:
608 jmc 1.1383 - add code to monitor statistics of dynamical fields at OB.
609     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
610     - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
611     - change default: balance the Net inflow through all OB (instead of balancing
612     each OB separately); keep the old method if setting OBC_balanceFacX < 0.
613     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
614     to match Nortern OB inflow (OBCS_balanceFacN=0).
615 dimitri 1.1382 o pkg/seaice:
616     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
617 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.113):
618     - reverting seaice_growth to v 1.111 in order to have code with exact bit
619     compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
620     CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
621     runtime flag SEAICEareaFormula is kept but is inactive
622 jmc 1.1380 o model/src:
623     - add new param to scale curvilinear grid distance and area when using
624     a different sphere radius from the grid-files.
625     - test/check multi-threads EXCH applied to local variable (cg2d_x)
626 heimbach 1.1385 o adjoint:
627     - enable adjoint of Stevens OB
628     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
629     (a bit delicate because of potentially modified adj. common block structure;
630     current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
631 jmc 1.1380
632 jmc 1.1379 checkpoint62s (2011/02/15)
633 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.112):
634 gforget 1.1378 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
635 jmc 1.1379 computing the ice cover tendency from effective thickness tendencies. Include
636     Ian Fenty's formula.
637     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
638     SEAICEareaFormula.
639 gforget 1.1378 - simplify notations for the various d_HEFF/d_AREA terms.
640 jmc 1.1377 o pkg/gmredi:
641     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
642     from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
643     add a verification test-run (front_relax.bvp) to test GM_useBVP.
644 dimitri 1.1381 o pkg/seaice (seaice_growth v 1.111):
645 gforget 1.1376 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
646 jmc 1.1379 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
647     also melt ice.
648 jmc 1.1377 o pkg/seaice:
649 gforget 1.1375 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
650     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
651 jmc 1.1374 o pkg/cheapaml:
652     - from Nico Wienders: New version of this package.
653 jmc 1.1372 o pkg/flt:
654     - add CPP options to prevent floats to re-enter the opposite side of
655     a periodic domain (default: keep periodicity)
656 jmc 1.1370 o pkg/gmredi:
657     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
658     (needed for multi-dim advection).
659 jmc 1.1371 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
660 jmc 1.1370 o model/src:
661     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
662 heimbach 1.1373 o tutorial_tracer_adjsens
663     - extend to NLFS and replace maskC by hFacC
664     (change reference output accordingly)
665 jmc 1.1370
666 jmc 1.1369 checkpoint62r (2011/01/24)
667 jmc 1.1368 o testreport:
668     - add option -deloutp (-do) to remove output file after successful run
669     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
670     extract exact list of procs from this file ; adjust COMMAND by
671     replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
672 mlosch 1.1367 o pkg/ecco: replace old ineffective way of penalizing deviations from
673     first guess (of obcs) with code by Matt Mazloff
674 jmc 1.1368 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
675 mlosch 1.1366 exf/cal
676     - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
677     and handle case of obcs?period == 0
678     Not affected by these changes: There is still an inconsistency in
679 jmc 1.1368 the computation of start/endrec for the obcs variables for ALLOW_CAL
680 mlosch 1.1366 defined (see comment by Menemenlis, 7-Mar-2003)
681     - make S/R ctrl_get_gen_rec return something meaningful even if
682     ALLOW_CAL is not defined
683 jmc 1.1368 - ctrl_getobcs?: simplify code so that it does not need to use
684 mlosch 1.1366 S/R exf_swapfields
685 jmc 1.1365 o testreport:
686     allow to test MPI with different number of processors for each experiment:
687     create file "SIZE.h.mpi" in each build dir.
688     Note: update of "-command" argument not yet implemented.
689 gforget 1.1364 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
690     alleviate the need for additional 3D tapes when using
691     the non-inear free surface in the adjoint. This is done
692 jmc 1.1368 by adding an 'update' of hfacc etc. to their current
693     value at the beginning of forward_step.F.
694 mlosch 1.1362 o pkg/seaice
695     seaice_lsr: move stress-divergence computations out of outer pseudo-
696 jmc 1.1363 timestepping loop
697 mlosch 1.1362 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
698     up, so that the calls of the ctrl_* subroutines are really at the end
699     of the routine.
700 jmc 1.1363 o pkg/gmredi:
701     allow to specify a 2-D horizontal map and a 1-D vertical profil
702     as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
703 gforget 1.1364 o pkg/seaice:
704     move lsr iterations from seaice_dynsolver to seaice_lsr.
705     o pkg/seaice:
706     reduce memory footprint of seaice mutldim advection tapes,
707     by using a 2D tape independent of the generic_advdiff ones,
708     and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
709 mlosch 1.1362
710 jmc 1.1361 checkpoint62q (2010/12/29)
711 jmc 1.1360 o model/src:
712     - check horizontal grid-spacing for unset or zero/negative values.
713     - change AD test hs94.1x64x5 to be truly a 2-D set-up.
714 jmc 1.1359 o pkg/flt:
715     - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
716     - precision of input and output files set according to readBinaryPrec
717     and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
718     - initial float position from tiled file was not converted to index space
719     (looks like a bug): fixed to make it similar to initial pos. global file.
720 jmc 1.1358 o global_ocean.cs32x15:
721     change SIZE.h of AD set-up to get same tiling as with MPI.
722     Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
723     o model/src:
724     add flag to control printing of domain fields (bathymetry, hFac ...) in
725     ini_mask_etc (call to plot_fieds_xy*).
726     o pkg/thsice:
727     if useEXF, some forcing fields are not valid in overlap: fixed by computing
728     over the interior only + apply EXCH at the end (like with SEAICE advection).
729 jmc 1.1357 o pkg/mdsio:
730     - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
731     to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
732     - change barrier call for safe multi-threads access to 3-D shared buffer.
733     - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
734     - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
735     remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
736 jahn 1.1356 o pkg/flt:
737     - add fourth-order Runge-Kutta integration
738     - add basic exch2 support (only 1 facet supported so far!)
739 jmc 1.1355 o pkg/mdsio+rw:
740     new S/R to read local (or tile independent) vector (read counterpart of
741     mds_writevec_loc, and front-end write_glvec_rl/rs).
742 gforget 1.1354 o global_ocean.cs32x15: additional input_ad.seaice experiment
743     that uses pkg/seaice rather than pkg/thsice.
744     (using multidim advection for seaice)
745 jmc 1.1353 o towards more F95 syntax for array specification in namelist:
746     - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
747     of all verification experiments.
748     e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
749     was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
750     - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
751 gforget 1.1352 o global_ocean.cs32x15: additional input.seaice experiment
752     that uses pkg/seaice rather than pkg/thsice.
753 jmc 1.1353
754 jmc 1.1350 checkpoint62p (2010/12/17)
755 gforget 1.1351 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
756     to THSICE_SIZE.h to avoid conflict with pkg/seaice.
757     o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
758     allow for use of multim. advection in seaice adjoint.
759 mlosch 1.1349 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
760     - first attempt to close budgets by taking into account the freshwater
761 jmc 1.1350 flux implied by the sublimation of snow and ice. So far only the
762 mlosch 1.1349 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
763     SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
764 jmc 1.1348 o eesupp/src:
765     new S/R with new option (NML_EXTENDED_F77) to change array specification
766     from F95 standard to commonly accepted extended F77 form.
767     This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
768     and to revert back to the original syntax (with -DNML_EXTENDED_F77)
769     for less tolerant f77 compiler (e.g., pgf77, g77).
770 jmc 1.1346 o globalFiles:
771     commented out in parameter file "data" since it's not safe with MPI
772     (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
773     in this case); no longer commented out in restart test (tst_2+2).
774     o add adTapeDir to specify a special directory where adjoint tapes are
775     written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
776 mlosch 1.1345 and cannot be used together with mdsioLocalDir.
777 jmc 1.1343 o nesting pkgs:
778     - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
779     - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
780     - add parameter files + utils dir + output from short run on beagle.
781 gforget 1.1344 o pkg/seaice:
782     fix seaice_growth.F store directives; update results of exp. lab_sea.ad
783 jmc 1.1343 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
784 mlosch 1.1342 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
785    
786 jmc 1.1341 checkpoint62o (2010/11/25)
787 jmc 1.1340 o pkg/exf:
788     - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
789 jmc 1.1341 o pkg/seaice:
790     - seaice_ocean_stress: split a loop for better vectorization of the
791     adjoint code
792 mlosch 1.1337 - seaice_growth.F: fix bug in conservation of freshwater connected to
793 mlosch 1.1338 capping of heff, put contribution into d_HEFFbyNEG
794 mlosch 1.1337 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
795     by something more sensible (parameters that are what their name implies)
796     - change some defaults, so that by default exf-parameters are used for
797     things like rhoAir, cpAir,latent/sensible heat parameters, in order
798     to reproduce the old results, many data.seaice now contain funny values
799     for cpAir and latent heat of sublimation
800 jmc 1.1341 o packages_readparms.F: move exf_readparms up in line so that
801 mlosch 1.1337 exf-parameters are visible for other packages (e.g. seaice)
802 jmc 1.1336 o debugMode & debugLevel=2:
803     - differentiate between debugMode & debugLevel=2:
804     debugMode: controls printing of debug messages (sequence of S/R calls).
805     debugLevel: controls printing of algorithm intermediate results and stats.
806     - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
807     => allows to print debug-stats without all sequence of call messages.
808     - switch control of debug print from debugLevel to debugMode in many S/R.
809     o pkg/obcs (obcs-sponge):
810     fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
811     call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
812 jmc 1.1335 o pkg/generic_advdiff:
813     - record overlap minimum size for each advection scheme;
814     - refine criteria on overlap minimum size;
815     - check and stop (in gad_check) if overlap size is too small.
816     o pkg/obcs:
817     - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
818     once, in ptracers_implicit.F)
819     - with seaice: remove test on empty file name in obcs_apply_seaice (always
820     apply OB values when tile has OB)
821 jmc 1.1334 o model/src, coriolis setting:
822     - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
823     useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
824     files (selectCoriMap=3) with any grid.
825     - add parameter "fPrime" for constant second Coriolis coeff (default=0).
826     o pkg/seaice/seaice_growth.F:
827     a few cosmetic changes that reduce the number of lines of code
828 mlosch 1.1332 o pkg/obcs: add boundary conditions following Stevens (1990)
829     - the code follows old MOM/NAOSIM code
830     - so far it is only implemented for the eastern and western boundaries
831     and NOT for pTracers
832 jahn 1.1331 o pkg/rbcs:
833     - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
834     beginning of the first rbcs forcing period.
835     - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
836     offline package, i.e., one file per time, labeled by iteration number;
837     deltaTrbcs sets the timestep with which the data was generated;
838     rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
839     - rbcsForcingCycle=0 makes forcing non-cyclic.
840     - make arithmetic safe for negative times and odd forcing periods.
841    
842 jmc 1.1330 checkpoint62n (2010/11/09)
843 mlosch 1.1327 o pkg/seaice:
844 jmc 1.1329 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
845     o pkg/obcs:
846     New S/R to copy tracer value from the OB location to narrow band region
847     (width = same as overlap) beyond the OB: preserve OB value (needed for
848     high-order scheme) which were overwritten by EXCH call if in overlap
849     region. Applied to theta, salt, ptracer and advected seaice variables.
850     With seaice: use maskInC in similar way as in gad_advection.F,
851     in seaice_advection.F and advect.F.
852     Update output of experiment seaice_obcs and change exp4 to test OBCS with
853     4th order Adv.Scheme. for pasive salt and ptracer.
854     o tools/genmake2:
855     - when looking for an optfile (not specified), only search for Fortran compiler
856     (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
857     - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
858     (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
859     - set default for CPP to "cpp -traditional -P" (was the case without specifying
860     an optfile, but otherwise default was just "cpp".
861     - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
862     - when "CC" is not set in the optfile, look for possible C compiler
863     (instead of just setting CC=cc)
864     - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
865     => add a ".F" to ".o" rule for source files with no "#include" (such as
866     port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
867     - move gfortran before g77 in list of possible Fortran compiler (consistent
868     with reference compiler switch from g77 to gfortran)
869     o pkg/seaice:
870     o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
871 mlosch 1.1327 seaice_check that stops the model, when the CPP flag is used.
872     o seaice_growth.F: make capping of ice volume conserving by returning the
873     capped ice as freshwater to EmPmR. This does not change the verification
874     experiments but will change runs where the capping is acutally active
875 jmc 1.1326 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
876     (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
877     global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
878     lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
879     o tools/genmake2:
880     - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
881     - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
882     - clean previous genmake log files before anything else.
883     - change Makefile to remove testreport log files (*.tr_log) and genmake log
884     files only with "CLEAN" target (instead of "Clean");
885 jmc 1.1324 o pkg/generic_advdiff:
886     Change OBCS in multiDim advection (gad_advection.F):
887     Use maskInC to prevent intermediate update of tracer-field in OB regions,
888     thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
889     which were applying future time-step OB values.
890     This way, all explicit calculations use current-time-step OB values
891     (simpler and more consistent).
892     Affects results when set-up uses time-varying OBC and multi-dim advection;
893     update output of experiment seaice_obcs.
894 jmc 1.1323 o pkg/seaice:
895     move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
896     this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
897     SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
898     Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
899     but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
900     unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
901 dfer 1.1322 o pkg aim (2010/10/26):
902     - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
903     formulation with obliquity, eccentricity, ... as run-time parameters,
904     - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
905     upward shortwave radition at the surface (all-sky and clear-sky).
906 jmc 1.1319 o pkg/obcs:
907 dimitri 1.1321 - writing sections with globalFiles=T does not work: switch to tiled-files
908     when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
909     - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
910     - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
911 jmc 1.1319
912 jmc 1.1318 checkpoint62m (2010/10/21)
913 mlosch 1.1316 o pkg/seaice: vectorize seaice_solve4temp.F
914     - move iterations loops outside of i/j-loops
915     - requires 2D arrays for TB and effConduct
916 jmc 1.1318 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
917 mlosch 1.1316 modified in this routine
918     - a little bit of clean up, adjusting indentation, etc.
919 jmc 1.1318 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
920     performance and '**TWO' by '**2' (because TWO is a float),
921 mlosch 1.1316 replaced ONE, ZERO
922 jmc 1.1314 o eesupp/src:
923     fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
924 gforget 1.1313 o pkg/seaice/seaice_growth.F
925 jmc 1.1314 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
926     merging process. The merged routine has two branches, and one activates the 'evolution'
927 gforget 1.1313 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
928     In summary, here is what the '10/10 revision' did consist of
929 jmc 1.1314 part 1: seaice_growth.F revisions 1.71 to 1.75
930 gforget 1.1313 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
931 jmc 1.1314 The emphasis here was on improving readability (e.g. by trying to use meaningful
932 gforget 1.1313 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
933 jmc 1.1314 part 1.5:
934     - revising the lab_sea experiment to make it a more useful (i.e. stable
935     and representative of an actual model run). This was done by generating a
936     (winter) pickup to start from, switching back the main experiment dynamic
937 gforget 1.1313 solver from evp to lsr, having one of the experiments use the free drift solution.
938 jmc 1.1314 part 2: seaice_growth.F revisions 1.76 to 1.85
939 gforget 1.1313 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
940 jmc 1.1314 - Sorting out the various fields units and sign (set early on and reset at the end)
941     to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
942     fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
943     - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
944 gforget 1.1313 and simplifying logical expressions to further improve readibility.
945     part 3: seaice_growth.F revisions 1.86 to 1.89
946     - Re-organize the blocks of code more logically.
947     - Merging the '_if.F' pieces that add something new.
948 jmc 1.1314 o pkg/thsice:
949     - vectorize thsice_solve4temp and thsice_get_exf.
950 mlosch 1.1312 Problem: thsice_solve4temp has an unvectorizable statement that
951     might also be problematic for TAF
952 jmc 1.1314 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
953     does not change the verifcation experiment, but will change all
954 mlosch 1.1312 experiments that have this flag undefined (not tested in verification);
955     a little reorganization to save a few 2D fields and recomputations
956 heimbach 1.1315 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
957 heimbach 1.1317 - 2nd step: fix some store dirs
958     o seems to work somewhat, i.e. using ifort but not g77
959     o likely cause are incomplete init. or recomputation
960     o start verification/global_ocean.cs32x15/input_ad.thsice
961 jahn 1.1311 o pkg/obcs: add support for exch2
962     - the position of the boundary and prescribed values are specified using
963     a global domain with exch2 facets stacked
964     - in x for N,S boundaries (like W2_mapIO=-1)
965     - in y for E,W boundaries (so E,W boundaries do not overlap)
966     o pkg/mdsio: add support for writing global sections with exch2
967     file layout is as for obcs described above:
968     - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
969     - for y-z sections, facets are stacked in y
970 jmc 1.1309 o pkg/thsice:
971 mlosch 1.1310 - change a few routines for better vectorization: thsice_albedo.F,
972     thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
973     not affected, but in particular the latter routine has changed
974     dramatically (not necessarily easier to read now).
975     - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
976 jmc 1.1309 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
977 gforget 1.1308 o verification/lab_sea:
978     - overhaul of the forward model experiments. The main motivation
979 jmc 1.1314 for this revision is that lab_sea has proven quite fragile (when
980 gforget 1.1308 changing the sea-ice code, and switching platforms) to a point
981     when failures were very hard to attribute to specific code problems.
982 jmc 1.1314 - the suspected reason for this fragility is noise amplification by evp so,
983 gforget 1.1308 to start with, we decided to replace evp with lsr in the main experiment.
984     - the input.lsr experiment thus became obsolete and was removed.
985 jmc 1.1314 - it was replaced with the input.fd experiment that uses an
986 gforget 1.1308 analytical "free drift" solution as the ice velocity field.
987     - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
988     will hopefully allow us to discriminate problems due to dynamic solvers
989     from problems due to the thermodynamic code. input.salt_plume (lsr) allows
990     us to test additional options, along with the salt plume package.
991 jmc 1.1314 - Finally a pickup was generated (at the end of a one year run) to
992 gforget 1.1308 make the tests more representative of an actual model run. Previously
993     the tests starting point was a 1m thickness of ice everywhere.
994 jmc 1.1314 o pkg/seaice:
995 gforget 1.1308 - introducing S\R seaice_freedrift.F that compute the
996 jmc 1.1314 analytical solution to an approximate ice momentum
997 gforget 1.1308 equation (i.e. the simple stress/coriolis balance).
998     - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
999 jmc 1.1314 of the free drift velocity field, and enable its use.
1000     To actually use the free drift solution as the model ice
1001     velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
1002 mlosch 1.1307 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
1003    
1004 jmc 1.1306 checkpoint62l (2010/10/04)
1005 jmc 1.1305 o pkg/seaice:
1006     -fix the USE_ORIGINAL_SBI version (for variable freezing point);
1007     -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
1008     version (with USE_ORIGINAL_SBI undef);
1009 mlosch 1.1304 o add hooks for new packages OASIS, the package will follow
1010     (hooks exclude the seaice pkg for now)
1011 gforget 1.1303 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
1012 jmc 1.1305 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
1013 gforget 1.1303 rather than mdsio_readvector.F/mdsio_writevector.F, within
1014     adread_adwrite.F to read/write adjoint-related tapes to disk.
1015 jmc 1.1305 o eesupp and pkg/mdsio: ALLOW_WHIO
1016     Option to write/read 2D fields to files including tiles halos.
1017     The main purpose is for adjoint related "tape I/O".
1018 gforget 1.1302 The secondary purpose is for debugging phases.
1019     A word on those rather specifically intended purposes.
1020     The code was meant to be stripped down to the bare minimum.
1021 jmc 1.1305 Typically, there is a unique and basic mapping to the global
1022 gforget 1.1302 buffer (tile by tile, then proc by proc, then level by level), and
1023     byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
1024 jmc 1.1305 meant to generate user friendly outputs of various shapes and forms.
1025 gforget 1.1302 Rather it is intended, for the knowledgeabale developers,
1026     to be largely independent of the many mdsio options, to allow
1027 jmc 1.1305 outputs of tiles+halos in debugging phases and in adjoint runs,
1028 gforget 1.1302 and to allow some flexibility in tuning (adoint) I/O depending on each
1029 jmc 1.1305 file system behavior. With regard to tuning, most of the potential knobs
1030 gforget 1.1302 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1031     to specify directories, to specify the typical size of I/O calls, etc.)
1032     are not yet included, and will be added if they prove useful.
1033 jmc 1.1300 o pkg/seaice:
1034 jmc 1.1301 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1035     o pkg/seaice:
1036 jmc 1.1300 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1037     code (seaice_budget_ice_if.F) which enable to recover old standard
1038     code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1039     temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1040     o model/src (rStar):
1041     use simple average (not area weighted) of rStarFac at U,V point when using
1042     vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1043     update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1044 jmc 1.1299
1045 jmc 1.1298 checkpoint62k (2010/09/17)
1046 heimbach 1.1297 o adjoint
1047     * changed verification/global_ocean.cs32x15 ; adjoint now tests
1048     Adams-Bashforth 3 + NLFS + RSTAR
1049     * some more modifs required for ECCO-GODAE v4
1050 dimitri 1.1296 o pkg/seaice
1051     add SEAICE_AGE_VOL option to use volume instead of area for
1052     integrating SEAICE_AGE
1053 jmc 1.1295 o model/src:
1054     first check-in of sigma & hybrid-sigma coordinate code ; also includes
1055     non-linear free-surface parts ; but pressure-gradient not yet coded.
1056 jmc 1.1294 o pkg/ptracers:
1057     option for ptracer to convert Salt Relax into additional EmP.
1058     tested in exp. global_ocean.90x40x15.dwnslp (update output)
1059    
1060 jmc 1.1293 checkpoint62j (2010/08/25)
1061 jmc 1.1292 o pkg/ggl90:
1062     other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
1063 mlosch 1.1291 o pkg/dic: car_flux.F, phos_flux.F
1064     - reduce number of exp-calls in order to improve performance
1065 jmc 1.1292 - clean up a little (replace fields by their macros, etc., fix
1066 mlosch 1.1291 typo in CPP-flag)
1067 gforget 1.1290 o pkg/ggl90: minor changes
1068     - GGL90diffKrS was removed --> always use GGL90diffKr
1069     - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1070 jmc 1.1292 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1071     (commented out for now)
1072 gforget 1.1290 - change in max/min operations to ensure that smoothing is ok
1073     - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1074     - always use diffKrNrT as background profile (i.e. never use diffKr field)
1075 mlosch 1.1289 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1076 mlosch 1.1286 o pkg/dic:
1077 mlosch 1.1288 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1078     vectorization
1079 mlosch 1.1287 - small bug fix in insol for the unlikely case of a cartesian grid
1080     - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1081     + now vectorize, which also removes adjoint recomputations;
1082     + replace integer maksp1 by _RL maskp1
1083 mlosch 1.1288 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1084 mlosch 1.1286
1085 jmc 1.1285 checkpoint62i (2010/07/21)
1086 jmc 1.1284 o pkg/flt:
1087     - with OBCS: stop floats which enter the OB region
1088     o model/src:
1089     - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1090     for implicit vertical advection.
1091 jmc 1.1283 o pkg/seaice:
1092     - account for melting in seaice age evolution.
1093 jmc 1.1284 - remove double counting of seaice ridging effect on seaice age.
1094 jmc 1.1283
1095 jmc 1.1282 checkpoint62h (2010/06/18)
1096 jmc 1.1281 o pkg/exch2:
1097     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1098     o tools/genmake2
1099     - remove "-pdefault" option: redundant with the use of "packages.conf";
1100     - remove file pkg/pkg_default : set the default as a pkg group
1101     ("default_pkg_list") defined in pkg/pkg_groups;
1102     - fix for case pkg/pkg_depend is missing (was hanging before);
1103     - add option "-pgroups" to specify a different pkg_groups than the default.
1104 jmc 1.1280 o verification/adjustment.cs-32x32x1:
1105     add a "minimal" set-up test (code_min & input_min) which only compiles
1106     eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1107 jmc 1.1279 o tools/genmake2
1108     - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1109     - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1110 mlosch 1.1277 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1111     files are nearly the same anyway.
1112     Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1113     - redefinition of tau(i,i) (by a factor of ustar)
1114     - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1115     - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1116     - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1117 jmc 1.1278 - replace
1118 mlosch 1.1277 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1119     shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1120     by
1121     shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1122     (changes results)
1123 jmc 1.1278 -> exf_bulkformulae v1.22,
1124 mlosch 1.1277 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1125     (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1126 jmc 1.1278 output.txt 1.63
1127 mlosch 1.1277 offline_exf_seaice: output.seaicetd.txt 1.7
1128     seaice_obcs: output.txt 1.10)
1129     Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1130     -> exf_bulkformulae v1.23,
1131     unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1132     and global_ocean.cs32x15.icedyn (only 11 matching digits)
1133 jmc 1.1278 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1134 jmc 1.1276 o adjoint of exch-1:
1135     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1136     (note: was already like this when using EXCH-2) and remove flow dir
1137     and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1138     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1139     - update pkg/exch2 diff list.
1140    
1141 jmc 1.1275 checkpoint62g (2010/05/19)
1142 jmc 1.1274 o eesupp/src (exch-1):
1143     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1144     and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1145     (renamed to exch1_*rx_cube.F).
1146     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1147     to call new exch1 S/R ; update Makefile and .cvsignore.
1148     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1149     exch2_xy_rx later)
1150     Note: after updating your code, need to run "make clean" in eesupp/src
1151 jmc 1.1273 o test experiment bottom_ctrl_5x5:
1152 jmc 1.1274 new output_adm.txt with fewer grdchk & less monitor output.
1153 jmc 1.1273 o model/src:
1154     remove the call to ini_cori in initialise_varia.F (just keep the usual one
1155 jmc 1.1274 in initialise_fixed.F). More consistent with coriolis & horizontal grid
1156 jmc 1.1273 beeing treated in the same way (ini_grid is not called a 2nd time).
1157 jmc 1.1274 o pkg/exf:
1158 mlosch 1.1272 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1159 mlosch 1.1271 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1160 mlosch 1.1272 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1161     - cosmetic changes to exf_bulkformulae.F to make it look more like
1162     exf_bulk_largeyeager04.F
1163 jmc 1.1270 o eesupp/src (exch-1):
1164     - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1165     - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1166     array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1167     (even without using MPI).
1168     - Message mode: move RecvAck setting (indicator of buffer being ready)
1169     from send_put to recv_get S/R (was useless before, but not sure if
1170     it's much more useful now);
1171 jmc 1.1273 - Switch the order of sync: MPI-proc 1rst and then threads;
1172 jmc 1.1270 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1173 jmc 1.1273 - fix AD code for communication mode ='get' (but not used).
1174 jmc 1.1269 o model/src:
1175     initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1176     not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1177 mlosch 1.1268 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1178 mlosch 1.1267 o pkg/ctrl: require a specific set of control variables and exf-flags for
1179     adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1180 gforget 1.1264 o model/src:
1181 jmc 1.1266 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1182     1rst forward sweep, to avoid over-writing output files during recomputations
1183     recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1184     b) 2nd version:
1185     - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1186     - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1187     writePickupAtEnd) + seaice & ptracers output;
1188     - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1189 jmc 1.1265 o model/src:
1190 gforget 1.1264 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1191 jmc 1.1263 o pkg/exch2:
1192 jmc 1.1265 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1193 jmc 1.1263 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1194 jmc 1.1262 o pkg/autodiff & exch2:
1195     process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1196     (for now, only if ALLOW_EXCH2 is defined).
1197 jmc 1.1261 o pkg/autodiff:
1198 jmc 1.1265 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1199 jmc 1.1261 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1200     + clean-up comments (_RS is not always real*4)
1201     - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1202     - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1203     was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1204 jmc 1.1260 o testreport (AD-tests):
1205     no longer link files from dir "../input" (1rst link files from
1206     "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1207    
1208 jmc 1.1259 checkpoint62f (2010/04/29)
1209 mlosch 1.1258 o model/src/the_main_loop.F:
1210     adjust store directives for seaice evp and multicategory according to
1211     pkg/ecco/the_main_loop.F
1212 heimbach 1.1256 o adjoint:
1213 jmc 1.1260 global_sum_ad was incomplete (noted many times by many people ;)
1214 heimbach 1.1256 nice description by Jean U. as follows:
1215 jmc 1.1260 * allreduce(var) in global_sum.F can be interpreted as
1216     reduce(sum) followed by broadcast of sum.
1217     * The adjoint of that is
1218     sum(adjoint) followed by broadcast(summed adjoint value)
1219 heimbach 1.1256 or in other words, allreduce(sum, adjoint vars)
1220     We were missing the sum(adjoint)!
1221     Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1222     (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1223     The fix should produce 16-digit accuracy between
1224     single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1225     multi-CPU single-tile (e.g. nSx=1, nPx-2)
1226     We'll probably change this yet again shortly
1227 jmc 1.1257 o eesupp/src:
1228     - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1229 dimitri 1.1255 o pkg/icefront
1230     - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1231     specification of addmass array based on a 2D field, which is added
1232     at bottommost wet level at each horizontal location.
1233 jmc 1.1254 o model/src:
1234     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1235     layout; (not always compatible with delX,delY setting; commented out for now).
1236 jmc 1.1253 o pkg/exch2:
1237     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1238     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1239    
1240 jmc 1.1252 checkpoint62e (2010/04/15)
1241 jmc 1.1251 o pkg/obcs:
1242     - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1243 jmc 1.1250 o pkg/dic:
1244     -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1245     (note: not presently tested in any forward verification exp.)
1246     update tutorial_global_oce_biogeo AD output file.
1247     o pkg/exf:
1248 gforget 1.1249 - account for the variation of albedo as a function of zenith angle
1249 jmc 1.1250 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1250 jmc 1.1248 o build_options:
1251     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1252     o pkg/dic:
1253     change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1254     - use binary pickup file for restart;
1255     - initialise atmos-CO2 box from dic_pCO2 parameter;
1256     - fix multi-threaded.
1257 jmc 1.1247 o pkg/rbcs:
1258     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1259     change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1260     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1261     and update output.txt
1262 jmc 1.1246 o pkg/kpp:
1263     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1264     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1265 jmc 1.1248 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1266 jmc 1.1246 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1267     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1268     KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1269 dfer 1.1244 o pkg/offline:
1270 jmc 1.1245 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1271     (bug was added in version 1.10 on 2007-08-23).
1272     o pkg/offline:
1273 dfer 1.1244 - no need to specify periodicExternalForcing, etc ... to use offline pack
1274     - offline input files no longer just single prec --> parameter offlineLoadPrec
1275 heimbach 1.1242 o verification/lab_sea:
1276 jmc 1.1245 change AD test to multi-tile setup and update all 4 AD output.
1277 heimbach 1.1242 NOTE: while cost function values remain very similar,
1278     gradients are very different, although gradient checks are self-consistent
1279     Should try to get to the bottom of this (cost function summation order?)
1280 jmc 1.1241 o pkg/dic:
1281     in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1282     a weakness of TAF that drops part of double precision in log10 derivative.
1283 jmc 1.1243 <= changes removed since problem has been fixed in current TAF version 1.9.71
1284 jmc 1.1241 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1285 jmc 1.1240 o pkg/ecco:
1286     add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1287     update all 4 lab_sea AD output.
1288    
1289 jmc 1.1239 checkpoint62d (2010/03/22)
1290     o build_options:
1291     remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1292 jmc 1.1238 o remove unbalanced quote (single or double) in commented line of source code
1293     (may cause some warning with some preprocessor/makedepend versions).
1294     o pkg/seaice:
1295 jmc 1.1237 fix seaice_model.F for adjoint (gael) and update AD results of experiments
1296     lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1297 jmc 1.1236 o testreport:
1298     add option '-runonly' (short: '-ro') to just do the run part (without make).
1299 jmc 1.1235 o eesupp: remove JAM communication code (obsolete).
1300 jmc 1.1234 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1301     (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1302     to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1303     (update also the output).
1304    
1305 jmc 1.1233 checkpoint62c (2010/03/02)
1306 jmc 1.1232 o tools/build_options :
1307     move (some) old optfiles from build_options/ to build_options/unsupported/
1308 gforget 1.1231 o model/src and pkg/exf
1309     surface relaxation -- separating data and data.exf options
1310     The point is to ensure that we specify the surface relaxation
1311     either in data or in data.exf (but not half and half) and to
1312     avoid an accidental relaxation to 0 (which happened if a time
1313     scale was specified but the file name was left empty)
1314 gforget 1.1230 o model/src model/inc and pkg/mom_common
1315     ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1316     => addition to the viscosity field as computed by others schemes
1317 jmc 1.1229 o tools/build_options:
1318     - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1319     but keep the former optfile for few weeks for smooth transition
1320 gforget 1.1228 o pkg/ecco
1321     - allow user defined cost function contributions
1322 dfer 1.1322 CPP: ALLOW_USERCOST_CONTRIBUTION
1323     USAGE: compute contributions in cost_usercost_all.F
1324 gforget 1.1228 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1325     the two options are complementary.
1326 gforget 1.1227 o pkg/smooth
1327     - migration from contrib to the main repository
1328 jmc 1.1229
1329 jmc 1.1226 checkpoint62b (2010/01/26)
1330 jmc 1.1225 o pkg/monitor:
1331     - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1332     (in case someone forgot to update customized pieces of code)
1333     o nonHydrostatic:
1334 jmc 1.1224 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1335     - add a simple 2-D experiment (short_surf_wave) to test it.
1336     o pkg/icefront:
1337     adding the shell of, and the hooks to, a new package that
1338 dimitri 1.1223 will model melting and freezing of vertical glacier ice fronts
1339 jmc 1.1224 o momentum:
1340 jmc 1.1222 add diagnostics of momentum tendency from Hydrostatic pressure gradient
1341     (without surf.pressure term: would need a 2nd filling since implicit term).
1342 jmc 1.1224 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1343     two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1344     cannot deal with the former
1345 jmc 1.1220 o cleaning:
1346 jmc 1.1222 - remove all (except OpenAD) old TLM output from results_ad dirs.
1347 jmc 1.1220 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1348     - comment out maskH definition (replaced by maskInC)
1349     o pkg/monitor:
1350     - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1351 jmc 1.1225 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1352 jmc 1.1220
1353 jmc 1.1219 checkpoint62a (2010/01/15)
1354 jmc 1.1218 o model/src:
1355     - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1356 jmc 1.1217 o pkg/diagnostics:
1357     - add optional level number diagnostics (i.e., level number to be define
1358     explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
1359     - strictly check for valid parser-code(10) ;
1360     - check if adding diag to the list from the right place.
1361 jahn 1.1216 o pkg/longstep:
1362     - change parameters and fix tracer conservation with rstar/nonlinear free surface
1363 jmc 1.1215 o diagnostics:
1364     - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
1365     S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
1366 jmc 1.1214 o pkg/diagnostics:
1367     - Add option for writing vertical integral (sum of selected levels) of an output
1368     field instead of writing output field levels. Activate this option on a per
1369     output-file basis, by setting the 2nd character of fileflag to 'I'.
1370     - Add field-specific information relative to level integral in 3rd postion
1371     of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
1372     vertically (x level-thickness x hFac), "r"=same but without hFac.
1373 jmc 1.1213 o do_the_model_io:
1374     - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
1375     in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
1376     writing pickups and stopping.
1377     o pkg/diagnostics (for now, only with mdsio):
1378     - write time information to meta file (and modify accordingly rdmds.m) :
1379     time-averaged diagnostics output: write starting and ending time of the
1380     time-averaging interval ; snap-shot diagnostics output remains unchanged;
1381 jmc 1.1212 o pkg/timeave:
1382     - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
1383     always Nr), now assumed to be equal to number of levels of averaged field;
1384     only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
1385     o pkg/sbo:
1386     - fix ocean bottom pressure global-average & 2-D time-ave output (was
1387     neither initialised nor filled).
1388     - add starting iteration in suffix of global-average output file
1389     (to avoid over-writing the file after a restart)
1390     - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
1391     o time-average:
1392     - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
1393     (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
1394     ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
1395     this fix DIC_COST cumulative-time array (previously: bi,bj,k)
1396     - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
1397     - fix missing accumulation for pkg/opps.
1398     - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
1399     (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
1400     - fix initialisation of time-ave vars and do only full time-step increment
1401     (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
1402 jmc 1.1211 o pkg/layers:
1403     - use standard RW pkg S/R to write the output
1404     and remove local write_fld version (which had a problem).
1405     - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
1406     - fix LAYERS_CALC argument list.
1407     o pkg/timeave:
1408     - store cumulative-time in a simple tiled array (drop the level index)
1409     - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
1410 jmc 1.1210 o pkg/ocn,aim_compon_interf
1411     - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
1412    
1413 jmc 1.1209 checkpoint62 (2009/12/23)
1414 jmc 1.1208 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
1415     (was not previously tested in any other exp.)
1416 jmc 1.1207 o pkg/monitor:
1417     - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
1418 jmc 1.1209 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
1419 jmc 1.1207 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
1420     - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
1421     - change del2 calculation.
1422     - use interior masks (instead of maskH, <- to be remove).
1423     - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
1424     o mask & obcs:
1425     - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
1426 jmc 1.1209 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
1427 jmc 1.1207 (called after packages_init_fixed)
1428 jahn 1.1206 o pkg/obcs:
1429     - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
1430     Fixes bug in obcs+exf with nSx*nSy.GT.1
1431     - fix multi-tile handling in obcs balance code
1432 jmc 1.1205 o nonHydrostatic:
1433     - Implement AB-3 for non-hydrostatic vertical momentum ;
1434     (change ordering of var. stored in pickup file when using NH)
1435     - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
1436     - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
1437     (in prep. for new NH free surface form).
1438 jmc 1.1204 o pkg/obcs:
1439     add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
1440 jmc 1.1209 o model/src:
1441 jmc 1.1204 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
1442    
1443 jmc 1.1203 checkpoint61z (2009/12/01)
1444 jmc 1.1202 o nonHydrostatic:
1445     Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
1446     a spurious source of energy in simple baroclinic adjusment test case.
1447     Update all non-hydrostatic exp output.
1448     o model/src (3-d solver):
1449     Change again 3-D solver free-surface RHS term when exactConserv=T:
1450     simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
1451     (which was not the case with previous formulation).
1452     To recover previous version, just reset "oldFreeSurfTerm" to previous value.
1453     Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
1454     o nonHydrostatic:
1455     - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
1456     for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
1457     - change 3-D solver to work with r* (for now, only with linear free-surf.)
1458     - add few debug diagnostics (cg3d_x, residual)
1459 jmc 1.1201 o model/src:
1460     fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
1461     update output of exp. global_ocean.cs32x15.viscA4
1462 jmc 1.1200 o update output of exp. global_ocean.cs32x15.icedyn after removing
1463     #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
1464     o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1465 mlosch 1.1199 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
1466     for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
1467 mlosch 1.1198 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
1468 jmc 1.1200 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
1469     runtime flag useSRCGSolver. Modify verification experiment global_with_exf
1470     to test this code
1471 jmc 1.1197 o pkg/cd_code:
1472     Change defaut D-grid time-stepping to get the same for D-grid momentum as for
1473     C-grid momentum. D-grid velocity used to be stepped forward in time with
1474     Adams-Bashforth only on surface pressure term. Tests show that using AB on
1475     D-grid coriolis term improves stability (as expected from CD-scheme paper).
1476     To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
1477     Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
1478     lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
1479     tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
1480     Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
1481 jmc 1.1204 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
1482 jmc 1.1196 o pkg/obcs:
1483 jmc 1.1197 - fix bug in initialisation (broken since Oct 1rst modification)
1484 jmc 1.1196 for useOBCSprescribe without useEXF.
1485    
1486 jmc 1.1203 checkpoint61y (2009/11/15)
1487 mlosch 1.1194 o pkg/seaice
1488     - change (once again) the discretization for the evp solver: rather than
1489     squaring the averages of strain rates, average the squares to give
1490     a better approximation to VP behavior (in simple test); this breaks
1491     verification experiments that use EVP (lab_sea and lab_sea.hb87)
1492     --> update outputs
1493 jmc 1.1195 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
1494 mlosch 1.1193 to improve vectorization of adjoint code on TARGET_NEC_SX
1495 dfer 1.1192 o verification/vermix:
1496 mlosch 1.1194 - change vermix to a more "classical" 1d column with high vertical
1497     resolution, seasonal heat flux forcing and constant wind forcing
1498     --> update outputs
1499 mlosch 1.1190 o pkg/seaice
1500     - fix diagnostics of principal stress components for EVP
1501     - add optional diagnostics of non-linear convergence for LSOR solver
1502 mlosch 1.1191 - make maximum zeta a runtime parameter
1503 jmc 1.1189 o model/src (3-d solver):
1504     Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
1505     which consisted in removing the Surf. Non-Hydrostatic pressure from the
1506     whole column and adding it to Eta (inspired from Casualli, 1999):
1507     Only affects 3-D solver initial guess and only if using ExactConserv,
1508     but tests did show a degradation of solver convergence. For this reason,
1509     decide to disable this piece of code.
1510     to recover previous version, just set zeroPsNH = exactConserv (line 78).
1511     Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
1512 jmc 1.1188 o pkg/ggl90:
1513     - fix previous modif (unfortunatly has not been documented here).
1514 mlosch 1.1182 o pkg/seaice/autodiff:
1515 mlosch 1.1185 - add CPP flag to include clipping of zeta in EVP code;
1516     although clipping of zeta is not necessary for EVP and not recommended
1517     it was done by default, now clipping is disabled by default
1518 mlosch 1.1184 - modify computation and store zetaC/Z in seaice_evp for TAF
1519 mlosch 1.1183 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
1520 mlosch 1.1190 - change seaice_calc_viscosities/strainrates for better
1521 mlosch 1.1183 vectorization after AD by TAF
1522 jmc 1.1187 - rearrange common blocks in SEAICE.h once again for easier dumps of
1523 mlosch 1.1182 adjoint output, adjust adcommon.h and g_common.h
1524     - change flux form of default advection scheme for better vectorization
1525     of adjoint code
1526     - modify lab_sea/input.lsr to test the flux form of default advection
1527     scheme
1528 mlosch 1.1181 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
1529     transition in checkpoint61r)
1530    
1531 jmc 1.1203 checkpoint61x (2009/10/19)
1532 heimbach 1.1179 o adjoint: adding two new verification experiments
1533     * tutorial_global_biogeo: an online dic sensitivity experiment
1534     (work with G. Forget)
1535     * tutorial_dic_adjoffline: an offline dic sensitivity experiment
1536     (an update of the Dutkiewicz et al., 2006 paper)
1537     Both use the same CO2FLUX cost function, but different controls
1538     Gradient checks look good, but some recomp. could still be traightened out
1539     Should add xx_dic control variable to test at some point
1540 jmc 1.1178 o model/src:
1541     add run-time parameters to check and/or mask initial Temp & Salt
1542 jmc 1.1177 o pkg/ptracers:
1543     apply zonal filter (if used) to all passive tracers
1544    
1545 jmc 1.1203 checkpoint61w (2009/10/12)
1546 heimbach 1.1175 o adjoint:
1547     * update and finish work on adjoint of dic package (G. Forget)
1548     * start adjoint of offline package
1549     * bug fix for cube-sphere TLM code (active_file_g.F)
1550 jmc 1.1173 o tutorial_global_oce_optim:
1551     now tested with 4 tiles (change data.grdchk and update output_adm.txt)
1552 jmc 1.1174 and add SIZE.h_mpi for MPI testing
1553 mlosch 1.1172 o pkg autodiff
1554     - fix bug in autodiff_restore
1555     - make genmake2 remove comments and empty lines from ad_input_code.f in
1556     order to reduce file size (new script file remove_comments_sed)
1557 jmc 1.1171 o allows to specify vertical profile of vertical viscosity (viscArNr)
1558 mlosch 1.1170 o pkg autodiff
1559     autodiff_ini_model_io: comment out writing of grid information to netcdf
1560     files, because at this time the grid fields are a bunch of zeros
1561     (this is analogous to ini_mnc_vars.F)
1562 mlosch 1.1169 o pkg seaice/autodiff:
1563     left-over from removing the 3-time-level fields:
1564     - small rearrangement of common blocks (SEAICE.h)
1565     - fix field declaration in order to get meaningful output in
1566     adseaice.*.nc (adcommon.h)
1567 jmc 1.1165 o pkg obcs:
1568     - go through NH code only if nonHydrostatic=T
1569     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
1570 jmc 1.1174 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
1571 jmc 1.1166 => Update output of experiment seaice_obcs
1572     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
1573 jmc 1.1167 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
1574 jmc 1.1168 - fix restart for useOBCSprescribe + useEXF
1575 mlosch 1.1164 o pkg ctrl
1576     - make obcs as control parameter work also with useSingleCPUio
1577     - replace a few sny and snx by Ny and Nx to be consistent with
1578     ctrl_set_globfld_x/yz.F
1579 mlosch 1.1163 o pkg seaice
1580     - re-introduce global field frWtrAtm for the case of
1581     ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
1582     - catch the case of an empty filename in seaice_cost_init_fixed.F
1583     o pkg ecco:
1584     - small bug fixes in the_main_loop
1585     . fix order of monitor arguments
1586     . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
1587     . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
1588     that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
1589     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
1590     imbalance diagnostics for wmean_h/sflux = 0
1591     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
1592     - catch the case of empty filenames in ecco_cost_init_fixed.F
1593     and ecco_readparms.F
1594     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
1595 mlosch 1.1164 to make this statement meaningfull in ecco_cost_weights.F
1596 jmc 1.1162 o pkg zonal_filt:
1597     - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
1598     - when using rStar, filter uVel*hFacW instead of uVel
1599     (tested without topography: fix a Pb of growing instability with NLFS)
1600 dfer 1.1161 o pkg/aim/thsice:
1601     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
1602     (works as SST restoring)
1603 dfer 1.1160 o pkg/thsice:
1604     -add specific parameter for salt restoring in slab mixed-layer
1605     (by default equal to the temperature restoring)
1606    
1607 jmc 1.1203 checkpoint61v (2009/09/21)
1608 mlosch 1.1158 o pkg/kpp:
1609     -add double diffusive contributions as a hack, turned off by default
1610     for now, and the code can be excluded with a CPP-flag
1611     EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
1612     -add a verification experiments to "vermix" to test this code
1613 dfer 1.1157 o pkg/mom_common:
1614     Move computation of length scales to mom_init_fixed.F (avoid recomputation
1615     at each time-steps*levels).
1616 rpa 1.1156 o pkg/layers:
1617     Created a new package for computing volume fluxes in temperature or
1618     [not yet implemented] density layers, e.g. for calculating residual
1619     overturning circulations.
1620 jmc 1.1155 o pkg/diagnostics:
1621     implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
1622     o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
1623 jmc 1.1154 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
1624     To avoid mixing type (RS/RL) of input/output array argument,
1625     replace single mixed-type array with a pair from each type (RS/RL).
1626 jmc 1.1153 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
1627     is now implemented for all pkgs (previously only done for the main pickup)
1628    
1629 jmc 1.1203 checkpoint61u (2009/08/25)
1630 mlosch 1.1150 o pkg/obcs:
1631 mlosch 1.1151 - change OB?eta from _RS to _RL and put them into a separate commen block
1632     - add code to read OB?eta from a file via obcs_prescribe_read: the code
1633     compiles and does not destroy any other experiments, the data is read
1634     properly, but the code is not tested in actual applications
1635 mlosch 1.1149 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
1636     create a meaningful unit attribute for the time coordinate variable
1637 jmc 1.1148 o pkg/ebm: add plenty of missing "_d 0" ;
1638     update results of experiment global_ocean_ebm (fwd + adjoint tests)
1639     Notes: several pieces of code only works for (very) specific set up
1640     (domain size, lat range, etc ...); should be documented & stop if one
1641     of those assumptions is not meet.
1642 jmc 1.1147 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
1643     update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
1644     and offline_exf_seaice (seaicetd + adjoint).
1645 jmc 1.1146 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
1646     update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
1647     seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
1648     o few changes to pass when compiling with strick checking of arguments
1649     across S/R (allow to find few bugs in S/R calls).
1650 mlosch 1.1145 o pkg/seaice:
1651     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
1652     2d-fields, for slightly better performance
1653 jmc 1.1146
1654 jmc 1.1203 checkpoint61t (2009/07/22)
1655 mlosch 1.1142 o pkg/seaice:
1656     - remove unused variables in seaice_evp
1657     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
1658 jmc 1.1141 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
1659     named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
1660 jmc 1.1144 each processor opens a different file (a fix from Matt).
1661 jmc 1.1140 o cg2d:
1662     use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
1663     this reduces number of EXCH calls by 2 when using exch2.
1664     For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
1665     directives and missing simple EXCH (exch_s3d_rx) adjoint code.
1666     o pkg/thsice:
1667     add code for Near Infra-Red albedo (from Jeff)
1668 jmc 1.1139 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
1669 jmc 1.1140 o ini_model_io:
1670     move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
1671     MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
1672     to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
1673 jmc 1.1139
1674 jmc 1.1203 checkpoint61s (2009/06/30)
1675 jmc 1.1137 o pkg/exch2 (exch2_rxN_cube*):
1676     remove last BARRIER (no need to synchronise after getting data from shared
1677     buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
1678 jmc 1.1136 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
1679     and generate new output (for the 2 tests) using default rotationPeriod.
1680 jmc 1.1135 o pkg/exch2:
1681     - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
1682     (was already the case with AUTODIFF_EXCH2 defined)
1683     - add bj in exch2 arrays and S/R.
1684 jmc 1.1136 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
1685     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
1686 jahn 1.1134 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
1687     - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
1688     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
1689     - verification experiment natl_box.longstep
1690 jmc 1.1133 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
1691     allow different versions of ifort (8 or 9) and different versions
1692     of mpi (mpich or mpich2) to be used with the same optfile.
1693     requires to load a netcdf module and set MPI_INC_DIR (see comments inside
1694     optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
1695 jmc 1.1135 o pkg/seaice:
1696     fix previous modif (3-level field removed) for old-pickup reading
1697 jmc 1.1133
1698 jmc 1.1203 checkpoint61r (2009/06/25)
1699 mlosch 1.1129 o pkg/seaice:
1700 mlosch 1.1130 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
1701     1. introduce fields for time step (N-1)
1702     2. do not use levels 2 and 3 anymore (but keep them)
1703     3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
1704     includes changes to pkg/thsice/thsice_get_velocity.F,
1705     model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
1706     pkg/obcs/obcs_apply_uvice.F.
1707     - completely remove code for leap-frog time stepping for second order
1708 mlosch 1.1129 advection
1709 heimbach 1.1131 - adjusted adjoint accordingly;
1710     gradient checks have improved by an order of magnitude!
1711 mlosch 1.1130
1712 jmc 1.1203 checkpoint61q (2009/06/22)
1713 mlosch 1.1128 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
1714     - the boundary conditions along open boundaries are unclear, because the
1715     associated masks are set to zero and are thus treated as closed when
1716     applying the slip-boundary conditions.
1717     - move initialisation of grid variables from seaice_init_varia to _fixed
1718 dimitri 1.1127 o adding doc/diags_changes.txt
1719 jmc 1.1126 o model/src:
1720     do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
1721     to avoid "_diags" naming if no relation to pkg/diagnostics.
1722     ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
1723     file and only call PLOT_FIELD_XYZ if debugMode=T.
1724     remove few PLOT_FIELD_XY calls outside initialisation.
1725     remove few unnecessary BARRIER.
1726 dimitri 1.1125 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
1727     of salt_plume package in Southern Ocean
1728 jmc 1.1124 o pkg/thsice:
1729     - fix hOceMxL in overlap (needed for sea-ice advection);
1730     update output of experiment global_ocean.cs32x15.icedyn.
1731 mlosch 1.1123 o pkg/seaice:
1732     - make the (placeholder-)tracer IceAge a little more meaningful
1733 mlosch 1.1122 by avoiding ridging of age due to convergent ice flow
1734 dimitri 1.1127 - add diagnostics for surface temperature, atmospheric and oceanic
1735     heat flux, and atmospheric and oceanic ice growth
1736 mlosch 1.1122
1737 jmc 1.1203 checkpoint61p (2009/06/10)
1738 jmc 1.1120 o eesupp (global_max & global_sum):
1739     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
1740     - remove starting & endding barrier (no longer needed)
1741 jmc 1.1119 o pkg/mdsio, writelocal:
1742     works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
1743     (remove the STOP): uses shared buffer IO to store data from all threads
1744     and then let master-thread write nThreads tiles.
1745 jmc 1.1118 o pkg/mdsio (read/write field):
1746     - tiled IO done in 1 piece (all levels at a time);
1747 jmc 1.1119 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
1748 jmc 1.1118 - multi-threaded: allow to read/write local (non-shared) array
1749     (was already working with singleCpuIO ; now works also without);
1750     => no longer needs barrier call after reading a file (added inside
1751 jmc 1.1119 mds_read/write field).
1752 jmc 1.1118 - move barrier calls outside gather/scatter_2d to mds_read/write_field
1753 mlosch 1.1115 o pkg/obcs/exf
1754 mlosch 1.1116 - exf_getffieldrec.F: add a few ". _d 0" and
1755     add code to catch the case fldperiod = 0.
1756 mlosch 1.1115 - obcs_precribe_read.F: change if statements so that they match
1757     the variable type (_RL)
1758     - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
1759     exf_iprec) as part of namelist EXF_NML_01
1760 jmc 1.1114 o pkg/mdsio:
1761     - read/write tiled (local) files: read/write 1-level tile chunk at a time
1762     (instead of segment of length sNx); expected to speed up tiled IO.
1763     o pkg/exch2:
1764 jmc 1.1113 - take buffer copy from/to array out of S/R exch2_send/recv into new
1765     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
1766     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
1767     - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
1768 jmc 1.1114 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
1769 jmc 1.1113 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
1770     including Topology header file (and common blocks).
1771     - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
1772     remove 2nd exch call in exch2_s3d_rx (no longer needed).
1773     - document S/R arg. list (+ update some comments)
1774 dimitri 1.1117 o pkg/seaice:
1775     - added SEAICE_CLIM_AIR code, which permits modulation of surface air
1776     temperature and humidity over sea ice based on climatological values.
1777 mlosch 1.1111 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
1778     of LSR (this change is expected to change the results slightly because now
1779     it uses slightly difference moduli from the second last LSR solution, but
1780     that is more consistent with the stress computations; this part of the code
1781     is not tested in the verification experiments)
1782 mlosch 1.1110 - fix diagnostics for flux of ice in case of B-grid
1783     - turn strain rates eij and press into global fields within global
1784     common block in SEAICE.h for more straighforward diagnostics
1785     - fix diagnostics for principal stress components, press, zeta, eta
1786     to give something meaning full
1787 jmc 1.1109 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
1788     new output (all 4 tests) using default rotationPeriod.
1789 dfer 1.1112 o pkg KPP:
1790     - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
1791     - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
1792     and normal grid from 1 to Nr)
1793 dfer 1.1108 o Fix computations of L4rdt in mom_calc_visc.F
1794 jmc 1.1107 o eesupp:
1795     new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
1796     should be called before a "stop" if we know that all process are going
1797     to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
1798    
1799 jmc 1.1203 checkpoint61o (2009/05/26)
1800 jmc 1.1106 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
1801     o model/src/ini_curvilinear_grid.F:
1802 mlosch 1.1104 compute angleSin/CosC when they are not read from a file
1803 jmc 1.1106 o pkg/seaice:
1804 mlosch 1.1104 add pseudo time stepping for LSOR
1805 jmc 1.1103 o pkg/exch2:
1806     temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
1807 dimitri 1.1102 o pkg/seaice:
1808 dimitri 1.1105 Adding separate sea ice albedo, drag coefficients, and HO in Southern
1809     Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
1810 jmc 1.1101 o SingleCpuIO:
1811     fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
1812     o pkg/seaice:
1813 jmc 1.1100 put exchanged variable in (local) common block for MPI+Multi-Threads
1814     to work (necessary with exch1, and for now with exch2 too).
1815 jmc 1.1099 o verification: to get more experiments tested with mpi, mth and mpi+mth,
1816     change tiling of:
1817     aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
1818     hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
1819     update output of exp:
1820     exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
1821     tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
1822     + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
1823     (note: output.txt generated on faulks using only 1 tile)
1824 jmc 1.1098 o eesupp & mdsio (SingleCpuIO):
1825     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
1826     parameter "W2_useE2ioLayOut" (read from file "data.exch2").
1827     Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
1828     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
1829     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
1830     gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
1831 jmc 1.1097 o pkg/exch2:
1832     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
1833     read parameter file "data.exch2" if it exists; otherwise try default regular
1834     cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
1835     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
1836     with new code (not to be used, just as a backup solution).
1837 jmc 1.1098 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
1838     in utils/exch2/input.
1839 jmc 1.1097
1840 jmc 1.1203 checkpoint61n (2009/05/12)
1841 jmc 1.1095 o eesupp & mdsio (SingleCpuIO):
1842     - move mapping to global io-buffer inside gather_2d/scater_2d: this save
1843     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
1844     receive real*4 array (instead of real*8) to read/write 32.bit files.
1845     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
1846     and remove new mapping S/R)
1847 jmc 1.1094 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
1848     - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
1849     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
1850     when using exch2. Add S/R to map global io-buffer to global model array.
1851     - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
1852    
1853 jmc 1.1203 checkpoint61m (2009/04/29)
1854 jmc 1.1094 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
1855     and add 3 other S/R for other types (R4,R8,RS).
1856 jmc 1.1092 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
1857     o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
1858     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
1859     - reduce number of macro definitions (keep only those which are used);
1860     can always call directly the corrresponding S/R if needed.
1861 jmc 1.1094 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
1862 jmc 1.1092 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
1863     Fixed wrong type of arg in:
1864 jmc 1.1094 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
1865 jmc 1.1092 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
1866     To fix: global_sum of var in common block is wrong (multi-threaded) in:
1867     dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
1868     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
1869 jmc 1.1094 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
1870     "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
1871 jmc 1.1091 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
1872     o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
1873     edges are closed (zero depth); might happen with "blank tiles";
1874 jmc 1.1094 for now, disabled if using OBCS.
1875 jmc 1.1091 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
1876 jmc 1.1090 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
1877 jmc 1.1091 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
1878 jmc 1.1089 to reduce length of 1.D array print in STDOUT.
1879 jmc 1.1088 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
1880     + use 48 tiles (16x8): this will allow to test "blank tiles".
1881     o start to test MPI + multi-threaded (change testreport to skip tests
1882     where number of tiles do not match).
1883     o genmake2: add option "-omp" to turn on Open-MP ;
1884     passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
1885 jmc 1.1086 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
1886     and keep the original tile numbering. Note: compatible with old
1887     W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
1888    
1889 jmc 1.1203 checkpoint61l (2009/04/07)
1890 jmc 1.1085 o Overlaps had been forgotten in calculating ijk keys : fixed
1891     o fix cyrus makedepend for gcc 4.4
1892 jmc 1.1084 o experiment fizhi-cs-aqualev20:
1893     switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
1894 jmc 1.1088 and generate new output. Note: new output is much closer to the old
1895     one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
1896 jmc 1.1084 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
1897     o pkg/fizhi:
1898     - change to avoid indices going deliberately over array-bounds
1899     - remove unnecessary MPI stuff
1900     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
1901     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
1902     does not go over array-bounds and therefore returns reliable output.
1903     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
1904     this S/R has 4 output arguments, which are used inside "get_alarm";
1905     when it is called with the same variable "ndum" in place of several
1906     output arguments, this produces weird side effect inside "get_alarm"
1907     (e.g., datein=dates(n) is overwritten by timein=times(n) since both
1908     datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
1909     address) and produces error.
1910 jmc 1.1090 o tools/gemake2: (March 27-29 2009)
1911     with option "-mpi": link *_mpi files from "MODS" dir (this is what
1912     testreport does).
1913 jmc 1.1083 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
1914 jmc 1.1084 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
1915 jmc 1.1083 update lab_sea.lsr & lab_sea.salt_plume results
1916 mlosch 1.1079 o pkg/seaice:
1917     Major overhaul of the LSOR solver: change discretization from original
1918     finite differences to finite volume. The old routine is still in the
1919     file seaice_lsr.F and can be turned on with the CPP-flag
1920     SEAICE_OLD_AND_BAD_DISCRETIZATION
1921     Along with this change, the discretization of the strain rates is changed.
1922     The same flag turns on the old discretization in seaice_calc_strainrates.F
1923     All verification experiments with seaice are affected (except for
1924     seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
1925     results by setting the above flag.
1926     Further changes involve changes in defaults:
1927     - ALLOW_FLOODING is defined and turned on by default
1928 heimbach 1.1087 - SEAICEadvSnow = .true. is now the default
1929     - SEAICEadvSalt = .true. is now the default
1930     - SEAICEadvAge = .true. is now the default
1931 mlosch 1.1081 - SEAICE_clipVelocities = .false. is now the default
1932     (as per J. Zhang's recommendation)
1933 mlosch 1.1079 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
1934     is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
1935     - seaice_growth: replace computation of UG by a simple copy from wspeed
1936    
1937 jmc 1.1203 checkpoint61k (2009/03/18)
1938 mlosch 1.1078 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
1939     seaice_lsr: fixed a few metric terms,
1940     affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
1941     add more debugging diagnostics
1942     seaice_evp: removed superfluous many metric terms of FV discretization
1943     of stress divergence
1944     affects lab_sea, lab_sea.hb87
1945     seaice_ocean_stress: removed superfluous many metric terms of FV discretization
1946     of stress divergence for non-evp solver
1947     (this part is not tested anywhere)
1948     seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
1949     they were effectively only half slip
1950     affects lab_sea.hb87
1951 jmc 1.1082 updated all relevant verification experiments (except lab_sea//output_adm.txt
1952     which was left over, but fails at level 7 & 6)
1953 mlosch 1.1078
1954 jmc 1.1203 checkpoint61j (2009/03/17)
1955 mlosch 1.1076 o pkg/seaice: turn a few hard wired parameters into run time parameters
1956 mlosch 1.1075 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
1957     time in seconds as promised by the usints in seaice_monitor and exf_monitor
1958 mlosch 1.1074 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
1959     that are not cubed-sphere grids
1960 mlosch 1.1073 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
1961 jmc 1.1072 o pkg/ctrl:
1962     fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
1963 jmc 1.1071 o non-hydrostatic (calc_gw.F):
1964     fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
1965     update output of exp. global_ocean.cs32x15.viscA4
1966     o remove backward compatibility for thetaMin,phiMin
1967 jmc 1.1070 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
1968 mlosch 1.1069 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
1969     interpolated wind field not only for curvilineargrid=.true., but also
1970     for a rotated grid (rotateGrid=.true.)
1971 mlosch 1.1068 o pkg/exf: add capability to bypass interpolation for runoff
1972     by setting yet another CPP-flag
1973 jmc 1.1070 o eesupp/src, B-grid exchange:
1974     add simple (6 tiles, non MPI) CS exch + standard interface S/R.
1975 heimbach 1.1067 o autodiff
1976     new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
1977     allows to switch to single-prec common blocks;
1978     corresponding switch occurs in tamc.h, integer isbyte
1979     TAF store directivs "byte" and "kind" seem equivalent;
1980     Most tamc.h have been updated correspondingly.
1981    
1982 jmc 1.1203 checkpoint61i (2009/02/13)
1983 heimbach 1.1066 o autodiff:
1984     fix autodiff_sore/_restore indices for obcs
1985     (spotted by I. Hoteit, M. Mazloff)
1986 heimbach 1.1065 o pkg/autodiff, pkg/ctrl:
1987     Add flag to reduce all tapelev I/O to single-prec.
1988     In data.ctrl set
1989     doSinglePrecTapelev = .TRUE.
1990 jmc 1.1070 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
1991     check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
1992 mlosch 1.1062 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
1993     real fresh water flux (not yet)
1994 jmc 1.1060 o pkg/mdsio & rw:
1995     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
1996     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
1997 jmc 1.1058 o pkg/flt:
1998     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
1999     init_fixed & ini_varia.
2000 jmc 1.1059 - clean-up & simplify linear interpolation S/R:
2001     move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
2002     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
2003 jmc 1.1060 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
2004 jmc 1.1061 - add vert. coordinate & horiz. indices to output files.
2005     - change vertical position in initial condition, from index to depth [m].
2006 jmc 1.1063 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
2007     (easier to get to a curvilinear grid) ; delX,delY no longer used.
2008 dfer 1.1057 o pkg/ggl90: a few modifications:
2009     - fix bottom boundary condition, and interpolation of KappaE
2010     near top and bottom
2011     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
2012     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
2013     - add a few options for mixing-length upper limit (--> mxlMaxFlag)
2014 jmc 1.1056 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
2015     (maintain temporary backward compatibility, until next checkpoint)
2016    
2017 jmc 1.1203 checkpoint61h (2009/01/27)
2018 jmc 1.1054 o pkg/diagnostics with "periodic averaging diagnostics":
2019     fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
2020 jmc 1.1053 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
2021 mlosch 1.1052 o pkg/obcs: fix loop ranges for balancing code
2022 jmc 1.1051 o pkg/flt:
2023     - improve criteria for finding which tile owns a float.
2024     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
2025 dfer 1.1050 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
2026     aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
2027     with ocean biogeo)
2028 jmc 1.1049 o pkg/flt:
2029     - do some cleaning and fix the restart ;
2030     - add output.txt in flt_example/results to get this pkg tested.
2031     o genmake2: add an EXTENDED_SRC option and flag.
2032     for now, cannot be turned on on command line (only through genmake_local)
2033 jmc 1.1048 o pkg/mdsio: read/write vector:
2034     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
2035 jmc 1.1049 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
2036 jmc 1.1048 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
2037     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
2038     (drop to 4 digits matching for grad). But this test does not look very
2039     reliable (was already failling on eddy, fc5, at 6.digits). Update output.
2040    
2041 jmc 1.1203 checkpoint61g (2008/12/29)
2042 jmc 1.1046 o pkg/flt:
2043     - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
2044     + make OPTIONS file more standard.
2045     - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
2046     - fix _BYTESWAPIO CPP-Flag
2047     - standard reading of file-parameter "data.flt"
2048 jmc 1.1047 - fix argument list of S/R FLT_RESTART
2049 jmc 1.1046 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
2050 mlosch 1.1045 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
2051 mlosch 1.1044 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
2052     a still unfixed compiler/optimization bug
2053    
2054 jmc 1.1203 checkpoint61f (2008/11/21)
2055 jmc 1.1042 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
2056     update results of global_ocean.cs32x15.icedyn test.
2057 jmc 1.1041 o move getcon.F from model/src to pkg/fizhi.
2058 jmc 1.1040 o pkg/exf: add parameter for extrapolation of temp up to the surface
2059     and option to prevent negative evap (in bulk_largeyeager04 only).
2060 jmc 1.1039 o Prather Advection scheme: fix tracer conservation for divergent flow
2061     (e.g., when using NonLin Free-Surface).
2062 dfer 1.1038 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
2063 jmc 1.1037 o gmredi (Visbeck-variable-K):
2064     - add more parameters to Visbeck-variable-K.
2065     - use a 5 points average for dSigmaR in Visbeck-K calculation
2066     (more "homogenous": same stencil and same weights as in dSigmaH)
2067     - update output of ideal_2D_oce experiment.
2068 mlosch 1.1034 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
2069     (#undef REAL4_IS_SLOW)
2070     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
2071     coordinate variable
2072     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
2073     (surface forcing fields), removes some of the functionality
2074     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
2075     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
2076     probably not all: copy _RS surface flux fields to RL field before
2077     calling DIAGNOSTICS_FILL
2078 mlosch 1.1035 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
2079     real*4 (CALL EXCH_*_RS) versions.
2080 jmc 1.1036 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
2081     (generate new output).
2082 mlosch 1.1034
2083 jmc 1.1203 checkpoint61e (2008/10/23)
2084 jmc 1.1032 o gmredi (Visbeck-variable-K):
2085     - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
2086     - change computation of Visbeck-K where Slope > Smax :
2087     now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
2088     previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
2089 jmc 1.1031 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
2090     to be the same as with Z-coord. (i.e., m/s & no-units respectively).
2091     o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
2092 jmc 1.1030 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
2093 jmc 1.1032 does not become too large (to avoid precision problems in implicit-diffusion
2094 jmc 1.1030 solver); update ideal_2D_oce output.
2095 dfer 1.1028 o pkg ggl90:
2096     - in ggl90_cal.F: compute only one set of visc/diff, used to
2097     step forward TKE/T/S/momentum
2098     - default value of GGL90viscMax/GGL90diffMax larger and equal (to
2099     have Prandlt =1)
2100 jmc 1.1032 o gmredi (fm07):
2101 jmc 1.1029 - add lower limit on Transition layer thickness + lower limit on 1/lambda
2102 jmc 1.1027 - allow to set few more params from data.gmredi
2103 dfer 1.1026 o pkg ggl90:
2104     - add missing sqrt(2) factor in computation of mixing length
2105     scale in ggl90_calc.F
2106     (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
2107    
2108 jmc 1.1203 checkpoint61d (2008/09/25)
2109 heimbach 1.1025 o adjoint modifs
2110     - adapt to new field rhoInSitu
2111     - allow to revert from StoreDynVars2D, StoreDynVars3D
2112     to individual fields
2113     (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
2114 jmc 1.1024 o store 3-D (in-situ) density in commom block (DYNVARS.h)
2115     - save 1 rho computation.
2116     - no longer modify T & S inland when using down_slope pkg.
2117 jmc 1.1023 o gad_som : allow to switch to SOM advection for T & S without corresponding
2118     pickup files (using new S/R: MDS_CHECK4FILE).
2119     o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
2120     (for useSingleCpuIO to work in multi-threaded)
2121 mlosch 1.1022 o pkg/shelfice:
2122     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
2123     with SHELFICEtopoFile in data.shelfice
2124     - move code for reading ice shelf topography and modifying hFacC into separate
2125     subroutines of the shelfice package
2126     - separate initialisation of "fixed" and "variable" variables
2127     - kTopC is not (yet) replaced by kSurfC, although this is possible
2128 jmc 1.1023 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
2129 jmc 1.1020 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
2130     and rename:
2131     ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
2132     ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
2133     o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
2134    
2135 jmc 1.1203 checkpoint61c (2008/08/30)
2136 jmc 1.1018 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
2137     to add mass source/sink of fluid in the interior (3-D generalisation
2138     of oceanic real-fresh water flux).
2139     o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
2140 jmc 1.1017 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
2141 jmc 1.1016 o new pkg: down_slope
2142     density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
2143     - presently, modify T & S inland (dwnslp_calc_rho.F).
2144     can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
2145     - implementation for ocean in P-coords not tested.
2146     - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
2147     o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
2148 jmc 1.1015 (to facilitate conversion of oceanic pkg to p-coordinate).
2149 jmc 1.1014 o change FIND_RHO to FIND_RHO_2D :
2150     pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
2151     o new pkg: cheapaml
2152    
2153 jmc 1.1203 checkpoint61b (2008/08/05)
2154 jmc 1.1011 o exch2:
2155 jmc 1.1012 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
2156     - no longer depend on the order sequence (N,S,E,W).
2157     - 3rd exchange no longer needed (tested with 24 tiles).
2158     - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
2159     - exch_UV_A-grid readily available (but not yet tested).
2160     comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
2161     (both are no longer needed) in exch_uv: no effect in forward run; but
2162     get truncation error differences with adjoint exch.
2163     o exch2:
2164 jmc 1.1011 - change index-bounds storage (moved from target to local tile,
2165     more intuitive this way) ; rename/remove some variables.
2166 jmc 1.1012 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
2167 jmc 1.1011
2168 jmc 1.1203 checkpoint61a (2008/07/29)
2169 jmc 1.1009 o exch2/matlab-topology-generator:
2170     fix bug in index bounds for N-S internal exchange (hard to tell if this
2171     had any effect on the solution).
2172 mlosch 1.1008 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
2173     is exceeded
2174 mlosch 1.1007 o testreport: modify syntax of awk, so that it works also with
2175     awk, and not only with nawk and gawk
2176    
2177 jmc 1.1203 checkpoint61 (2008/06/24)
2178 heimbach 1.1005 o autodiff
2179     Change default for TAF usage by removing argument '-nonew_arg'
2180     This changes TAF subroutine argument list (ordering of active var.)
2181     Omission of this flag leads to incompatibility w.r.t. TAMC
2182     To restore TAMC-compatibility, need following modifs:
2183     * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
2184     * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
2185     Tested TAF version is 1.9.22
2186     N.B.: exch2 hand-written adjoint code currently not TAMC compatible
2187    
2188 jmc 1.1203 checkpoint60 (2008/06/19)
2189 heimbach 1.1004 --->>> This is the last checkpoint for which generating the adjoint
2190     --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
2191     --->>> by default.
2192     --->>> Future checkpoints will ommit this flag by default.
2193 jmc 1.1003 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
2194 gforget 1.1002 o pkg/grdchk: Add gradient check to etan0 perturbations.
2195 gforget 1.1001 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
2196 gforget 1.1000 o pkg/autodiff: more flexibility in zeroadj.
2197     model/src: modifying do_oceanic_phys.F accordingly.
2198 gforget 1.999 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
2199     o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
2200     special setup of gmredi for which the adjoint is stable
2201     enough for parameter optimization.
2202 gforget 1.998 o bridging the gap between eddy stress and GM.
2203     -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
2204     along with a change in CPP option (now ALLOW_EDDYPSI).
2205     -> when using GM w/ GM_AdvForm:
2206     The total eddy streamfunction (Psi = eddyPsi + K x Slope)
2207     is applied either in the tracer Eq. or in momentum Eq.
2208     depending on data.gmredi (intro. GM_InMomAsStress).
2209     -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
2210     The key modifications are in model/src/taueddy_external_forcing.F
2211     pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
2212 jmc 1.1003
2213 jmc 1.1203 checkpoint59r (2008/05/29)
2214 jmc 1.996 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
2215     from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
2216     fix option to read coriolis(@ cell-corner) from files with CS-grid.
2217 mlosch 1.995 o pkg/mnc: add some attributes to standard 1D-coordinate variables
2218 mlosch 1.993 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
2219     mass points, when using mnc for output
2220     - add runtime parameter (missing_value, missing_value_int) to override
2221     default (which is the value of getcon('UNDEF'))
2222     o pkg/mnc: prepare mnc for the actual use of missing values with the
2223     diagnostics package: small fix in mnc_cw_readwrite.template and more
2224     initialisation of never used fields
2225 mlosch 1.994 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
2226     versions
2227     o pkg/thsice/thsice_ini_vars.F added default initial values so that
2228     thermodynamics sea ice solver does not blow up when some initial fields
2229     are missing.
2230 jmc 1.991 o move from external_forcing_surf.F to ini_forcing.F
2231     the p-coord. hack consisting in using pLoad to set phi0surf ;
2232     update output of tutorial_global_oce_in_p (affected @ truncation level).
2233 dfer 1.990 o Freshen up a bit hs94.1x64x5, notably:
2234 mlosch 1.994 remove rotationPeriod and tRef=5*0. (adjoint only), and add
2235     exactConserv=.TRUE.
2236 jmc 1.989 o pkg/generic_advdiff:
2237     change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
2238     applies to files where Temperature & Salinity 2nd Order moments are used.
2239 jahn 1.988 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
2240     this uses a dynamically allocated internal state data structure
2241     (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
2242     and requires a fortran 90 compiler
2243    
2244 jmc 1.1203 checkpoint59q (2008/05/06)
2245 jmc 1.986 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
2246     (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
2247 dfer 1.985 o Refresh tutorial_global_oce_biogeo, notably:
2248     - change bathymetry (put back seamounts in ACC, use hFacs)
2249     - change EOS (POLY3 --> JMD95Z)
2250     - use Bryan-Lewis vertical diffusivity
2251     - use multidimensional advection
2252     - remove old virtual virtual in dic pkg, now done through ptracer pkg
2253     - change a couple of parameters in dic pkg
2254 gforget 1.984 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
2255 mlosch 1.982 o pkg/obcs: change default to OBCSfixTopo = .true.,
2256 mlosch 1.983 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
2257     - replace "debugMode" with "debugLevel .GE. debLevB"
2258 gforget 1.981 o implementation of TAF directives for gchem,cfc,dic
2259 jmc 1.980 o remove "exp5" (replaced by tutorial_deep_convection).
2260 mlosch 1.979 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
2261     this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
2262     the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
2263 mlosch 1.982 --> changes results in exp4, seaice_obcs
2264 jmc 1.980 o tutorial_deep_convection :
2265 jmc 1.978 update the set-up and increase resolution and domain size ; start
2266     from pseudo initial conditions = output at t=120mn in order to see
2267     something happening when running testreport.
2268 mlosch 1.976 o pkg/seaice: add os7mp as an advection scheme
2269     add check for advection schemes
2270 mlosch 1.977 add a flag for restoring T and S underneath sea ice
2271 mlosch 1.975 o pkg/my82: add netcdf-support and diagnostics
2272 dfer 1.974 o thsice pkg:
2273 mlosch 1.979 - Now hsMax limits snow height by turning it into ice following
2274 dfer 1.974 flooding scheme (and now conserving energy)
2275     - Slight rewriting of the formula in thsice_calc_thick.F
2276     - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
2277 jmc 1.980 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
2278 dfer 1.974
2279 jmc 1.1203 checkpoint59p (2008/04/10)
2280 jmc 1.973 o gchem / dic / cfc :
2281     - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
2282     - add new parameter files: "data.dic" & "data.cfc" ;
2283     - various re-arrangement in initialisation & header file ;
2284     - fix tutorial_global_oce_biogeo for multi-threaded test.
2285     o pkg/dic: test for "pickup_dic" file when restarting ;
2286     if no pickup-file, can restart with a re-initialised pH (same as it did
2287 jmc 1.972 before) providing pickupStrictlyMatch is set to False.
2288 jmc 1.971 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
2289     + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
2290 jmc 1.970 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
2291     and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
2292     o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
2293     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
2294     (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
2295 jmc 1.969 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
2296     scheme to use for vorticty-term ;
2297     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
2298     (with default selectVortScheme, return to original discretisation)
2299     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
2300 mlosch 1.968 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
2301 jmc 1.967 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
2302     bottom ; only used with variable horizontal viscosity and non-hydrostatic.
2303     also fix diagnostics VISCAHW & VISCA4W.
2304    
2305 jmc 1.1203 checkpoint59o (2008/03/07)
2306 jmc 1.965 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
2307 mlosch 1.964 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
2308     move a few statemens out the main loop into separate loops
2309 mlosch 1.962 o pkg/shelfice:
2310     - sort out freshwater flux; convert freshwater fluxes to mass fluxes
2311     (kg/m^2/s), does not break tests, because in verification/isomip,
2312     rhoConstFresh=rhoConst (by accident)
2313 mlosch 1.963 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
2314     - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
2315     new file model/src/seawater.F, so that they are available for all pkgs.
2316     - convert potential temperature into in-situ temperature. This changes the
2317     isomip tests => update tests
2318 mlosch 1.961 o add a flag writePickupAtEnd (default=true) to be able to suppress
2319     writing a pickup at the last timestep
2320 jmc 1.966 o tools/mpack-1.6 :
2321     - disable automake (not working) and autoconf (not needed).
2322     - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
2323     also cleaner with much less compilation warnings.
2324 gforget 1.960 o pkg/profiles:
2325     rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
2326     (for "less than 32 characters name" compiler requirement)
2327 dimitri 1.959 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
2328     conditions that have a different sampling frequency than S/T/U/V obcs
2329 jmc 1.958 o pkg/diagnostics (stats-diags):
2330     - fix global Min/Max in case 1 processor get only empty tiles
2331 mlosch 1.957 o genmake2: replace (4 times)
2332     make genmake_tc_1.o >> genmake_warnings 2>&1
2333     with
2334     COMM="$CC $CFLAGS -c genmake_tc_1.c"
2335     echo $COMM >> genmake_warnings
2336     $COMM >> genmake_warnings 2>&1
2337     to make genmake2 always see the value of CC as specified in the optfile.
2338 jmc 1.956 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
2339     - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
2340     - modify verification advect_cs test to test SOM-advection on CS-grid.
2341 gforget 1.955 o pkg/ctrl:
2342     - Rewrite of ctrl_map_ini_ecco.F,
2343     introducing a generic routine (ctrl_map_ini_gen.F).
2344     - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
2345 jmc 1.956
2346 jmc 1.1203 checkpoint59n (2008/02/09)
2347 jmc 1.953 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
2348     number in dedicate array "hdiag":
2349     - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
2350     with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
2351     - many small changes (integer format) for large number of diagnostics
2352     - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
2353     a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
2354 mlosch 1.952 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
2355     usingSphericalGrid, this allows to define the rotated grid coordinates
2356     via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
2357     geographical coordinates according to the inverse of the rotation defined
2358     by the Euler angles, so that Coriolis parameter and online-interpolation by
2359     exf works with the geographical coordinates on XC/YC/XG/YG.
2360     Naturally, this feature does not work with all packages, so some
2361     combinations are prohibited in config_summary (flt, flt_zonal, ecco,
2362     profiles), because there the coordinates are assumed to be regular
2363     spherical grid coordinates.
2364 gforget 1.951 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
2365     - introduce isopycnal diffusion coefficient control.
2366     o tools/adjoint_options:
2367     - additional control vector components.
2368 mlosch 1.950 o pkg/mnc: have mnc create marginally meaning full coordinate variables
2369     (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
2370 jmc 1.948 o pkg/mypackage:
2371     - add example of read/write pickup for state-var ;
2372     - add entry points to the main code for state-vars diags & write-pickup.
2373 dimitri 1.946 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
2374     transitions for useExfYearlyFields
2375 mlosch 1.947 - add new subroutine that determines the file to read from for
2376     use*YearlyFields = .TRUE. and .FALSE.
2377 mlosch 1.949 - add a verification experiment to global_with_exf that tests
2378     useExfYearlyFields with USE_EXF_INTERPOLATION defined
2379 mlosch 1.945 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
2380     analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
2381     subroutines (which could be generated from a template, because they are
2382     almost identical), for now they are included in obcs_prescribe_read.F for
2383     simplicity
2384 mlosch 1.943 o pkg/exf:
2385     - add a little more diagnostic to exf_interp_read (in analogy to
2386     mds_read_field, can be turned off with debugLevel < debugLevA=1)
2387     - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
2388 mlosch 1.944 ugly but fast by unrolling short inner loops, inserting a unroll=8
2389     directive in routine lagran, and splitting a loop and making do while the
2390     outermost loop (the latter requires the intoduction of index arrays)
2391 dimitri 1.942 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
2392 dimitri 1.941 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
2393     http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
2394 dimitri 1.940 o verification/seaice_obcs: updated for restart test and latest options
2395 mlosch 1.939 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
2396     ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
2397     for now this is only available for the C-grid code and also within
2398     #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
2399    
2400 jmc 1.1203 checkpoint59m (2008/01/14)
2401 dimitri 1.936 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
2402     and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
2403 dimitri 1.937 o gad_som : fix flux output (& diagnostics) to have same units as other
2404     advection scheme fluxes (was previously multiplied by deltaT).
2405 dimitri 1.933 o added verification/seaice_obcs both to test seaice open boundaries
2406     and to provide an example matlab scrpt for generating them
2407     o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
2408 atn 1.931 o pkg/salt_plume: clean up salt_plume_frac.F to
2409     remove redundancy in PlumeMethod 1 and 4
2410 atn 1.930 o pkg/kpp: added saltplume diagnostics
2411 dimitri 1.929 o pkg/obcs and pkg/seaice:
2412     - do not set uice and vice to zero when OB*icefile are unspecified
2413     - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
2414     - moved seaice tracer obcs after call to seaice_growth
2415 dimitri 1.927 o pkg/salt_plume: added various options for salt plume depth
2416     criterion and for vertical distribution of the salt
2417 jmc 1.928
2418 jmc 1.1203 checkpoint59l (2007/12/18)
2419 jmc 1.925 o pkg/ptracers: new version of ptracers pickup:
2420     read meta file and write only fields which are needed to restart.
2421     ( same logic as main pickup file ; also using pickupStrictlyMatch )
2422 dimitri 1.924 o pkg/seaice:
2423 mlosch 1.923 - add timescale for melting due to warm mixed layer as a means of
2424     setting SEAICE_availHeatFrac more conveniently
2425     - add a CPP-flag/runtime parameter check for flooding algorithm
2426 dimitri 1.924 - reformulated availHeat in seaice_growth.F to be independent of AREA
2427 mlosch 1.923 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
2428     unit changes
2429 dimitri 1.921 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
2430 mlosch 1.919 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
2431     SX vector computer.
2432 dimitri 1.920 o pkg/seaice:
2433     - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
2434     seaice forcing fields can now be read only through pkg/exf
2435     - removed some unused halos
2436 jmc 1.917 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
2437 dimitri 1.922 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
2438     or U/VICE from U/VWIND before computing U/VSTRESS
2439 dimitri 1.916
2440 jmc 1.1203 checkpoint59k (2007/11/30)
2441 dimitri 1.914 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
2442     dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
2443 jmc 1.913 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
2444 jmc 1.925 all experiments pass when compile with un-initialised var. checking option.
2445 dimitri 1.912 o added pkg/salt_plume
2446 jmc 1.911 o script to test restart (for now, in MITgcm_contrib/jmc_script)
2447     o pkg/seaice: new read/write pickup version.
2448     read meta file and write only fields which are needed to restart.
2449     ( same logic as main pickup file ; also using pickupStrictlyMatch )
2450 mlosch 1.910 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
2451 jmc 1.909 o lab_sea.hb87: modify the domain & update output.hb87.txt :
2452     lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
2453     at j=1 & j=Ny+1 : this case is not treated correctly in the restart
2454     process. Fixed here by closing the domain at the Northern boundary.
2455     o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
2456     o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
2457     a set of consecutive levels in/from a 3-D array.
2458 jmc 1.908 o pkg/ptracers:
2459 jmc 1.909 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
2460 jmc 1.908 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
2461    
2462 jmc 1.1203 checkpoint59j (2007/11/09)
2463 jmc 1.906 o in pkgs: dic, obcs, offline, rbcs:
2464     standard way to compute coeff. for time interpolation between 2 time reccords
2465     which retains full precision (& make results less dependent on compiler).
2466     update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
2467 mlosch 1.905 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
2468     packages instead of reading ice cover and wind speed separately
2469 jmc 1.904 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
2470     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
2471     to allow to compile customized code before the update)
2472 jmc 1.903 o cleaning-up:
2473     - fix CPP instruction syntax in pkg/obcs
2474     - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
2475     add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
2476     - fix some threads issue in IO parts.
2477 dfer 1.901 o pkg/dic:
2478     - add tons of "_d 0" (--> much better testreports !)
2479     and then update outputs of tutorial_global_oce_biogeo
2480 jmc 1.900 o pkg/mom_fluxform:
2481     add a special version of momentum advection intended to conserve momentum
2482     next to a bathymetry step or a coastline edge. (default = off = #undef)
2483 jmc 1.898 o new read/write pickup version:
2484     - for now, only implemented for main (mdsio) pickup file.
2485     - write out only what is needed to restart; merge pickup_nh , pickup_ph
2486     and main pickup together.
2487     - read meta file; read only what is needed to restart; stop if a field
2488     is missing (if pickupStrictlyMatch=T, = the default) or try to restart
2489     if it make sense (even if the restart is not perfect).
2490     - if no meta file, assume that pickup to read corresponds exactly to
2491     a pickup that would currently be written.
2492     - read pickup written in the old format (until checkpoint59i) if it
2493     recognizes an old meta file (no field-list).
2494     - add a meta file in exp. which starts from a pickup: 2 cases:
2495     a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
2496     e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
2497     b) a meta file describing the content of the associated pickup file
2498     e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
2499     o pkg/mdsio & pkg/rw:
2500     - new routine to read a meta file ; new set of routine to read
2501     Multiple-fields file (with meta file).
2502 dimitri 1.899 o added open boundary conditions capability for seaice
2503     HSNOW, HSALT, UICE, and VICE
2504 dimitri 1.897
2505 jmc 1.1203 checkpoint59i (2007/10/21)
2506 heimbach 1.895 o adjoint:
2507     * fix multiDimAdvection adjoint
2508     (partial recomputation problem by TAF for fVerT(:,:,kDown)
2509     and comlev1 size definition (maxpass vs. max. number of tracers)
2510     * verification/global_ocean.90x45x15 adjoint now tests
2511     NLFS and multiDimAdvection using DST3 (=30)
2512     * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
2513 jmc 1.894 o pkg/kpp: add "_d 0" to real constant (if missing);
2514     update output of exp: natl_box (10.digits); vermix (std, 7.digits)
2515     and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
2516 jmc 1.893 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
2517     for internal parameters related to restart process (formerly from PARAMS.h)
2518     and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
2519     o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
2520     as argument. (only atm2d & obcs write_pickup have not yet been updated)
2521 jmc 1.892 o pkg/monitor:
2522     - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
2523     - fix mon_stats_rs (statistics over the full domain, even where field is zero)
2524     - account for deep Atmosphere factor and density factor (anelastic)
2525 dimitri 1.891 o added open boundary conditions capability for seaice HEFF and AREA
2526 mlosch 1.890 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
2527     thermodynamics
2528     - requires a little reorganization, which affects the testreport results
2529     of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
2530     so that now the conservative form is tested
2531     - add a few comments
2532 jmc 1.892 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
2533 mlosch 1.888 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
2534 mlosch 1.887 o add new diagnostics to seaice: advective, diffusive fluxes (only for
2535     multidim-advection, for scheme 2 they are not filled) and transports,
2536     thermodynamic growth rates
2537 jmc 1.902 o change units of EmPmR (inside the code, + within coupling interface)
2538     from m/s to kg/m2/s (mass flux) but leave input file unchanged.
2539     Affects results @ truncation level (cg2d match) and update output of
2540     experiments: lab_sea(6), global_ocean.90x40x15(10),
2541 jmc 1.886 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
2542     + adjoint results: global_ocean_ebm(11) and lab_sea (12).
2543 jmc 1.902 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
2544 jmc 1.886 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
2545    
2546 jmc 1.1203 checkpoint59h (2007/09/29)
2547 mlosch 1.884 o pkg/exf:
2548     - improve vectorization by moving if-statement out of loops in
2549     exf_mapfields, exf_radiation
2550     - exf_bulkformulae.F: introduce 2D fields and vectorize code
2551 dimitri 1.881 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
2552 jmc 1.880 o testreport:
2553     - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
2554     monitor & update offline_exf_seaice exp. output.
2555     - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
2556 mlosch 1.879 o pkg/seaice:
2557     - bug fix in the evp solver: boundary conditions were affected be
2558     masking of zMax/zMin (changes results)
2559     - minor bug fix in boundary conditions in seaice_calc_strainrates
2560     (changes results for no_slip)
2561     - seaice_lsr.F: make interpolation of eta dependent on boundaries
2562     - replace hardcoded lower limit for zeta (zMin) by runtime parameter
2563     - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
2564     stress formulation and no-slip boundary conditions
2565 jmc 1.878 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
2566     in gad_calc_rhs.F ; add few safety stops in initialisation phase.
2567 dimitri 1.877 o pkg/seaice: a first HSALT time stepping equation has been checked in
2568 dimitri 1.875 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
2569     in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
2570     without requiring DO-IF statements
2571 jmc 1.876 o pkg/thsice:
2572     use continuous power-law function for partition of energy between lateral
2573     melting/freezing and thinning/thickening ; old code using step function
2574     still available with #undef THSICE_FRACEN_POWERLAW
2575     update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
2576     o testreport: change AD testing : check against results/output_adm.txt
2577     using same scripts as for forward test.
2578 dimitri 1.875
2579 jmc 1.1203 checkpoint59g (2007/09/17)
2580 jmc 1.873 o adjoint testing: in preparation for changing testreport:
2581     - output format: cost and grad written on separated lines
2582     - ad output results in directory "results" (instead of "results_ad")
2583 dimitri 1.872 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
2584 dimitri 1.871 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
2585 gforget 1.870 o pkg/ecco: allow user defined cost function contributions
2586 jmc 1.869 o testreport:
2587     Allow to choose (per experiment) the list of tested output variables
2588     and the main variable (used to issue a pass/FAIL ) ;
2589     - for now, done by adding the specific list in file: [exp]/input/tr_checklist
2590 jmc 1.873 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
2591 jmc 1.869 Also modify printing of summary:
2592     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
2593     b) echo the list of tested variables in the individual summary.txt of
2594     each experiment.
2595 jmc 1.868 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
2596     threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
2597     (but still depend on the tile decompostion of the domain).
2598 mlosch 1.867 o pkg/seaice: change a discretization detail to make the B-grid code
2599     "more symmetric". This change is likely to remove all "ridges/leads" that
2600     where quasi-aligned with the grid in B-grid solutions. It may also be
2601     the solution to the stress coupling issues with the B-grid.
2602 jmc 1.866 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
2603     remove .cvsignore from input dir. (since testreport no longer run here).
2604 jmc 1.865 o pkg/thsice:
2605 jmc 1.866 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
2606 jmc 1.865 - fix reshaping of sea-ice just after advection:
2607     melt all the ice only if ice-volume is too small.
2608     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
2609     prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
2610     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
2611 jmc 1.864 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
2612     tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
2613 jmc 1.863 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
2614     forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
2615     (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
2616     and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
2617     of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
2618     -> update output.txt
2619     o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
2620     this affects truncation error: -> update output.txt of exp:
2621     global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
2622     ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
2623    
2624 jmc 1.1203 checkpoint59f (2007/08/21)
2625 gforget 1.861 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
2626     o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
2627     a bounded range (in forward mode)
2628 gforget 1.860 o pkg/ecco, ctrl, autodiff and mom_common:
2629     internal parameter controls, completements of implementations
2630 jmc 1.859 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
2631 jmc 1.862 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
2632     (not seem any difference in testing results).
2633 jmc 1.859 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
2634     at face corners.
2635 jmc 1.858 o pkg/generic_advdiff:
2636     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
2637     loop range indices for computing vertical advection tendency
2638     and do the calculation in the interior only (no overlap) ;
2639     for now, only implemented for SOM advection (to save CPU time).
2640     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
2641 heimbach 1.855 o exch2 adjoint
2642     First set of changes:
2643     - add exch2 hand-written adjoint templates
2644     - exch2 hand-written no longer use TAF-flag 'nownew_arg'
2645     This will require cleanup in pkg/autodiff/*.F
2646     (changed routines currently kept separate in verif. code/)
2647     - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
2648     that used to hide exch2 or cubed-sphere specific code
2649     (commented via 'cph-exch2')
2650 dimitri 1.856 o pkg/seaice
2651     - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
2652 jmc 1.857 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
2653     output of global_ocean.cs32x15.thsice .
2654 heimbach 1.855
2655 jmc 1.1203 checkpoint59e (2007/07/26)
2656 jmc 1.853 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
2657     for B-grid vector (not yet tested) and C-grid vector (<- only used
2658     when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
2659 dimitri 1.852 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
2660     (#ifdef ALLOW_SALT_PLUME)
2661 dimitri 1.851 o gather_2d/scatter_2d: removed halo regions
2662 jmc 1.845 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
2663     scheme and the corresponding test case (under front_relax dir). For now,
2664     only available with Skew-flux form and not yet tested in realistic set-up.
2665 heimbach 1.847 adjoint: store directives updated, but gradient checks deteriorated,
2666     so maybe GM/Redi adjoint is now broken.
2667 heimbach 1.844 o seaice adjoint
2668     * add AREA, HEFF, HSNOW as control variable
2669     (should not change lab_sea results)
2670     * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
2671 dimitri 1.848 o pkg/seaice:
2672     * added computation of saltFlux in seaice_growth;
2673     For time being, sea ice salinity is assumed constant
2674     contribution of snow flooding to freshening of sea ice is neglected.
2675     SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
2676     defaults to 0.0 in order to maintain backward compatibility.
2677     Typical values for SEAICE_salinity are 4 to 10 g/kg.
2678     * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
2679     * added SEAICE_availHeatFrac, which specifies fraction of surface level
2680     heat content used to melt or grow ice
2681 dimitri 1.849 * commented out cap of HICE: it helps keep ice thinner
2682     * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
2683 dimitri 1.850 * applied OBCS T/S mask to HEFFM sea ice mask
2684 heimbach 1.844
2685 jmc 1.1203 checkpoint59d (2007/06/21)
2686 jmc 1.842 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
2687     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
2688     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
2689     o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
2690     and change default value of parameter "GM_Small_Number";
2691     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
2692     global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
2693     tutorial_global_oce_biogeo, tutorial_global_oce_latlon
2694 gforget 1.841 o pkg/ecco: cost function when applying pkg/smooth to controls
2695     o pkg/ctrl: add forcingPrecond run time parameter
2696 mlosch 1.839 o pkg/seaice:
2697     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
2698     - fix bug in metric terms of u-equation in LSR solver (implicit part),
2699     changes verification/lab_sea
2700     - rearrange implicit part of u-equation in LSR solver to make it easier to
2701     read, understand, and debug. This causes changes at the truncation level.
2702     - fix (serious) bug in the boundary conditions (sign error in the implicit
2703     part) of the LSR solver. Changes all LSR results.
2704 dimitri 1.840 - fixed problem with HSNOW initialization to avoid thick snow when AREA
2705     is initilized with small values - does not change lab_sea results.
2706     - added HsnowFile initialization capability
2707 gforget 1.838 o pkg/smooth: addition to model/src and pkg/ctrl so allow
2708     initialization of pkg/smooth and application to control vector
2709 mlosch 1.837 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
2710 gforget 1.836 o dependencies: pkg/profiles requires pkg/cal
2711 gforget 1.835 o pkg/profiles:
2712     - added option ALLOW_PROFILES_GENERICGRID
2713     -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
2714     that interpolation information (grid points and coefficients) is provided
2715     within the netcdf input files.
2716     -> sample matlab scripts can be found in MITgcm_contrib/gael
2717     that allow you to prepare netcdf input files.
2718     - also modified: cleaner include statements, cleaner error print statements,
2719     cleaner stops when error, and more tests of the netcdf input files consistency.
2720 jmc 1.834 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
2721 mlosch 1.830 o pkg/seaice:
2722 mlosch 1.833 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
2723     requires a new routine: seaice_diagnostics_fill.F
2724 mlosch 1.832 - make sure that seaice does not move if not forced (pressure replacement
2725     method, Hibler and Ip, 1995), changes results
2726 mlosch 1.830 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
2727     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
2728     It is turned off by default (=-1.), because it changes the results.
2729 mlosch 1.831 - make it possible to read AREA from a file, too.
2730 mlosch 1.830
2731 jmc 1.1203 checkpoint59c (2007/06/04)
2732 jmc 1.828 o add S/R and diagnostics for oceanic mixed-layer depth
2733     o move GMRedi call after all vertical mixing schemes (including KPP)
2734     o pkg/thsice:
2735     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
2736     (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
2737 mlosch 1.824 o pkg/obcs:
2738     - bug fix for balance code
2739 mlosch 1.822 o pkg/seaice:
2740 mlosch 1.825 - allow values of SEAICE_elasticParm > 1
2741 mlosch 1.826 - add new parameter SEAICE_evpTauRelax as an alternative
2742     to SEAICE_elasticParm
2743 mlosch 1.825 - make lsr boundary conditions free slip (by default), changes result
2744 mlosch 1.823 - add code for no slip boundary conditions for lsr
2745 mlosch 1.822 - set minimum of zeta to zero (and not 4e8) (changes results)
2746 mlosch 1.826 - add a cap on AREA after advecting AREA if seaice_growth is not called
2747 jmc 1.821 o change calculation of Visbeck K:
2748     - no longer depend on tapering scheme; instead, compute slope (limited
2749     by GM_maxSlope). this is equivalent to what was comuted before with
2750     clipping or linear tappering.
2751 jmc 1.828 - fix vertical averaging (wrong by 1/2 level)
2752 jmc 1.821 - leave the old version (but will not be maintained) within
2753     #ifdef OLD_VISBECK_CALC / #endif
2754 jmc 1.828 - update output of exp. ideal_2D_oce
2755 mlosch 1.820 o change error catch in calc_r_star to improve vectorization
2756 jmc 1.819 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
2757     add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
2758 heimbach 1.827 o adjoint:
2759     Re-organized adjoint checkpointing according to Matt Mazloff
2760     (but with modifs/completions/cleanups)
2761     Storing is now bundled into large arrays to optimized I/O
2762     (and second step in cleanup of the_main_loop)
2763 jmc 1.819
2764 jmc 1.1203 checkpoint59b (2007/05/16)
2765 jmc 1.818 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
2766     - export/import (between ocean & coupler) fields needed for ocean DIC.
2767 mlosch 1.817 o pkg/seaice:
2768     - get rid of three more exchanges seaice_calc_viscosities (required
2769     different loop boundaries in seaice_lsr and seaice_ocean_stress)
2770     - bug fix in seaice_ocean_stress (update of lab_sea required)
2771     - reduce loop boundaries to necessary minimum also in seaice_evp
2772     - go back to the old way of computing deltaC/Z as the adjoint likes that
2773     better
2774 dfer 1.816 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
2775     passive tracer to an Age Tracer) + update output.txt
2776 jmc 1.814 o pkg/exf:
2777 jmc 1.815 - implement A-grid / C-grid selection for wind-stress input files.
2778     - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
2779     for now, in exf_bulk_largeyeager04.F only :
2780     - change implementation for case where windspeed + 2. components wind-stress
2781     are read-in. AND use rhoConstFresh to convert evap.
2782     o pkg/seaice:
2783     - use correct EXCH_UV for wind-forcing (on A-grid).
2784     - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
2785     SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
2786     o pkg/exf:
2787 jmc 1.814 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
2788     EXF_INTERPOLATION:
2789     - merge global_with_exf/code version of exf_interp_read.F
2790     to the main code ;
2791     - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
2792     reading the file ; Important: This options needs to be defined to recover
2793     previous code.
2794     otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
2795     - no longer loose real*8 precision along the way when using exf_iprec=64.
2796 mlosch 1.811 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
2797 mlosch 1.813 - change discretisation of evp-solver in order to avoid another exchange
2798     (changes lab_sea) and clean up a little
2799     - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
2800     help the adjoint (this also changes the results slightly)
2801     - add a few "_d 0" where they had been missing in seaice_evp.F
2802     - cleaning up: remove unused seaice_calc_rhs.F
2803 jmc 1.810 o pkg/exf: some cleaning-up:
2804     - change various "constants" into runtime parameters
2805     - cleaned-up Large&Yeager04 routine which should eventually
2806     replace exf_bulkformulae.F (changed names of S/R and CPP)
2807     and merged various ALLOW_ATM_WIND options
2808     only used with thsice pkg (in thsice_get_exf.F):
2809     - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
2810     which are used when useStabilityFct_overIce=TRUE (= the default)
2811     - change default values of ice & snow emissivity and scale downward LW
2812     by ice & snow emissivity.
2813     o pkg/thsice:
2814 jmc 1.809 fix few little problems, in thsice_calc_thickn.F:
2815     - growth vertically (and not laterally) if iceFrac == iceMaskMax
2816 jmc 1.828 - melt only laterally if hIce < hThinIce (as the comments say)
2817 jmc 1.809 and in thsice_extend.F:
2818     - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
2819     - start to form ice as soon as the minimum ice-volume is reachable.
2820     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
2821     and cpl_aim+ocn
2822 mlosch 1.807 o pkg/kpp
2823 jmc 1.809 - move computation of surface related input fields to KPP into a new
2824     subroutine kpp_forcing_surf.F
2825 jmc 1.808 - remove wrong (within bi,bj loops) EXCH calls.
2826     - little cleaning (add argument myThid in last position, cvs header ...)
2827 jmc 1.809 - for now, fix conservation problem by exchanging KPPviscAz (may not
2828     be the best fix)
2829 mlosch 1.806 o pkg/seaice
2830     - check for inconsistent evp parameter/cpp-flag combination
2831     - remove leftover errIO flat for obsolete name list error handling
2832 heimbach 1.812 o OpenAD
2833     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
2834 mlosch 1.806
2835 jmc 1.1203 checkpoint59a (2007/05/01)
2836 mlosch 1.803 o pkg/seaice: some parameter clarifications and a little bit of clean up
2837 jmc 1.802 o pkg/thsice: rename run-time parameters:
2838     himin -> hIceMin
2839     himin0 -> hThinIce
2840     hihig -> hThickIce
2841     i0 -> i0swFrac
2842     transCoef -> bMeltCoef
2843     frac_energy -> fracMelting
2844     add new parameters: hNewIceMax, fracFreezing, dhSnowLin
2845     with default values (for now) that do not change the results.
2846     remove old version of thsice vars advection in pkg/seaice.
2847 jmc 1.801 o in FFIELDS.h:
2848     - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
2849     - make pLoad & sIceLoad always available (but still only used if
2850     ATMOSPHERIC_LOADING is #define).
2851 dimitri 1.799 o pkg/kpp: replaced _KPP_RL with _RL
2852 dimitri 1.798 o bug fixes for vertical diffusivity computations when both KPP and
2853 dimitri 1.883 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
2854     are no longer updating the vertical diffusivity array
2855     (passed as argument) but are (re-) setting those arrays.
2856 mlosch 1.795 o pkg/seaice: fix bug in evp solver, while doing that
2857     - change (improve?) discretization of stress computations for both
2858     cgrid-lsr and evp solver
2859     - add a new routine to compute strain rates
2860 mlosch 1.796 - the above changes lab_sea results
2861     - add no slip conditions for evp solver (off by default), lsr-version
2862     may follow
2863     - fix exchange for shear at Z-points (does not change lab_sea)
2864     - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
2865     (to force the user to pick a time step since there is not "safe" way
2866     of choosing it)
2867 mlosch 1.797 - add principal stress diagnostics
2868 mlosch 1.800 - rearrange fields for evp a little to avoid having to call a: too many
2869     exchanges and b: exchanges for stress trensor components which we do
2870     not have.
2871     - modify Hibler+Bryan (1987) stress coupling so that it reuses information
2872     of evp, complete rewrite for lsr case (latter is does not yet work
2873     in all cases)
2874 mlosch 1.794 o pkg/kpp: add code to have mixing in shelf ice caverns
2875 mlosch 1.804 - add myThid to all kpp routines (long overdue)
2876 mlosch 1.794
2877 jmc 1.1203 checkpoint59 (2007/04/19)
2878 heimbach 1.792 o pkg/exf:
2879     - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
2880     ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
2881     - move exf header files from lower_case.h to UPPER_CASE.h ;
2882     add missing cvs Header & Name
2883     - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
2884 heimbach 1.793 - add namelist param. selectStressGridPosition, exf_monFreq
2885     - retire many _CLIM routines, and remove data.exf_clim
2886     + params moved to data.exf
2887     + climsst, climsss now handled by exf_set_gen, i.e.
2888     climss?period=0 refers to constant field,
2889     climss?period=-12 to monthly forcing
2890     - split up namelists in data.exf
2891 mlosch 1.788 o pkg/seaice:
2892     - remove seaice_exch and seaice_exch_uv
2893     - remove superfluous exchange of theta
2894     - add myThid to seaice_budget_ocean/ice
2895 mlosch 1.790 - add new interface for atmospheric wind forcing (C-grid only)
2896     + new routine
2897     + two new field (taux, tauy for stress over ice)
2898     + removed one global field (DAIRN) for C-grid case only
2899 heimbach 1.792 o pkg/thsise
2900     - 2nd set of modifs for thsice adjoint in conjunction with exf
2901 heimbach 1.793 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
2902 mlosch 1.788
2903 jmc 1.1203 checkpoint58y_post (2007/04/15)
2904 dimitri 1.785 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
2905 dimitri 1.786 vertical diffusivity, similar to that in MOM4; turned on using
2906     #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
2907     diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
2908 dimitri 1.782 o Added capability for 3D specification of background vertical diffusion
2909     coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
2910     in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
2911     "data" file that contains the 3D vertical diffusivity coefficients.
2912 jmc 1.784 o ice dynamics (pkg/seaice) with thsice thermodynamics:
2913     - add code within pkg thsice to advect & diffuse sea-ice fields
2914     similar to (and will replace) what has been added in seaice_advdiff.F,
2915     but: - conserving Mass, Heat & Salt.
2916     - better when using non-linear advection scheme (not yet fully tested)
2917     - can also be used in atmospheric set-up (for now, only the diffusion).
2918 dimitri 1.783
2919 jmc 1.1203 checkpoint58x_post (2007/04/04)
2920 jmc 1.779 o IO option for global-file compact format:
2921     - add options when generating topology (utils/exch2/matlab-topology-generator)
2922     - add I/O capability (pkg/mdsio).
2923     - adapt utils/matlab/rdmds.m to read this format.
2924     for now long-line format not yet supported by pkg/mdsio (& exch2).
2925 mlosch 1.778 o shelfice: add a few diagnostics
2926    
2927 jmc 1.1203 checkpoint58w_post (2007/03/13)
2928 jmc 1.776 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
2929     rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
2930     (and replace horiVertRatio in NH code).
2931     Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
2932     and tutorial_plume_on_slope (sensitive to truncation)
2933 mlosch 1.774 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
2934     directly to drive seaice model (C-grid only)
2935     o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
2936     - reintroduce computation of wind from stress,
2937     - compute tau (in exf_bulkformulae.F) from windstress averaged to
2938     mass points to avoid tau = 0
2939 mlosch 1.775 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
2940 mlosch 1.774 o rdmnc.m: make it work with "global" files created with gluemnc
2941 jmc 1.773 o rdmnc.m : some improvements in dealing with singleton dimension
2942     (tested on all testreport mnc output files).
2943     o genmake2: disable pkg/profiles if netcdf test fails.
2944 jmc 1.772 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
2945 mlosch 1.771 o move call to cal_readparms up to make calendar parameters/variable available
2946     to all packages
2947    
2948 jmc 1.1203 checkpoint58v_post (2007/02/08)
2949 jmc 1.770 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
2950     useDynP_inEos_Zc tested.
2951 dimitri 1.769 o pkg/exf: changes to properly interpolate/mask/scale initial fields
2952 dimitri 1.768 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
2953     and portions thereof. See read_cs.txt for description and examples.
2954 jmc 1.767 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
2955     add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
2956     following the great-circle arc between those 2 points.
2957     o trap un-initialized variable with pathscale compiler on weddell.mit.edu
2958     (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
2959 jmc 1.766 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
2960     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
2961     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
2962     - still needs work (not working with some options ; efficiency to improve)
2963     and serious testing.
2964     - use this scheme for temperature & salinity in 2 advection test exp.:
2965     advect_xy & advect_xz, respectively.
2966    
2967 jmc 1.1203 checkpoint58u_post (2007/01/12)
2968 jmc 1.765 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
2969 jmc 1.764 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
2970     o testreport: add option "-skipdir" to skip some test.
2971     o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
2972     momentum calculation.
2973     o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
2974     o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
2975     remove checkpoint.F and the_correction_step.F (no longer used);
2976     do the k loop inside CYCLE_TRACER (supposed to be more efficient).
2977     o add option (linFSConserveTr) to correct for tracer source/sink due to
2978     Linear Free surface
2979 mlosch 1.763 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
2980     o pkg/thsice: fix reading mnc-pickups
2981    
2982 jmc 1.1203 checkpoint58t_post (2006/12/30)
2983 jmc 1.761 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
2984     o pkg/mdsio:
2985     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
2986     move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
2987     mdsio_write_field.F (S/R MDS_WRITE_FIELD);
2988     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
2989     - collect old S/R in one file: mdsio_rw_field.F (now just a call to
2990     either MDS_READ_FIELD or MDS_WRITE_FIELD )
2991     - new S/R (to replace MDSWRITEMETA), which allows to write more
2992     informations (variable names, time ...) to meta files.
2993     - modify rdmds.m to give back the meta file content.
2994 jmc 1.760 o pkg/diagnostics: change vertical interpolation to be safer, and more
2995     flexible (define p-levels to interpolate to in data.diagnostics);
2996     add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
2997     diagnostic pointer.
2998 mlosch 1.759 o pkg/seaice: more cleaning up of seaice_growth, added many comments
2999 mlosch 1.763 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
3000 mlosch 1.757 o fix multi-category seaice:
3001     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
3002     SEAICE_MULTICATEGORY
3003     - fix short wave heat flux
3004 jmc 1.758 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
3005     and allow to use EVP solver. Change forward lab_sea: test both EVP
3006     solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
3007 heimbach 1.756 o Initial check-in of lab_sea adjoint
3008     (very similar to natl_box_adjoint/code_seaice)
3009     * used C-grid and EVP solver
3010     * used KPP, GM/Redi
3011     * uses inAdExact=.TRUE.
3012     * gradient checks fail for both ADM and TLM
3013     due to sensitive snow melt code in seaice_grwoth (look for "JZ")
3014     f.d. gradients actually seem more problematic than ADM, TLM gradients;
3015     issue is related to forward mismatch between g77 an ifort
3016 mlosch 1.755 o pkg/seaice: overhaul of thermodynamics
3017     - growth.F and groatb.F are replaced by new routine seaice_growth.F
3018     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
3019     - move a few global fields out of SEAICE.h into seaice_growth.F and
3020     make them 2D (FICE/QNETO/ ...)
3021     - remove FO (it is the same as QNETO)
3022     - introduce a few local fields to avoid modifying external fields such
3023     as atemp, etc.
3024    
3025 jmc 1.1203 checkpoint58s_post (2006/12/11)
3026 dimitri 1.753 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
3027     changed exf_set_gen.F so that
3028     genperiod=0 means input file is one time-constant field and
3029     genperiod=-12 means input file contains 12 monthly means
3030 jmc 1.752 o CG2D: use pre-computed solver main-diagonal (stored in common block);
3031     this affects truncation error ; generate new output file for exp. which
3032     fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
3033     global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
3034     ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
3035     MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
3036     tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
3037     vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
3038 jmc 1.751 o start implementation of deep-atmosphere and anelastic formulation
3039 jmc 1.750 o verification: remove 2nd copy of input files and use script "prepare_run"
3040     to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
3041 mlosch 1.749 o mom_common/vecinv/fluxform: fix a few initialisation isssues
3042 gforget 1.748 o profiles: fix for multithreaded case
3043    
3044 jmc 1.746 o diagnostics: rename few diags:
3045     s/'PRESSURE'/'RCENTER '/g
3046     s/'TICE '/'oceFreez'/g
3047     s/'TAUX '/'oceTAUX '/g
3048     s/'TAUY '/'oceTAUY '/g
3049     s/'SWFLUX '/'oceQsw '/g
3050     s/DIFx/DFxE/g
3051     s/DIFy/DFyE/g
3052     and add few ocean-forcing diagnostics:
3053     atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
3054 dimitri 1.747 o modifications to pkg/seaice/growth.F and budget.F, which change results of
3055     lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
3056     as actual snow thickness. It now refers everywhere to effective snow
3057     thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
3058 jmc 1.746
3059 jmc 1.1203 checkpoint58r_post (2006/11/17)
3060 dimitri 1.744 o modifications to pkg/seaice/growth.F, which change results of
3061     lab_sea experiment: fixes pertain to melting snow over open water, to
3062     masking EVAP under sea ice, and to using the correct AREA variable for
3063     computations of EVAP, PRECIP, HSNOW, and GHEFF
3064 edhill 1.743 o add ability to read bathy, salt, and theta using MNC (off by def)
3065 mlosch 1.742 o add flooding algorithm and advection of HSNOW for pkg/seaice;
3066     both are turned off by default and do no change any results
3067 jmc 1.741 o seaice advection with pkg/thsice: a step toward the use of non-linear
3068     advection scheme, but #ifdef or commented out for now (requires more EXCH).
3069 jmc 1.739 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
3070     (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
3071     in natl_box (affects results @ truncation level: update output.txt)
3072     o multi-threading and IO:
3073 jmc 1.738 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
3074     - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
3075     (needed to work with SingleCpuIO): tested in all verif. exp.
3076 jmc 1.737 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
3077     affects the results (but none of the verification test uses this scheme).
3078 heimbach 1.736 o Adding some pkg/diagnostics capability to pkg/seaice
3079     (will certainly be subject to changes)
3080 heimbach 1.740 o ctrl: adding new control variables:
3081     lwflux, lwdown, evap, snowprecip, apressure, runoff
3082 heimbach 1.736
3083 jmc 1.1203 checkpoint58q_post (2006/10/20)
3084 dimitri 1.734 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
3085     1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
3086     high_res_cube configuration by 4% on Columbia.
3087 jmc 1.733 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
3088     add (in global_with_exf/code) a version of EXF_INTERP_READ without
3089     dynamical allocation (seems to work in multi-threaded).
3090     o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
3091     single CPU io) so that TAF does not have to see EESUPPORT.h
3092 jmc 1.727 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
3093    
3094 jmc 1.1203 checkpoint58p_post (2006/09/08)
3095 mlosch 1.726 o obcs: stop if obcs is used with useCDscheme = .true.
3096 mlosch 1.723 o shelfice:
3097     - fix a sign error so that no slip at shelfice interface works
3098     - remove stop for combination non-hydrostatic code and shelfice. That does
3099     not mean, that the results are correct, but at least they are numerically
3100     stable
3101 dfer 1.721 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
3102 heimbach 1.724 o added adjoint exch routined for all exch*3d* routines
3103     and updated flow directives
3104 dfer 1.721
3105 jmc 1.1203 checkpoint58o_post (2006/08/28)
3106 jmc 1.720 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
3107     remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
3108 jmc 1.719 o change controling S/R for writing pickup file (new S/R do_write_pickup)
3109     and clean-up reading/writing of pickup files.
3110     o fix local version of read/write pickup (NH part) in rotating_tank/code
3111 jmc 1.718 o simplify EXCH interface:
3112     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
3113     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
3114 edhill 1.717 o added the regrid package
3115 mlosch 1.716 o shelfice:
3116     - add a simple boundary layer scheme to reduce noise
3117     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
3118 jmc 1.718
3119 jmc 1.1203 checkpoint58n_post (2006/08/14)
3120 jmc 1.713 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
3121     local variable (not in common block).
3122 jmc 1.712 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
3123     - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
3124     - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
3125     to work with SingleCpuIO.
3126 jmc 1.711 o add "_d 0" to real constant of pkg/cfc subroutines ;
3127     update exp. cfc_exemple & tutorial_cfc_offline output files.
3128 jmc 1.710 o multi-threading and IO:
3129     - all threads call READ_FLD S/R (needed if using SingleCpuIO):
3130     (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
3131     - barrier before and after reading.
3132     - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
3133     - avoid using MDS_WRITELOCAL for LAND pkg output.
3134     - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
3135     common-block variables ; Allows multi-threading with master-thread IO.
3136 jmc 1.709 o change default MAX_NO_THREADS from 32 to 4 ;
3137     and stop cleanly when MAX_NO_THREADS is too small.
3138     o add S/R BAR_CHECK to check multi-threaded barrier synchronization
3139    
3140 jmc 1.1203 checkpoint58m_post (2006/07/17)
3141 jmc 1.707 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
3142     and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
3143 jmc 1.706 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
3144     keep global_ocean.90x40x15 (for AD testing) with former secondary test
3145     (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
3146     o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
3147     add MITgcm_tutorials (= code + all the tutorials)
3148 gforget 1.705 o ecco, option to compute cost for total ssh (mean+anom)
3149 gforget 1.704 o consistent with addition of ptracer and ssh in pkg/profiles
3150 gforget 1.703 o profiles: adding ptracer and ssh
3151 jmc 1.702 o testreport: change multi-test output-file name
3152     (from output.txt.{name} to output.{name}.txt)
3153 jmc 1.712 o profiles: now ok for mutli-tiles case
3154 mlosch 1.700 o seaice: add 4 parameters for different advection schemes for area,
3155     (effective) seaice thickness, enthalphy, and snow height. Their default
3156     is the standard parameter SEAICEadvScheme
3157 jmc 1.699 o calc_gw:
3158     - add cosFacU in zonal viscous flux (harmonic.visc.).
3159     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
3160     of tutorial_plume_on_slope.
3161     o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
3162 jmc 1.698 o calc_gw: true flux-form, account for horizontal grid spacing.
3163     update rotating_tank results, but not plume_on_slope (affected at
3164     truncation level, 11 digits).
3165    
3166 jmc 1.1203 checkpoint58l_post (2006/07/12)
3167 jmc 1.698 o calc_gw:
3168     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
3169     - remove side-drag for now (need to fix it); update plume_on_slope results.
3170     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
3171 heimbach 1.695 o commit code to make SST/SSS weights spatially variable
3172     (based on either variable in-situ or variable initial T/S weights)
3173 heimbach 1.696 o pkg/ecco:
3174     * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
3175     now based on horizontally varying weights wthetaLev, wsaltLev
3176     * cost_averagesflags now returns year indices in addition to day, month
3177     * sflux balance is performed on annual basis
3178     (sflxumm, sfluxmm2, bal_sfluxmm)
3179     * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
3180     including separate counting and multipliers
3181 heimbach 1.697 o pkg/rbcs
3182     * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
3183 jmc 1.694
3184 jmc 1.1203 checkpoint58k_post (2006/07/06)
3185 jmc 1.692 o testreport:
3186     - always build in dir. "build" (if not there, mkdir build instead of building
3187     & running in input)
3188     - run in dir run (if it exists), in build otherwise.
3189     - call prepare_run (if input/prepare_run exists)
3190     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
3191 dimitri 1.691 o pkg/exf modifications to interpolation and rotation routines for more
3192     reasonable treatment of North Pole singularity: for tracers North Pole
3193     value is set to northernmost zonal-mean value, for zonal velocity it is
3194     set to zero, and for meridional velocity it is set to northernmost value.
3195 mlosch 1.690 o pkg/exf/exf_check_range.F
3196     - add tile index to diagnostics and move stop statement to the very
3197     end of the routine.
3198 jmc 1.689 o pkg/diagnostics: (diagnostics_main_init.F)
3199     define title of isomorphic variables according to the current config.
3200 jmc 1.687 o pkg/thsice with pkg/seaice dynamics:
3201 jmc 1.688 - fix domain of computation (interior only, required for exf) and do exchanges
3202     - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
3203 jmc 1.686 o towards a standard way of dealing with multi-threading in MONITOR
3204     and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
3205 baylor 1.685 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
3206     to W momentum equation in nonhydrostatic and quasihydrostatic runs.
3207 jmc 1.684 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
3208 jmc 1.683 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
3209     o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
3210     (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
3211 jmc 1.682 o tracer advection:
3212     - clean-up and simplify calc_common_factors.F
3213     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
3214     advection subroutine (but still not used within DST advection S/R)
3215 jmc 1.681 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
3216    
3217 jmc 1.1203 checkpoint58j_post (2006/06/15)
3218 heimbach 1.680 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
3219     from file (collects calls previously in FORWARD_STEP)
3220     o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
3221 heimbach 1.679 o adjoint store dir. adjusted accordingly
3222 heimbach 1.680 o genmake2
3223     replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
3224 heimbach 1.679
3225 jmc 1.1203 checkpoint58i_post (2006/06/14)
3226 mlosch 1.677 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
3227     on wind stress (SEAICEstressFactor defaults to 1.)
3228 jmc 1.676 o Total number of Timers is finite (<=40): comment out 2 non-essential one
3229     in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
3230 jmc 1.675 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
3231     on CS-grid: no longer loosing mass.
3232 jmc 1.674 o exf & curvilinear-grid: no longer modify longitude xC & xG.
3233 mlosch 1.670 o pkg/ggl90: fix sloppy output and fix a bug
3234 dimitri 1.672 o pkg/seaice: added SEAICEuseEVPpickup parameter
3235     - Set to false in order to start EVP solver with
3236     non-EVP pickup files when using SEAICEuseEVP
3237 mlosch 1.673 - fix sign error in diffusion in seaice_calc_rhs
3238 mlosch 1.670
3239 jmc 1.1203 checkpoint58h_post (2006/06/07)
3240 heimbach 1.669 * Modifications for bottom topography control
3241     o replace hFacC by _hFacC at various places
3242     o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
3243     o add non-self-adjoint cg2d_nsa
3244     o update autodiff support routines
3245     o re-initialise hfac after ctrl_depth_ini
3246     o works for 5x5 box, doesnt work for global_ocean.90x40x15
3247     * Adding verification for 5x5 box (4-layer) bottom topography control
3248    
3249 jmc 1.1203 checkpoint58g_post (2006/06/07)
3250 jmc 1.671 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
3251     used for mean seasonal cycle, mean diurnal cycle); add an example
3252     in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
3253 mlosch 1.667 o pkg/ggl90:
3254     - add parameter (minimum surface kinetic energy)
3255     - fix bug (avoiding division by zero)
3256 mlosch 1.665 o couple pkg/thsice to pkg/seaice:
3257     - modify advection in seaice to accomodate new scalar fields to be advected
3258     - only muliDimAdection scheme work with seaice/thsice
3259     - mapping of thsice-variables to seaice-variables, back and forth
3260     - does not break the verification experiments, but does not give the
3261     desired results either
3262     o pkg/seaice
3263     - make (default) second order advection a bit less confusing?
3264    
3265 jmc 1.1203 checkpoint58f_post (2006/06/05)
3266 mlosch 1.662 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
3267     to pkg/seaice):
3268     - new routines thsice_map_exf and thsice_get_exf provide the interface
3269     - add an additional formal parameter to thsice_solve4temp
3270 heimbach 1.661 o pkg/exf:
3271     - add new fields wspeed, snowprecip (to be able to couple to thsice)
3272     - correct Stefan-Boltzmann constant
3273     - new parameter for longwave surface emittance
3274     - separate some stuff from exf_bulkformulae into new routines
3275     exf_radiation, exf_wind
3276 mlosch 1.662 - add new parameters and constants: longwave emissivity for ocean, ice
3277     and snow, evaporation parameters over ice
3278 mlosch 1.663 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
3279     either wind from stress or stress from wind
3280 jmc 1.660 o pkg/thSIce:
3281     - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
3282     - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
3283     and THSICE_CALC_THICKN
3284     - for now, call to THSICE_GET_BULKF remains inside i,j loops.
3285     - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
3286     to make debugging easier.
3287     - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
3288     o pkg/bulk_force:
3289     - clean-up comments and parameters ;
3290     - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
3291 jmc 1.659 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
3292     generate new output for test-experiment: aim.5l_cs.thSI
3293 jmc 1.658 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
3294 heimbach 1.661 testreport accordingly
3295 jmc 1.658
3296 jmc 1.1203 checkpoint58e_post (2006/05/17)
3297 heimbach 1.656 o SEAICE_CGRID adjoint done
3298 heimbach 1.654 o R_STAR adjoint implemented.
3299     * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
3300     * need to sort out init. of h0facc, etc.
3301 heimbach 1.655 o Make pkg/profile fully independent of ecco,cost, etc. stuff
3302     to be able to use it in pure forward.
3303 heimbach 1.653
3304 jmc 1.1203 checkpoint58d_post (2006/04/21)
3305 jmc 1.651 o upgrade simple test-experiment to tutorial example:
3306     step.1: duplicate the experiment and (step.2) will remove the old copy.
3307     tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
3308     tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
3309     tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
3310     tutorial_global_oce_biogeo <- copy of dic_example
3311     tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
3312     tutorial_plume_on_slope <- copy of plume_on_slope
3313     tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
3314     tutorial_global_oce_optim <- empty for now (David ?)
3315     tutorial_global_oce_in_p <- copy of global_ocean_pressure
3316     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
3317 gforget 1.650 o correct a sign problem in cost_scat.F
3318 mlosch 1.649 o obcs and ptracers: fix boundary conditions for advections schemes
3319     with larger stencil
3320 heimbach 1.648 o thsice adjoint: start
3321 mlosch 1.647 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
3322     completeness
3323 mlosch 1.646 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
3324     and COSINEMETH_III, add comments in default CPP_OPTIONS.h
3325 heimbach 1.645 o ptracers adjoint:
3326     * avoid extensive recomputatations
3327     * fix missing re-init. of gptr (missed by TAF)
3328 mlosch 1.644 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
3329     me to turn off the excessive output to STDOUT that this package produces
3330 jmc 1.643 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
3331     and add those terms in Vector-Invariant formulation.
3332 gforget 1.642 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
3333     if the control period (xx_hfluxperiod etc) is 0
3334     o in profiles pkg, clean routines and fix details
3335     o in ecco pkg, reading ssh data:
3336     fix problem in case the model does not start at iter0=0
3337 mlosch 1.640 o fix mnc-pickup/restart for ptracers
3338 heimbach 1.641 o new package prifiles:
3339     code to compute profile-based cost by Gael Forget
3340 heimbach 1.639 (modifs in ecco, ctrl, autodiff)
3341 heimbach 1.641 o Benign bug fix in initialization (spotted by M. Mazloff) of
3342     ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
3343 heimbach 1.639
3344 jmc 1.1203 checkpoint58c_post (2006/03/23)
3345 heimbach 1.638 o adjoint: finish NLFS adjoint and provide reference output in
3346     verification/global_ocean.90x40x15/results_ad_nlfs
3347 mlosch 1.637 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
3348     documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
3349     SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
3350     with SEAICE_CGRID defined.
3351 jmc 1.636 o move calendarDumps from "data" to "data.cal" and clean-up the code
3352     with a simple call to pkg/cal S/R: CAL_TIME2WRITE
3353     o add useEXF & useCAL flags (for now, set in hard-coded way)
3354 jmc 1.635 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
3355     (were missing in NH mode, and wrong in quasihydrostatic mode).
3356     waiting for Chris updated version of calc_gw to add those CALLs.
3357     o fix bug in quasihydrostatic S/R ;
3358     add a test for this option: global_ocean.90x40x15.qshyd
3359 jmc 1.634 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
3360     (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
3361     o add on/off flag useOffLine for package OFFLINE
3362 mlosch 1.630 o seaice:
3363     - modify advection so that it works also on the C-grid
3364     - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
3365     problem in multi-tile runs with C-grid
3366 mlosch 1.633 - add flags for clipping ice velocities and/or masking solver forcing
3367 mlosch 1.631 - fix drag (ocean on ice) formulation and a bug that caused noise in the
3368     C-grid solver
3369 mlosch 1.632 - added a few comments to seaice_diffusion.F
3370     - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
3371     are now exclusive)
3372     - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
3373     required re-ordering the code a little:
3374     + make DAIRN global variable (defined in SEAICE)
3375     + move computation of the viscosities eta and zeta into a new separate
3376     routine (because I need to recompute them in seaice_ocean_stress.F)
3377 mlosch 1.629
3378 jmc 1.1203 checkpoint58b_post (2006/03/13)
3379 jmc 1.627 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
3380     update output.txt of exp. aim.5l_cs.thSI
3381 edhill 1.626 o various mnc cleanups and improvements:
3382     + shrink lookup tables by factor of ~4
3383     + better error reporting when running out of lookup space
3384     + able to handle longer path/file names (up to 500 chars)
3385 heimbach 1.625 o adjoint:
3386     - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
3387     - TBD: "hidden" mom_vecinv recomp. in dynamics
3388 jmc 1.624 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
3389     (allow to differentiate between forcing components using new integer flags:
3390     momForcingOutAB=1/0 & tracForcingOutAB=1/0)
3391     and add new flag to put Dissipation tendency out of Adams-Bashforth.
3392 heimbach 1.623 o ecco
3393     - enable trend removal from SSH anomaly obs.
3394     o adjoint
3395     - a fix for PmEpR when #undef EXACT_CONSERV
3396     - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
3397     - try to fix "hidden" recomp. in forward_step for NLFS
3398     (NLFS seems broken sometimes after I checked it in)
3399 mlosch 1.622 o seaice:
3400     - add c-grid version of the dynamic solver:
3401     + three new routines that are the c-grid substitute lsr, dynsolver
3402     and ostres
3403     + put a few fields that were local to dynsolver into global common
3404     blocks, so that I can move the computation of stresses etc into
3405     seaice_lsr (saves coding but may break the adjoint).
3406     - replace more hardwired parameters by runtime parameters
3407     - add ice masks that mask the rhs of the implicit solvers where there
3408     is no ice (commented out in seaice_dynsolver, because i am not sure
3409     if this works properly), eventually this should replace the clipping
3410     of ice velocities in seaice_dynsolver to +/-40cm/s.
3411 edhill 1.621 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
3412     include it only where its needed
3413 mlosch 1.620 o move balancing of fluxes before the call of external_forcing_surf
3414 mlosch 1.619 o seaice:
3415     - correct units of turning angles (now they are really in degrees)
3416     - move computation of GWATX/Y out of main routine into dynsolver
3417     - initialize GWATX/Y in seaice_init
3418 jmc 1.618 o Apply mask on Fresh-Water flux (needed for SSH forcing).
3419 mlosch 1.619 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
3420 mlosch 1.617 o seaice: add runtime flags for turning angles (default to zero)
3421 heimbach 1.616 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
3422     and trend from exf forcing and ctrl control adjustments
3423     o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
3424     (since checkpoint57x_post)
3425 jmc 1.615 o change the default rotation period to 86164.s = the Earth rotation
3426 jmc 1.614 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
3427     and based on a reference stratification. Tested within hs94.cs-32x32x5.
3428 mlosch 1.613 o seaice advection: add code for choosing between the default (2nd order
3429     central differences) and multiDim advection schemes provided by
3430     pkg/generic_advdiff
3431 mlosch 1.611 o seaice:
3432     - removed all references to SEAICE_GRID.h fields from
3433     dynsolver, advect, diffus, lsr, without changing the results of lab_sea
3434     (cubed-sphere configuration will change a little)
3435     - grid computations in seaice_init are obsolete now.
3436     - cleaned up code a little so that is easier to read (hopefully).
3437 mlosch 1.613 - added new (better?) discretizations of default advection and diffusion
3438     (turn on with SEAICEuseFluxForm)
3439     - replace 1 in 3d global fields by kSurface in growth.F
3440 mlosch 1.611
3441 jmc 1.1203 checkpoint58a_post (2006/02/13)
3442 mlosch 1.612 o seaice:
3443     - bug fix in advect.F
3444 mlosch 1.608 o shelfice:
3445     - separate shelfice load anomaly from pload (breaks with time
3446     dependent forcing), => introduce constant field shelficeLoadAnomaly.
3447     Its default is 0., but it may be computed more cleverly from (unknown)
3448     t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
3449     done offline. A good approximation of the pressure load anomaly is
3450     necessary to avoid large initial adjustment processes underneath
3451     deep-reaching shelfice.
3452 mlosch 1.609 - small fix in ISOMIP shelfice_thermodynamics
3453     - add more sophisticated thermodynamics of Hellmer (1989), this is
3454     now the default
3455     - give a few constants more intuitive names
3456 mlosch 1.607 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
3457     if bulk formulae are used in long integration (especially EmPmR). Turn
3458     on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
3459     if balancePrintMean, the imbalance that is substracted is printed to
3460     STDOUT.
3461 jmc 1.606 o fix bug (typo) in obcs_apply_eta.F
3462 mlosch 1.605 o add a new package shelfice which enables us to model the circulation
3463     underneath shelf-ice with draughts of hundreds of meters.
3464     - works
3465     - to do: + include improved thermodynamics
3466     + check whether kSurfC (from model/inc/SURFACE.h) can be used
3467     instead of new field kTopC
3468     + can we use topoFile, Ro_surf and existing code in ini_depth.F
3469     instead of new field R_shelfIce and new code in ini_depth.F
3470     and ini_mask_etc.F?
3471 mlosch 1.608 + adjust vertical mixing schemes?
3472 mlosch 1.604 o seaice pkg:
3473     - add a cpp-flag to include a simple formula for a salinity dependent
3474     freezing point of sea water at the surface
3475     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
3476     meridional stresses are now different (and hopefully correct)
3477 jmc 1.602 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
3478     update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
3479     and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
3480 jmc 1.601 o pkg/diagnostics: add options and parameters for regional-statistics
3481     diagnostics ; define regions by reading a region-mask from a file
3482     (might add other options later)
3483 jmc 1.600 o pkg/bulk_force:
3484     - add option and parameters to use AIM surface-flux formulae.
3485     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
3486     others forcing fields (defined in PARM05, parameter file "data") are loaded
3487     from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
3488     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
3489     - use the right EXCH call for uwind,vwind (to work on CS-grid).
3490     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
3491     and parameters (note: calcWindStress replaces .NOT.readwindstress).
3492     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
3493    
3494 jmc 1.1203 checkpoint58 (2006/01/12)
3495 edhill 1.598 o add "--embed-source" option to genmake2 which, when the supporting
3496     tools can be compiled (as determined by genmake2) will turn on the
3497     embed_files package which then embeds the entire MITgcm source code
3498     (*.[fFhc] + Makefile) used for the build within the executable
3499     - requested by CNH but off by default
3500     - adds a paltry <9MB to the mitgcmuv executable in most cases
3501     - only writes the output when useEMBEDSRC in eedata is true
3502 heimbach 1.597 o clean up 3-dim. relaxation codes:
3503     * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
3504     * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
3505     * Thanks to Tom Haine for testing!
3506    
3507 jmc 1.1203 checkpoint57z_post (2005/12/31)
3508 jmc 1.593 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
3509     affects output (@ truncation level) of exp. plume_on_slope ; updated.
3510 mlosch 1.592 o fix the pickup behavior for obcs in combination with ptracers
3511     o fix a bug in ptracers_external_fields_load
3512     o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
3513     affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
3514     o transfered surface NH pressure to eta field (if exactConserv).
3515 jmc 1.589 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
3516     and update lab_sea output.txt file.
3517 heimbach 1.590 o completing 3-dim. relaxation code: additional term
3518     1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
3519     in S/R EXTERNAL_FORCING_T (file external_forcing.F)
3520     * At compile time, in "EXF_OPTIONS.h" set
3521     #define ALLOW_CLIMTEMP_RELAXATION
3522     #define ALLOW_CLIMSALT_RELAXATION
3523     * At runtime in "data", under &PARM03 set (e.g., units in seconds)
3524     tauThetaClimRelax3Dim = 15552000.0,
3525     tauSaltClimRelax3Dim = 15552000.0,
3526     * 3 cases:
3527     1) Use a constant-in-time 3-dim. field
3528     2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
3529     3) Real-time relax. to time-evolving prescribed field
3530 heimbach 1.595 o Adding Laplacian-type smoothness constraint on
3531     initial and boundary (forcing) controls (ic, bc)
3532     * enable at compile-time via
3533     ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
3534     * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
3535 heimbach 1.594 * Absolute scale somewhat unclear so far
3536     * no area weighting was included since no other cost term does so far
3537 jmc 1.589
3538 jmc 1.1203 checkpoint57y_post (2005/12/08)
3539 heimbach 1.588 First step for a NLFS adjoint
3540     o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
3541     o new init. routines for calc_r_star, calc_surf_dr
3542     o still need to deal with ini_masks_etc
3543     o testreport seemed happy
3544 jmc 1.1203 checkpoint57y_pre (2005/12/08)
3545 heimbach 1.587
3546 jmc 1.586 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
3547 stephd 1.585 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
3548 stephd 1.584 o add new offset feature to offline pkg (plus minor cleanup)
3549     o cfc fixes for final year of integration
3550     o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
3551     be in GCHEM_OPTIONS).
3552    
3553 jmc 1.1203 checkpoint57x_post (2005/12/04)
3554 jmc 1.583 o fix testreport Pb in multiple test experiment.
3555 edhill 1.582 o cleanup our namelist syntax in verification:
3556     - make it more F95 standards compliant (some work still needed)
3557     - allows the vast majority of our tests to work with gfortran
3558 jmc 1.580 o Non-Hydrostatic:
3559     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
3560     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
3561 jmc 1.579 o Allow to apply AB on T,S rather than on AB(gT,gS):
3562     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
3563     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
3564     time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
3565     - need a "clever" read_pickup to restart from the other AB formulation
3566 jmc 1.578 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
3567     o remove some unused variables (reduces number of compiler warnings)
3568 heimbach 1.581 o adjoint
3569     * Disable useVariableViscosity for adjoint for time being
3570     (there are a number of extensive recomputations)
3571     * Initialize certain variables needed for adjoint
3572 jmc 1.578
3573 jmc 1.1203 checkpoint57w_post (2005/11/03)
3574 jmc 1.576 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
3575     fix the singleCpuIO RS version of MDSWRITEFIELD
3576     and add a WARNING if using globalFiles=T with multi-processors.
3577 jmc 1.575 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
3578     using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
3579 jmc 1.576 o tracer advection scheme:
3580 jmc 1.574 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
3581     those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
3582     was not very convenient).
3583     add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
3584     (further tests needed for the implicit DST & Flux-Limiter schemes).
3585 mlosch 1.573 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
3586     and sRef for convenience, handy, when you want to initialize
3587     ptracers in a large domain with a constant non-zero value. Also,
3588     untangle ptracers_init.F a little.
3589    
3590 jmc 1.1203 checkpoint57v_post (2005/10/13)
3591 jmc 1.572 o change dome exp. to use variable viscosity in side-drag terms.
3592 edhill 1.570 o remove all the files from the cfc_offline test since they are now
3593     incorporated into tutorial_cfc_offline which has been producing
3594     identical results for a few days of testing
3595 jmc 1.571 o add new parameter: sideDragFactor to enable half-slip-side BC
3596     and change side-drag S/R to use viscosity from mom_calc_visc
3597     (can switch back by setting sideDragFactor=0.); affects results at
3598     truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
3599     global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
3600 jmc 1.569 o vorticity & strain are now computed without masking, to account for
3601     no-slip-side BC in variable viscosity calculation ; mask is applied
3602     anyway later on, before computing advection/coriolis terms.
3603 mlosch 1.573 o modify exp4 to test new obcs support for reading from external files
3604 mlosch 1.568 and for passive tracers
3605 mlosch 1.567 o fix behavior of ptracers_monitor when monitor output is written to a
3606     netcdf-file; still not independent of monitor.F (writes in the same
3607     file).
3608 jmc 1.566 o change default value of tRef (put a uniform, meaningful value for ocean
3609     & atmos) and initialize sRef (was missing, as Martin mentioned).
3610 baylor 1.565 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
3611     to be proportional to enstrophy dissipation length. Thus,
3612     viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
3613     This is now consistent with Smagorinsky and with the manual.
3614    
3615 mlosch 1.564 checkpoint57u_post
3616 mlosch 1.562 o OBCS and PTRACERS: add open boundary support for passive tracers
3617     - either use homogenous (pseudo) v.Neumann conditions or prescribe
3618     OB-values from file; this is not different from the way theta and salinity
3619     are treated
3620     - however, Orlanski-radiation conditions are not supported, and the model
3621     will stop if you use pTracers and Orlanski at the same time.
3622     - beefed up the rountine obcs_external_fields_load: now only those open
3623     boundary values are overwritten with values from files for which there
3624     are really files, otherwise the OB-fields remain untouched. This makes
3625     it possible to use different OBs at different ends of the domain (as
3626     with EXF)
3627 jmc 1.561 o reduce number of exch calls in shap_filt (s2).
3628 jmc 1.560 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
3629     truncation level) 4/5 MLAdjust test results (11&12 digits match).
3630    
3631 jmc 1.1203 checkpoint57t_post (2005/10/03)
3632 jmc 1.558 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
3633     o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
3634     same truncation, independent of the face number: affects affects several
3635     test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
3636 jmc 1.557 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
3637 jmc 1.558 note that biharmonic viscosity + no-slip was not tested in any experiment.
3638 jmc 1.556 o fix bug in non-linear free-surf side-drag ; generate new output for
3639     global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
3640 edhill 1.555 o make mnc honor the writeBinaryPrec flag for most kinds of output
3641 edhill 1.554 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
3642 jmc 1.553 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
3643     error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
3644 jmc 1.552 o add brackets in multi-terms sum to get same truncation, independent of
3645     the face number (manage to get exactly same value of gU,gV at the cs-edge)
3646     affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
3647 baylor 1.551 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
3648     and viscA4Remax, which allow one to limit the minimum viscosity by specifying
3649     a maximum grid-scale Reynolds number. Also, changes all length calculations
3650     in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
3651     Suggested values of viscosity parameters found in mom_calc_visc.
3652     Many new viscosity diagnostics available.
3653 jmc 1.550
3654 jmc 1.1203 checkpoint57s_post (2005/09/20)
3655 baylor 1.549 o Add clearing-house for viscosity calculations, mom_calc_visc and
3656     correct numerous bugs in LeithD and Smagorinsky discretizations.
3657     mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
3658     used simultaneously, and to be used in mom_vecinv and mom_fluxform.
3659     Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
3660     and with Strain-Tension viscous term calculation (mom_hdissip.F).
3661     The Strain-Tension form is now called with useStrainTensonVisc=.true.
3662     ViscAhStrain and viscAhTension are now retired.
3663 jmc 1.550 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
3664 edhill 1.547 o In response to JMC's bug report, genmake2 now ignores any soft-links
3665     that it finds in the *current* directory when searching for files.
3666     Soft-links found in any other source directories will still work as
3667     they did before.
3668 edhill 1.546 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
3669     a C routine to unlimit the stack size
3670 edhill 1.545 o mnc-ify pkg/aim snapshot vars
3671 edhill 1.544 o mnc-ify pkg/land as requested by Daniel
3672 edhill 1.543 o various changes to mnc including:
3673     - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
3674     - output can now be grouped so that all files within a group
3675     change the ITER portion of their names in lock-step together
3676     - can now read ("global") PER-FACE (in addition to PER-TILE) files
3677     and works with both EXCH1 and EXCH2 (but needs more testing)
3678     - writing works for all verification test cases w/ g77 on Linux
3679    
3680 jmc 1.1203 checkpoint57r_post (2005/09/07)
3681 edhill 1.541 o make MNC variable initialization happen earlier
3682 jmc 1.540 o add diagnostics for (almost) each term of the momentum Eq.
3683 jmc 1.537 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
3684 jmc 1.536 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
3685     o remove MINIMAL_TAVE_OUTPUT option ;
3686     add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
3687 jmc 1.535 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
3688     allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
3689 heimbach 1.538 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
3690     o add time-dependent SST, SSS control
3691 heimbach 1.539 o cost terms in ecco/ modularized (new cost_generic.F)
3692     o cost_averages routines are modularized (new cost_averagesgeneric.F)
3693     o new infrastructure for seaice model vs. obs misfits in seaice/
3694     * driver from the_main_loop.F is seaice_cost_driver.F
3695     * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
3696     * gradient check in Exp. 6a of natl_box_adjoint/
3697     o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
3698     (see README file)
3699 jmc 1.535
3700 jmc 1.1203 checkpoint57q_post (2005/08/19)
3701 jmc 1.533 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
3702 edhill 1.531 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
3703     - bug was reported by Jean-Michel and Ian Fenty
3704 jmc 1.532 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
3705     update exp. cpl_aim+ocn output.
3706 heimbach 1.530 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
3707     Needed for high-res. runs with large global files
3708     to be able to limit tapelev size
3709     o Changed some tests for adjoint:
3710     * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
3711     * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
3712     * global_ocean.90x40x15/ back to default 3-level checkpointing
3713 heimbach 1.534 o Modifications to enable scripted COMMON to MODULE conversion
3714     * verification/OpenAD/code/ has necessary scripts and description;
3715     * converts, compiles and runs successfully;
3716 heimbach 1.530
3717 jmc 1.1203 checkpoint57p_post (2005/08/01)
3718 jmc 1.529 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
3719     o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
3720     (already the case for some pkgs, including recent MNC_init, e.g. thsice)
3721     o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
3722 jmc 1.527 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
3723     (was already the case for dissipation with mom_vecinv,
3724     and also the case for grad.PhiHyd when staggered-timeStep)
3725     This will allow to put dissipation out-off the AB time-stepping.
3726     Unfortunately, affects truncation error. Update output of exp. that "fails"
3727     (cg2d matching number) and leave the others for later: front_relax(10),
3728     global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
3729     matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
3730    
3731 jmc 1.1203 checkpoint57o_post (2005/07/30)
3732 edhill 1.525 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
3733     (2) its ready to be documented during the 20050801 DocFest
3734 edhill 1.524 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
3735     for ideal_2D_oce and lab_sea on linux_ia32_g77
3736 heimbach 1.526 o set to #undef CTRL_SET_OLD_MAXCVARS_30
3737     in global1x1_tot/code_seaice_adj to access indices 32, 33
3738     (worth another tag)
3739 edhill 1.524
3740 jmc 1.1203 checkpoint57n_post (2005/07/29)
3741 heimbach 1.521 o adding precip control xx_precip 32
3742     o adding swflux control xx_swflux 33
3743 heimbach 1.522 o Replacing 10 forcing penalty cost routines by 1 generic.
3744     o Implementing partitioning in time-mean and variable adjustment
3745     for atmos. state.
3746     o Time-mean constant error is now read in data.ecco (instead of hard-coded)
3747 heimbach 1.519 o in natl_box_adjoint:
3748 heimbach 1.522 * updated exp 1 to 10
3749     (but does not have time-mean vs. variable split results yet)
3750 heimbach 1.523 o updated global1x1/*_seaice_adj/
3751     to incorporate latest changes
3752 heimbach 1.520 o enable useSingleCpuIO for mdsio vector routines
3753     (applies in particular to tapelev I/O)
3754     o removed inefficient K-loop in all active_file*control*.F
3755 heimbach 1.518
3756 jmc 1.1203 checkpoint57m_post (2005/07/28)
3757 jmc 1.516 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
3758     and advect_cs (use EXCH-2 and standard cs-32 grid files).
3759 jmc 1.515 o pkg/exch2: filling of face-corner halo regions is optional
3760     (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
3761    
3762 jmc 1.1203 checkpoint57l_post (2005/07/14)
3763 jmc 1.514 tag before updating tutorials (pre-release-2)
3764 jmc 1.513 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
3765     for output and interpolation of input fields onto model grid)
3766     o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
3767     Affects results of exp. rotating_tank ; update output.txt.
3768 jmc 1.511 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
3769 jmc 1.512 and taking the square quantity and/or using a fraction-weight field.
3770 jmc 1.511 o fix aim_diagnostics_init.F mate numbers.
3771     o add mnc output capability to diagnostics/diagstat and update
3772 edhill 1.510 our cvsignore files for the ACSII output generated
3773    
3774 jmc 1.1203 checkpoint57k_post (2005/07/02)
3775 heimbach 1.509 o lab_sea now uses diagnostics package and provides a suite of
3776     new EXF diagnostics output.
3777    
3778 jmc 1.1203 checkpoint57j_post (2005/06/30)
3779 heimbach 1.508 o exf
3780     * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
3781     Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
3782     terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
3783     * extended diagnostics output
3784     - now includes all EXF variables
3785     - hs, hl moved to common block
3786     - separate S/R for diagnostics, called after ctrl vector is added
3787     - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
3788     - EXFqnet contains true Qnet (i.e. includes qsw)
3789     * updated verif. lab_sea, global_with_exf
3790     * Rearranging hflux (exf_mapfields -> exf_getforcing)
3791     to ensure that diagnostics sees a true EXFqnet
3792 jmc 1.507 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
3793 jmc 1.506 o diagnostics pkg: change pointers so that 1 diagnostic can be used
3794     several times with different frequencies.
3795 edhill 1.505 o mnc-ify the thsice package as requested by Daniel Enderton
3796     - the monitor--MNC output needs work
3797     - many attributes need to be added (most are currently blank)
3798     o mnc-ify theaim_v23 package as requested by Daniel Enderton
3799     - many attributes need to be added (most are currently blank)
3800 jmc 1.503 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
3801 jmc 1.502 o add Sadourny like discretization to the 4th.O vorticity advection scheme
3802 jmc 1.500 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
3803 jmc 1.501 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
3804     fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
3805 jmc 1.499 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
3806     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
3807    
3808 jmc 1.1203 checkpoint57i_post (2005/06/19)
3809 molod 1.497 o Diagnostics package was changed: diagnostic allocation is now deactivated
3810     by setting an empty file name in the namelist (used to be by setting 0 frequency)
3811 jmc 1.496 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
3812     add 1rst Order upwind vertical Shear.
3813 edhill 1.495 o add a quick fix for A/B checkpointing in OFFLINE mode
3814 edhill 1.494 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
3815     end-run around the C/Fortran linking horror in eesup/src/timers.F
3816 adcroft 1.493 o added pkg/runclock: allows user to terminate run based on wall clock
3817     o added non-hydrostatic scaling parameter: nh_am2
3818 mlosch 1.492 o pkg/my82: futile attempt to make results compiler-independent by adding
3819     some "_d 0", etc. no effect.
3820 edhill 1.491 o for mnc output, fill the 'T' coordinate var with myTime and create a
3821     separate 'iter' variable for iteration count
3822 jmc 1.489 o pkg/diagnostics:
3823 jmc 1.490 add new capability: output of Global/Regional & per-level statistics ;
3824     tested against monitor output (including land & thSIce) on various exp.
3825     o make seaice-pkg I/O type flags (MNC/MDS) more standard.
3826 jmc 1.489
3827 jmc 1.1203 checkpoint57h_done (2005/05/19)
3828 jmc 1.488 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
3829     data.diagnostics, data.gchem, data.ptracers) is done.
3830    
3831 jmc 1.487 o pkg/diagnostics: prepare for Global/Regional statistics.
3832     add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
3833 jmc 1.486 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
3834     and rename it: DIFFERENT_MULTIPLE
3835    
3836 jmc 1.1203 checkpoint57h_post (2005/05/14)
3837 jmc 1.485 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
3838 jmc 1.484 o pkg/diagnostics: change output frequency, now in seconds (instead
3839     of Nb of iterations). This requires to change data.diagnostics.
3840 jmc 1.1203 checkpoint57h_pre (2005/05/12)
3841 jmc 1.483
3842 edhill 1.482 o in mnc, let the user create the output dir if both mnc_outdir_date
3843     and mnc_outdir_num are false
3844 edhill 1.481 o add fflags() to pkg/diagnostics which allows one to specify, on a
3845     per-file basis, the file precision [default behavior is unchanged]
3846 dimitri 1.480 o added diagnostics to pkg/kpp, including computation of mixed layer
3847     depth based on a temperature/density criterion
3848     o updated verification/natl_box to test the new pkg/kpp diagnostics
3849 jmc 1.479 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
3850 jmc 1.478 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
3851 edhill 1.477 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
3852     not mnc -- this mistake was found by JMC and is now corrected
3853    
3854 jmc 1.1203 checkpoint57g_post (2005/04/15)
3855 jmc 1.476 o add Adams-Bashforth 3rd Order time stepping:
3856     - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
3857     - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
3858 jmc 1.1203 checkpoint57g_pre (2005/04/15)
3859 jmc 1.475
3860 heimbach 1.472 o make lambda[Theta,Salt]ClimRelax spatially varying
3861     (default remains spatially uniform constant based on tau)
3862 heimbach 1.473 o added new control variables
3863     * init. uVel, vVel, etanN
3864     * lambda[Theta,Salt]ClimRelax
3865     o separate masks used for ctrl_pack/unpack 'from write_grid' output
3866     (suggested by G. Forget)
3867 heimbach 1.472
3868 jmc 1.1203 checkpoint57f_post (2005/04/06)
3869 jmc 1.471 o add parameter "baseTime" = model base time = time at iteration zero
3870     new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
3871     account for baseTime shift
3872     o move Coriolis arrays from PARAMS.h to GRID.h
3873 jmc 1.1203 checkpoint57f_pre (2005/04/06)
3874 jmc 1.470
3875 edhill 1.468 o mnc-ifying the seaice package
3876 adcroft 1.467 o introduced an alternative length scale calculation for use in the limiting
3877     maximum viscosity (off by default, see mom_vi_hdissip.F for details)
3878 heimbach 1.466 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
3879 baylor 1.465 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
3880     as well as grad(vort3). Made it compatible with both approximate form
3881     for the cubed sphere and full form of these gradients. Added flag
3882     useFullLeith to select between approximate and full form.
3883 jmc 1.464 o add "d0" in getcon.F to reduce differences between compilers/platforms
3884     update output.txt of exp. fizhi-gridalt-hs
3885 jmc 1.463 o change port_rand funtion to allow to set the seed.
3886 edhill 1.462 o fix obscure MNC bug involving conversion between reals and integers
3887     - it caused no problems with certain (eg. gcc, ifc) compilers but the
3888     new version is now more standards-compliant
3889 heimbach 1.469 o adjoint-related modifications
3890     * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
3891     * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
3892     * mom_vi_hdissip: to be able to use Leith scheme in adjoint
3893 edhill 1.462
3894 jmc 1.1203 checkpoint57e_post (2005/02/28)
3895 heimbach 1.461 o Adding eddy stress controls a la Ferreira et al.
3896 jmc 1.474 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
3897 heimbach 1.460
3898 jmc 1.459 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
3899     update output.txt of exp. fizhi-gridalt-hs
3900 edhill 1.458 o add more "Z" dimensions and associated coordinate vars to MNC
3901 dimitri 1.457 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
3902 dimitri 1.456 o parameter calendarDumps: when set, approximate months (30-31 days) and years
3903     (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
3904     KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
3905     months and years. Requires pkg/cal.
3906 edhill 1.455 o diagnostics: add pickup functionality
3907     - off by default for backwards compatibility
3908     - current version only uses MDSIO -- MNC will be added
3909 jmc 1.454 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
3910 jmc 1.452 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
3911    
3912 jmc 1.1203 checkpoint57d_post (2005/02/11)
3913 jmc 1.451 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
3914 edhill 1.450 o modify verification/ideal_2D_oce so that it tests the creation of mnc
3915     output from the diagnostics package
3916 jmc 1.449 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
3917 edhill 1.448 o make genmake2 more portable by using ".$FS" instead of ".f" for more
3918     of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
3919 edhill 1.447 o add coordinate variables to the MNC output from the diagnostics package
3920 jmc 1.446 o change MNC-flags default value: true when useMNC=TRUE
3921 edhill 1.444 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
3922     the ability (off by default) to read the grid information using MNC
3923 jmc 1.445 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
3924 jmc 1.443 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
3925 jmc 1.442 o do snap-shot diagnostics at the middle of the time-interval (instead of
3926     at the end).
3927 jmc 1.441 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
3928     new test for AIM with thSIce + slab-ocean
3929 jmc 1.440 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
3930 jmc 1.439 o move state variable diagnostics to the beginning of the time step ;
3931     (note: still needs some work specially for snap-shot diagnostics)
3932     duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
3933    
3934 jmc 1.1203 checkpoint57c_post (2005/01/27)
3935 jmc 1.438 o Change testing option (-ieee) to get closer agreement between g77 & ifort
3936     o generate new output.txt files on faulks with g77 & the new -ieee option
3937 jmc 1.1203 checkpoint57c_pre (2005/01/27)
3938 jmc 1.437
3939     o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
3940 jmc 1.436 update output.txt of exp. global_ocean.90x40x15
3941 jmc 1.435 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
3942     results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
3943 jmc 1.432 o add saltFlux(+File) forcing capability with periodicExternalForcing
3944 jmc 1.431 o allow to use pkg diagnostics for GM-Redi & ThSIce output
3945     o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
3946 edhill 1.430 o improvements for the MNC output from DIAGNOSTICS:
3947     - correct handling of the unlimitied dimension
3948     - all dims now have associated coordinate variables
3949     - variables located at U, V, and Corner ("Z") points are now written
3950     with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
3951     *all* data points are output
3952 dimitri 1.429 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
3953 dimitri 1.428 o added pkg/seaice/seaice_monitor.F
3954 dimitri 1.427 o mdsio_readfield.F can now read files visible only to master MPI process.
3955 dimitri 1.426 o pkg/seaice: some test code for ice-modified ocean stress
3956 dimitri 1.425 o exf_getffields interpolation defaults to bilinear for all scalar forcing
3957     fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
3958     spurious negative numbers for precipitation and humidity. Will cause
3959     some small numerical differences for integrations using pkg/exf/exf_interp.F.
3960 heimbach 1.434 o pkg/ctrl/
3961     * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
3962     May be enabled via doPackDiag
3963     * introduce z-scaling of
3964     + gradient (doZscalePack) and
3965     + control (doZscaleUnpack)
3966     o pkg/mdsio/
3967     * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
3968     * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
3969 dimitri 1.425
3970 jmc 1.1203 checkpoint57b_post (2004/12/20)
3971 jmc 1.424 o simplify options in diagnostics_fill arguments (remove weird combinations)
3972 edhill 1.423 o fix MNC coordinate variables so that they now contain per-face index
3973     values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
3974     general, EXCH2 grids are only aligned to a "local" coordinate system
3975 jmc 1.422 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
3976     o Implement instantaneous output within pkg diagnostics:
3977     setting a negative frequency in data.diagnostics produces
3978     "snap-shot" output (as opposed to time-average if freq > 0)
3979 jmc 1.421 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
3980     NOTE: change ptracer diagnostics name: use 2 characters to work with
3981     more than 9 tracers. Add also diagnostics of advect & diffus flux.
3982 edhill 1.420 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
3983     becomes the coordinate variable for the 'T' dimension
3984 edhill 1.419 o add CF-style coordinate variables to MNC
3985     - just a first cut: numbers are meaningless on the cubesphere and
3986     missing along the T axis but otherwise it works!
3987 dimitri 1.418 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
3988 jmc 1.417 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
3989 jmc 1.416 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
3990     this is based directly on what the model compute, so that the content of
3991     each diagnostics might be affected by switching options (e.g., implicitDiffusion)
3992     o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
3993 mlosch 1.415 o clean up build options files for SunOS, in particular
3994     - remove -traditional from xmakedepend
3995     - change -xarch=v9 to -xarch=native for f77
3996     - restore use of make (not gmake)
3997     - add CC=gcc if using g77
3998 edhill 1.413 o changes per discussion of AM, JMC, & EH3 today:
3999     - move redundant "grid" variables out of "state" -- in preparation of
4000     creating proper CF-style coordinate variables and in recognition
4001     that any/all grid variables can be easily copied (eg. w/NCO) from
4002     the grid files into any of the other NetCDF files
4003     - *always* output grid variables with MDSIO (this will eventually be
4004     changed)
4005     - output MNC grid file if useMNC is true
4006 edhill 1.412 o every instance of _END_MASTER() has been found and replaced with
4007     _END_MASTER( myThid ) in order to satisfy certain picky Sun
4008     preprocessors
4009 jmc 1.411 o re-arrange diagnostics pkg initialisation:
4010     - allow each package to extend the available diagnostics list
4011     - add some checking and fix small problems (multi-threaded, ...)
4012     - new S/R diagnostics_fill (replace fill_diagnostics):
4013     look through the short list of active diag. (instead of the long list)
4014     create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
4015 edhill 1.381
4016 jmc 1.1203 checkpoint57a_post (2004/12/10)
4017 heimbach 1.410 o this set of changes restores TAMC compatibility
4018     tested for global_ocean.90x40x15 adjoint on trough
4019     (what a pain)
4020    
4021 jmc 1.1203 checkpoint57a_pre (2004/12/10)
4022 heimbach 1.409 o some modifs in tools/build_options for sunos
4023     o call ctrl_pack for ctrl at end for optimcycle=0
4024    
4025 jmc 1.1203 checkpoint57 (2004/12/09)
4026 mlosch 1.406 o add horizontal bi-harmonic viscosity for vertical velocity
4027     - new parameter viscA4W (defaults to viscA4)
4028     - affects only non-hydrostatic code
4029     - to be done: no-slip lateral boundary conditions
4030 dimitri 1.405 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
4031 jmc 1.404 o implement Implicit Vertical advection for pTracers
4032 jmc 1.401 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
4033 jmc 1.402 (implemented also for implicit vertical diffusion & advection)
4034 mlosch 1.400 o OBCS: extend application of tracer open boundary conditions
4035     to a strip beyond the boundary of width Olx/Oly
4036 heimbach 1.403 o add call monitor to TAF set of required calls (flow directives)
4037     and include in natl_box_adjoint
4038     o untangle a few ifdefs related to cost, ctrl, autodiff
4039     untangel a few ALLOW_ECCO_OPTIMIZATION
4040 heimbach 1.407 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
4041     (theta2, salt2 in ecco_cost_weights)
4042 mlosch 1.400
4043 jmc 1.1203 checkpoint56c_post (2004/12/03)
4044 mlosch 1.399 o OBCS as control variables
4045     - update ctrl_ad_diff.list, obcs_ad_diff.list
4046     - remove balance of obcs controls from default
4047     - fix index bug nobcs in ctrl_init
4048     - fix dummy fields filen in ctrl_pack
4049     - add dummy weights for obcs
4050     o lsopt: comment out fort.94 output
4051     o optim:
4052     - remove unnecessary header files
4053     - adjusted namelists
4054     - add xerbla.F to Makefile
4055     o exf:
4056     - multiple modifications of exf_check_range
4057     - unit change in exf_init_runoff from [m/year] to [m/s]
4058     o mdsio:
4059     - i/o-vector change debugLevel from debLevA to debLevB
4060    
4061 jmc 1.1203 checkpoint56b_post (2004/12/01)
4062 mlosch 1.397 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
4063     is called from DO_THE_MODEL_IO
4064     - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
4065     - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
4066     - clean up PTRACERS_WRITE_TIMEAVE a little
4067 mlosch 1.396 o add another verification experiment that tests both the cfc-pkg and
4068     the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
4069     reactive tendencies treated inline with regular timestepping
4070 mlosch 1.395 o testreport previously did a lousy job of comparing small numbers, so
4071     we (Ed and Martin) changed the way the cut-off of 1.e-12 is
4072     implemented in the little c-progam tmp_cmpnum.c which is embedded in
4073     testreport.
4074     o ptracers_monitor: bug fix for MPI
4075    
4076 jmc 1.1203 checkpoint56a_post (2004/11/28)
4077 mlosch 1.394 o GCHEM: finish reorganizating the package
4078     - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
4079     (introduces another 3D-array for each passive tracer, but only if
4080     GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
4081     gchemTendency is not needed because the timestep is done separately)
4082     - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
4083     - GCHEM is now---more or less cleanly---separate from PTRACERS
4084     - to bo done: handling of surfaceForcingPtr that is needed for KPP not
4085     so clear to me how that should be done in a general way.
4086     o CFC: improve formatting of output in CFC_ATMOS
4087     o PTRACERS:
4088     - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
4089     that ALL experiments with ptracers enable can be checked. This makes
4090     GCHEM_MONITOR obsolete.
4091     - include a runtime parameter PTRACERS_monitorFreq that defaults to
4092     monitorFreq
4093     - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
4094 edhill 1.393 o add PTRACERS (PTR0[1-5]) to testreport output
4095 heimbach 1.391 o exf_check_range:
4096     * default changed to .TRUE.
4097     * will check values for niter0 if debLevA, every timestep if debLevB
4098     * STOP in exf_check_range if 'out of range'
4099     * range chosen generous to allow for potential extema
4100     TBD: a version with stricter range
4101     permitted range would be runtime parameters
4102 jmc 1.390 o GMredi:
4103     - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
4104     - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
4105     - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
4106 mlosch 1.388 o GCHEM:
4107     - move call to GCHEM_FORCING_SEP, so that it is now called before
4108     the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
4109     - introduced a useGCHEM runtime flag and applied it everywhere.
4110 mlosch 1.392 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
4111     this flag is now only visible within GCHEM-pkg routines.
4112     - moved gchem_forcing_int temporarily into ptracers_forcing, this will
4113     be replaced by a 3D array that is computed before thermodynamics; for
4114     this, the tracer ID iTracer had to be included into the parameter list
4115     of ptracers_forcing
4116 mlosch 1.394 - set up forward_step to call gchem_forcing, that will replace
4117 mlosch 1.392 gchem_forcing_int in ptracers_forcing
4118     - cleaning up
4119 jmc 1.389 o small cleaning of exch2: remove files that are also in eesupp/src
4120 mlosch 1.387
4121 jmc 1.1203 checkpoint56 (2004/11/17)
4122 jmc 1.385 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
4123 edhill 1.384 o mnc: cleanup "full" files--fixes out-of-memory problem
4124 heimbach 1.386 o ECCO-GODAE
4125     * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
4126     * fully merged and updated from SIO code
4127     windstress sign change affects
4128     - exf_inscal_[u/v]stress
4129     - sign of xx_tau[u/v] adjustments
4130     - signs in cost_scat
4131     * ctrl_get_gen: avoid update of tau[u/v] for first few days
4132     * natl_box_adjoint updated and compressed
4133     * 2-level checkpoint switch added
4134     (tested in EXP. 1 of natl_box_adjoint)
4135     * new switch doInitXX to avoid init. of xx_... in optimcycle=0
4136     o SVD
4137     * first complete, non-hacked version for SVD calculations
4138     * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
4139     performed via direct access files admtlm_vector.it????
4140     (via ctrl_[un]pack)
4141     * optimcycle is used for ARPACK iteration counter
4142     (note: adxx_... is iterated, rather than xx_...; latter is constant!)
4143     * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
4144     and add linear transforms where necessary
4145     * controls are initial/final SST, SSS (can be extended; need to check
4146     ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
4147     o mdsio: filename info to both stderr, stdout
4148     o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
4149     from sign change
4150 edhill 1.384
4151 jmc 1.1203 checkpoint55j_post (2004/11/10)
4152 jmc 1.382 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
4153     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4154 edhill 1.381 o add consistent build directories and .cvsignore files to verification
4155 dimitri 1.380 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
4156 edhill 1.379 o make all subroutines 30 or less characters in length for certain older
4157     compilers to work (a thorough search only turns up two routines in
4158     pkg/ptracers)
4159 jmc 1.378 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
4160     affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4161    
4162 jmc 1.1203 checkpoint55i_post (2004/10/28)
4163 jmc 1.376 o change arrays for total vertical diffusivity (2.D if explicit,
4164     3.D if implicit) ; each ptracer uses its own background value.
4165 edhill 1.375 o added mnc/NetCDF output capability to ocn_compon_interf
4166     - added bits to verification/cpl_aim+ocn so that it can run on
4167     ITRDA and other clusters without the mpirun "-wd" option
4168 afe 1.374 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
4169     configuration
4170 edhill 1.373 o give MNC the ability to create additional files rather than
4171     exceeding a specified file size limit "MNC_MAX_FILESIZE"
4172     - the default is just less than 2GB which is a practical limit
4173     on many systems
4174 jmc 1.372 o Compute the non-local term using either KPP vertical diffusivity (=default)
4175     or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
4176 jmc 1.349
4177 jmc 1.1203 checkpoint55h_post (2004/10/20)
4178 jmc 1.371 o add verification test "vermix"
4179 edhill 1.370 o remove all the *_ioinc flags and replace with the single global
4180     outputTypesInclusive flag
4181 jmc 1.369 o allow to set a vertical profile of vertical diffusivity for T & S
4182 jmc 1.371 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
4183     o useMNC moved from data.mnc to data.pkg
4184 jmc 1.369
4185 jmc 1.1203 checkpoint55g_post (2004/10/14)
4186 heimbach 1.368 o Renaming carbon AD experiments to comply with testreport conventions
4187     o Updating adjoint of Held-Suarez hs94.1x64x5
4188     o Fixing directives for non-ECCO forward_step, after ECCO directives
4189     have been fixed to avoid recomp. of do_oceanic_phys
4190     Works well for global_ocean.90x40x15,
4191     but recomp. issue remains for carbon
4192     o Updating adjoint output for natl_box_adjoint after
4193     pkg/ecco has been modified (see taga c55d_post)
4194    
4195 jmc 1.1203 checkpoint55f_post (2004/10/13)
4196 edhill 1.367 o rename to timeave_init_fixed
4197    
4198 jmc 1.1203 checkpoint55e_post (2004/10/13)
4199 heimbach 1.366 o some delicate re-shuffle of store directives to avoid one
4200     extra call of do_oceanic_physics
4201     affects ecco_the_main_loop.F, do_oceanic_physics.F
4202     checkpoint_lev1_directives.h
4203     o NB: this may break global_ocean adjoint temporarily,
4204     but it is clear how to fix it. Will do later, need this now.
4205    
4206 jmc 1.1203 checkpoint55d_post (2004/10/11)
4207 heimbach 1.365 o ECCO specific cost function terms (up-to-date with 1x1 runs)
4208     o ecco_cost_weights is modified to 1x1 runs
4209     o modifs to allow observations to be read in as
4210     single file or yearly files
4211     o enable to read exf forcing fields as either
4212     single file or yearly files (flag useExfYearlyFields)
4213 jmc 1.1203 checkpoint55d_pre (2004/10/08)
4214 heimbach 1.365
4215     o switch between 2-level and 3-level checkpointing
4216 edhill 1.364 o add ability of MNC to write local and "partial" (eg. 2D slices where
4217     the full 3D field is never actually stored) arrays to NetCDF files
4218     with the correct (that is, the complete multi-dimensional) set of
4219     array indicies
4220     - used in mom_vecinv() to write the diagFreq output
4221     - tested (demonstrated) in verification/aim.5l_cs
4222 edhill 1.363 o further mnc-ification
4223     - add verification/lab_sea to the list with mnc setups
4224     - fix undefined mnc v-names in cd_code
4225     - add kpp to mnc output (both snapshot and timeave)
4226 mlosch 1.362 o non-hydrostatic code
4227     - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
4228     in calc_gw.F
4229     - defaults to viscAh
4230     - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
4231     friction or Leith) in non-hydrostatic mode, as long as there is
4232     no biharmonic friction and/or Leigth or equivalent for vertical velocity.
4233 heimbach 1.360 o pkg/cost
4234     extend simple cost functions to treat time mean quantities
4235     (T,U,V) via cost_accumulate_state from cost_tile
4236 jmc 1.358 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
4237     be 2 times larger than the minimum size the advection scheme requires.
4238     now get a perfect conservation of salt in advect_cs test-exp (updated)
4239 mlosch 1.356 o GGL90 (Gaspar's TKE mixed layer)
4240     - add horizontal diffusion of TKE, requires exchanges in
4241     do_fields_blocking_exchanges, horizontal diffusivity is zero by
4242     default. In OPA there is no horizontal diffusion of TKE but the
4243     mixing coefficients are computed from a horizontal average of TKE of
4244     6 points or so. I think that diffusion has a little more physical
4245     justification.
4246     - clean up ggl90_calc in the hope of reducing memory usage (this hope
4247     was in vain)
4248     - mask tke-variable in ggl90_init
4249 jmc 1.355 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
4250     o fix biharmonic diffusion on CS-grid.
4251 mlosch 1.354 o more obcs stuff
4252     - added obcs_external_fields_load as an alternative to the EXF-pkg option
4253     for reading boundary values. This routine is called from
4254     obcs_prescribe_read
4255     - updated obcs_check
4256 mlosch 1.357 - changed sponge layer relaxation parameter units for days to seconds
4257     - turned off sponge layer by default
4258 heimbach 1.359 - changed argument list of OBCS_CALC to myTime+deltaTclock
4259 mlosch 1.361 - fixed about 35 bugs in obcs_external_fields_load
4260 mlosch 1.354
4261 jmc 1.1203 checkpoint55c_post (2004/09/23)
4262 heimbach 1.352 o obcs stuff
4263     - new runtime flags useOBCSprescribe, useOBCSbalance
4264     - re-arranged obcs_calc
4265     - moved exf_getobcs to obcs_prescibe_read
4266     obcs_prescibe_read is called after ORLANSKI stuff
4267     and independent of it (executable can contain all).
4268     - updated obcs_check
4269 heimbach 1.353 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
4270     These may be necessary only if tangential velocities are
4271     prescribed at OB, not sure, needs testing.
4272 edhill 1.351 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
4273     which simplifies the calls and passes the ifc check-bounds test
4274    
4275 jmc 1.1203 checkpoint55b_post (2004/09/22)
4276 jmc 1.350 o add a 2D scalar, Z location, exchange_2 routine.
4277 jmc 1.349 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
4278     to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
4279     affects advect_cs results (for the wrong reason): update output.txt
4280 jmc 1.348 o use a more standard discretization for biharmonic viscosity ;
4281     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
4282     affects results of dome set-up: update output.txt
4283     o fix gad_advection.F (CubedSphere part), back to version 1.23
4284     o fix bug in mom_vi_del2uv.F (CubedSphere part).
4285 mlosch 1.341
4286 jmc 1.1203 checkpoint55a_post (2004/09/20)
4287 heimbach 1.347 o merged code to
4288     * prescribe/read time-dependent open boundaries
4289     (works in conjunction with exf, cal)
4290     * sponge layer code for open boundaries
4291     * each boundary N/S/E/W now has its own CPP option
4292     (healthy for the adjoint)
4293    
4294 jmc 1.1203 checkpoint55 (2004/09/17)
4295 heimbach 1.346 o up-to-date adjoint of previous breaks
4296     - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
4297     - global_ocean_ebm: adjoint still needs fix (TLM ok)
4298     - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
4299     - carbon: * remove tr1-related adjoint verification
4300     * add ptracer as control variable
4301     o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
4302     (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
4303    
4304 jmc 1.1203 checkpoint54f_post (2004/09/16)
4305 heimbach 1.345 o in verification/carbin/ remove experiment related to
4306     ALLOW_PASSIVE_TRACER (array tr1 etc)
4307     code_ad/ input_ad/ results_ad
4308    
4309 mlosch 1.344 o add two new packages
4310     - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
4311     + subject to optimization (memory)
4312     - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
4313     + subject to reordering (many GOTOs in the original code)
4314     + so far opps is called for every (i,j) point, and then operates in
4315     the vertical; one may want to reorder the scheme in order operate in
4316     horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
4317     fields)
4318 edhill 1.343 o overhaul of IO so that we now have flags for MDSIO and/or MNC
4319     - all verification tests compile and run with linux_ia32_g77
4320     - defaults are compatible with current input files--nothing
4321     should change if you were not previously using MNC
4322     - MNC output has been added in numerous places (eg. timeave)
4323     but there are still a few writes not yet do-able with MNC
4324     (this is in progress)
4325     - flags now allow for either/or/both use of MDSIO and MNC and
4326     documentation will soon follow
4327     - numerous small formatting cleanups for ProTeX
4328 edhill 1.342 o add version info (via BUILD_INFO.h) to MNC and stdout
4329    
4330 jmc 1.1203 checkpoint54e_post (2004/09/02)
4331 mlosch 1.341 o add two new packages
4332     - pp81 (Packanowski and Philander, 1981), Richardson number and
4333     stratification dependent mixing
4334     - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
4335     - these scheme operate in a similar manner as KPP (without ghat, of
4336     course), however there is only one diffusivity that is used for both
4337 mlosch 1.1068 temperature and salinity (and passive tracers)
4338 stephd 1.340 o add offline package
4339 edhill 1.339 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
4340     provided by Stephanie Dutkiewicz
4341 edhill 1.338 o genmake2: add ability to search for C compilers and cleanup test output
4342     - fixes recent SX-6 problems and should help with others (eg. HP-UX)
4343    
4344 jmc 1.1203 checkpoint54d_post (2004/07/27)
4345 adcroft 1.336 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
4346 jmc 1.337 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
4347     leading to additional shift by 5 days each year of integration
4348     (i.e. leading to considerable offset over the years)
4349 jmc 1.335 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
4350     o start with no AB and no initial filtering (staggerTimeStep):
4351     change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
4352     o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
4353     (external loading & cpl import/export stay in forward_step.F)
4354     o update coupling interface to work with new staggerTimeStep
4355     o change MDSIO ptracers_pickup.
4356 jmc 1.334 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
4357 edhill 1.333 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
4358 jmc 1.334 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
4359 edhill 1.333
4360 jmc 1.1203 checkpoint54c_post (2004/07/18)
4361 jmc 1.331 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
4362     this affects (truncation error) output.txt of test-exp:
4363     global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
4364     o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
4365 jmc 1.330 o change Qnet to always be the net heat flux, (+upward).
4366     affects (truncation error) output of natl_box exp.: updated
4367 jmc 1.329 o define the max number of passive tracers in PTRACERS_SIZE.h
4368     o start to test mnc routinely in exp0
4369     o add sea-ice loading (sIceLoad) as a new forcing field.
4370    
4371 jmc 1.1203 checkpoint54b_post (2004/07/08)
4372 edhill 1.327 o add testreport "-j JOBS" option for parallel builds (tested and pretty
4373     impressive on Altix and Opteron systems)
4374 edhill 1.326 o diagnostics can now write NetCDF files through the mnc package
4375 jmc 1.325 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
4376 jmc 1.324 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
4377 jmc 1.323 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
4378     affects (truncation error) output of lab_sea & natl_box exp.: updated
4379     o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
4380    
4381 jmc 1.1203 checkpoint54a_post (2004/07/06)
4382 jmc 1.322 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
4383     o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
4384     o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
4385     o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
4386     + internal_wave (shift in writing cg2d_ini_res)
4387 jmc 1.1203 checkpoint54a_pre (2004/07/05)
4388 jmc 1.321
4389 dimitri 1.320 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
4390     - modified verification/lab_sea and natl_box_adjoint accordingly
4391    
4392 jmc 1.1203 checkpoint54 (2004/07/02)
4393     checkpoint53g_post (2004/07/02)
4394 jmc 1.317 o prepare splitting of thermodynamics: store convect.counter in common block
4395 jmc 1.316 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
4396     output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
4397 dimitri 1.315 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
4398 jmc 1.314 o new parameter "nShapS": allow to treat differently S from T (nShapT)
4399     o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
4400 heimbach 1.318 o restore adjointability
4401 jmc 1.314
4402 jmc 1.1203 checkpoint53f_post (2004/06/25)
4403 jmc 1.313 o modifications that affect AIM experiment results (update output.txt):
4404     - no advection of S at top interface Nr (pkg/generic_advdiff)
4405     - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
4406 jmc 1.312 o AIM pkg:
4407     - include stability function into surf.Flux derivative relative to Tsurf
4408     - calculate clear-sky radiation & surface temp. change (for diagnostics)
4409 jmc 1.313
4410 afe 1.311 checkpoint53e_post
4411     o merged cylindrical coord configuration
4412     o added rotating_tank experiment
4413 afe 1.310 checkpoint53e_pre
4414    
4415 jmc 1.1203 checkpoint53d_post (2004/06/14)
4416 jmc 1.308 o faulks upgraded: re-generate output.txt that have changed:
4417     global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
4418 adcroft 1.307 o Added Bryan and Lewis, 1979, vertical diffusivity profile
4419 jmc 1.306 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
4420 adcroft 1.305 o added Sadourny discretization of Coriolis
4421     - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
4422     - re-enabled use of omega3 (useAbsVorticity)
4423 adcroft 1.304 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
4424 jmc 1.309 vector-invariant equations
4425 adcroft 1.304 - note: does *NOT* yet use same variable visc. for no-slip BC's.
4426 mlosch 1.303 o recoded the lateral boundary conditions for non-hydrostatic w, this time
4427     hopefully without new bugs
4428     - still to do: biharmonic friction for non-hydrostatic w
4429 adcroft 1.302 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
4430     o regenerated output for global_ocean_ebm (using -ieee)
4431 adcroft 1.301 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
4432     of mom_common/
4433     - simple re-arrangement of instructions within computing loop
4434 jmc 1.1203 checkpoint53d_pre (2004/05/21)
4435 mlosch 1.297
4436 jmc 1.1203 checkpoint53c_post (2004/05/21)
4437 jmc 1.299 o new version of coupler for AIM+thSIce and Ocean models
4438     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
4439     - land: change Evaporation of snow
4440     - aim with thSIce: fix bug in snow-precip.
4441 mlosch 1.297 o changes to calc_gw.F
4442     - bug fix for w^2 term near the bottom boundary
4443     - (hopefully) improve the lateral slip boundary condtions for use with
4444     partial/looped cells
4445     - because the bug fix changes two verification experiments anyway (exp5
4446     and plume on slope), change the lateral boundary condition from half slip
4447     to the value of no_slip_sides
4448 heimbach 1.298 o ebm package wasnt quite up to the parallel task. Fixed that.
4449 heimbach 1.300 o Adjoint of EBM package + verification
4450     * TLM OK
4451     * ADM not sufficient accuracy yet (needs further testing)
4452 heimbach 1.295
4453 jmc 1.1203 checkpoint53b_post (2004/05/14)
4454 heimbach 1.296 o Commiting new energy balance model to repository
4455     * package is pkg/ebm
4456     * verif. is verification/global_ocean_ebm
4457     * references are in ebm_driver.F
4458     C * X. Wang, P. Stone and J. Marotzke, 1999:
4459     C Global thermohaline circulation. Part I:
4460     C Sensitivity to atmospheric moisture transport.
4461     C J. Climate 12(1), 71-82
4462     C * X. Wang, P. Stone and J. Marotzke, 1999:
4463     C Global thermohaline circulation. Part II:
4464     C Sensitivity with interactive transport.
4465     C J. Climate 12(1), 83-91
4466     C * M. Nakamura, P. Stone and J. Marotzke, 1994:
4467     C Destabilization of the thermohaline circulation
4468     C by atmospheric eddy transports.
4469     C J. Climate 7(12), 1870-1882
4470     o Will need long integration testing.
4471 jmc 1.1203 checkpoint53b_pre (2004/05/14)
4472 dimitri 1.292
4473 adcroft 1.294 o created pkg/mom_common in preparation for variable viscosity code
4474     o renamed and split ini_mnc_io
4475 jmc 1.293 o pkg/land: only liquid water can diffuse or run-off
4476     o AIM using land: soil wetness availability account for snow
4477 dimitri 1.292 o added printMapIncludesZeros to EEPARMS namelist
4478 heimbach 1.290
4479 jmc 1.1203 checkpoint53a_post (2004/05/11)
4480 heimbach 1.290 o restore TAMC compatiility for exf_constants.h
4481     (no usage of _d in .h)
4482     o Additional storing in KPP in an attempt to fix
4483     TAMC problem with adjoint of KPP code.
4484     (no success...)
4485     Identical code works fine with TAF.
4486 dimitri 1.291 o Fixed verification/natl_box_adjoint experiments.
4487     Initial conditions for Experiments 4 and 5 are now
4488     set to "SEAICE_initialHEFF=0", which is more reasonable,
4489     and hence gives results closer to that of Experiment 2.
4490     Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
4491 cnh 1.289
4492 jmc 1.1203 checkpoint53 (2004/05/06)
4493 cnh 1.289 o stable checkpoint with up to date adjoint
4494     TLM tests only run for 1st grdchk at the moment. Its unclear if
4495     this is a code problem or a problem with resetting code for g_
4496     variables that is being autogenerated wrong.
4497     Otherwise:
4498     o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
4499     o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
4500     are both still in chaos following their security messes.
4501 jmc 1.279
4502 jmc 1.1203 checkpoint52n_post (2004/05/06)
4503 edhill 1.288 o various build (mostly genmake2) changes including:
4504     - ability to build/run more easily within Cygwin and MacOS X
4505     - more complicated Makefiles with a stronger dependence on Gnu Make
4506 dimitri 1.285 o pkg/seaice modifications
4507 dimitri 1.287 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
4508     of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
4509     and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
4510 dimitri 1.285 - changed proxy for geostrophic velocity and updated
4511 dimitri 1.286 verification/lab_sea/results/* accordingly
4512 dimitri 1.285 - removed ADI dynamic solver from pkg/seaice
4513     - replaced all occurrences of 1/CSTICE or 1/CSUICE
4514     they caused a segmentation fault under certain circumstances
4515 mlosch 1.283 - removed unused field WATR
4516 mlosch 1.282 o bug fix in exf-package:
4517     - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
4518     now reflect that.
4519 mlosch 1.281 o small fixes in the cal-package:
4520     - set reference date to first of January for the 'model'-calendar
4521     - failing of cal_CheckDate in cal_FullDate now actually results in a
4522     warning
4523 mlosch 1.280 o small modifications in exf-package to increase flexibility:
4524     - change climtempfreeze from a constant to a runtime parameter that
4525     is specified in data.exf_clim (default = -1.9)
4526     - introduce runtime parameter windstressmax (default = 2.0) that is
4527     specified in data.exf
4528 jmc 1.279 o fix in pkg/thsice:
4529     - update Evap (Tsf changes) to be consistent with Latent heat flux
4530     - maintain snow precipitation unchanged (even if Tsf >=0).
4531     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
4532 edhill 1.272
4533 jmc 1.1203 checkpoint52m_post (2004/04/18)
4534 mlosch 1.277 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
4535     this does not change any of the results, because myIter=0 in swfrac always
4536     lead to jwtype=2 (the default anyway), but the call makes little sense
4537     as a default
4538 jmc 1.276 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
4539 jmc 1.275 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
4540     atmospheric model (AIM) to use it ; add a "slab ocean" component.
4541     o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
4542     o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
4543 dimitri 1.274 o extending useSingleCpuIO option to work with new exch2 I/O format
4544     - old-style, missing-tile I/O is still accessible by defining CPP
4545     option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
4546 edhill 1.273 o monitor package can write to NetCDF files and/or STDOUT
4547     o fix re-definition bug in MNC_GRID_INIT_ALL()
4548 edhill 1.272 o doc/api_reference added
4549     - a framework for building an API Reference Manual using all
4550     the "protex" comments embedded in the code
4551     - see pkg/generic_advdiff, pkg/mnc for examples
4552 edhill 1.269 o MNC:
4553     - make myThid the last argument for all subroutines
4554     - new default for the grid files: NO halos
4555 edhill 1.270 - add useMNC and other run-time flags
4556     - separate per-file-group handling of the unlimited dimension
4557     - early initialization of MNC w/ flags read at the eeboot stage
4558     and lookup tables set in initialize_fixed
4559     - write all MNC output to a freshly-created directory
4560 jmc 1.268 o thermodynamics sea-ice (thsice) is now tested with testreport.
4561     o test exp. advect_cs: use the standard cs32 grid ; update output.
4562 heimbach 1.271 o Added functionality to grdchk:
4563     pick global i,j,k position (or nearest wet) where to perform check.
4564 jmc 1.266
4565 jmc 1.1203 checkpoint52l_post (2004/03/11)
4566 jmc 1.267 o new land formulation:
4567     a) use ground enthalpy as prognostic variable to ensure exact
4568     energy conservation.
4569     b) account for water temperature and for latent heat of freezing
4570     in all processes (rain, run-off, ground storage)
4571     c) compute surface and ground temperature implicitly.
4572     o aim_v23 modification for new land model:
4573     a) Treat separately land / ocean / sea-ice surface fluxes
4574     to allow implicit computation of land & sea-ice surface temp.
4575     b) add snow precipitation.
4576 jmc 1.1203 checkpoint52l_pre (2004/03/11)
4577 jmc 1.266
4578 jmc 1.265 o fix problem (when 1 tile is empty) in min/max monitor.
4579     o fix bug in timeAve (u,vZetatave in common block)
4580 dimitri 1.264 o no restoring terms under ice for pkg/seaice
4581 dimitri 1.263 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
4582     o bug fix for pkg/seaice pickups
4583 edhill 1.262 o change MNC call locations and add coordinate attributes
4584 jmc 1.260 o mask vorticity at the corner ; affects global_ocean.cs output
4585     o fix ini_curvilinear_grid ; test CS experiments with mpi
4586 jmc 1.259 o aim.5l_cs: modify sea-ice fraction input file ; update output
4587 heimbach 1.261 o exf: Adding simple range check routine for exf fields after read
4588 adcroft 1.256
4589 jmc 1.1203 checkpoint52k_post (2004/02/23)
4590 adcroft 1.256 o removed top-level directory "diags"
4591     - we migrated these functions to pkg/timeave a long time ago
4592     o fixed bug introduced in pkg/monitor
4593 heimbach 1.257 o accuracy ctrlprec = 32 insuffient for gradient checks using
4594     averaged fields (I/O via cost_averages)
4595     -> use ctrl.h in active_file*.F to control I/O precision.
4596     o paramter list of CALL ADTHE_MAIN_LOOP
4597     o added initial do_the_model_io to ecco
4598     o set all ...Freq to zero after cost_final
4599     taveFreq, dumpFreq, pChkptFreq
4600 heimbach 1.258 o MAIN and ECCO differentiability restored
4601 heimbach 1.255
4602 jmc 1.1203 checkpoint52j_post (2004/02/18)
4603 heimbach 1.255 o fix nchklev in tamc.h for global_ocean...
4604     o Bringing flow and store directives up-to-date
4605     o Really weird thing!
4606     call do_the_model_io from the_main_loop with parameters
4607     starttime, niter0, instead of mytime, myiter, screws up the adjoint:
4608     TAF places a faulty re-call of initialise_varia
4609     after cost_final call which should not be there!
4610 jmc 1.1203 checkpoint52j_pre (2004/02/03)
4611 jmc 1.253
4612 afe 1.254 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
4613     error messages
4614 jmc 1.253 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
4615 afe 1.252 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
4616     debug output
4617 afe 1.251 o modfied mdsio_writefield.F to handle non-global files under exch2
4618 jmc 1.250 o update AIM Cubed-Sphere exp (aim.5l_cs):
4619     use land, p*, and Franco.M forcing fields with fractional land-sea mask.
4620     o update AIM Equatorial Channel exp:
4621     use standard aim_v23 pkg and change the SST fields to be more realistic.
4622 afe 1.248 o globalFile now works with exch2
4623 afe 1.247 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
4624 jmc 1.253 mon_vort3.F to make exch2 friendly with >1 tile per cube face
4625 dimitri 1.249 o limit timeave output for hi-res integrations
4626 adcroft 1.245
4627 jmc 1.1203 checkpoint52i_post (2004/01/21)
4628 adcroft 1.245 o removed CPP_EEOPTIONS.h from verification/*/code
4629     o updated the tiling for global_ocean_pressure
4630 jmc 1.1203 checkpoint52i_pre (2004/01/20)
4631 jmc 1.246
4632     o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
4633     the old pkg/aim).
4634 afe 1.239
4635 jmc 1.1203 checkpoint52h_pre (2004/01/20)
4636 afe 1.243 o shortened offending lines in exch2_send_rx?.template
4637 afe 1.242 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
4638 edhill 1.240 o genmake2: add build & execute test for NetCDF code
4639 afe 1.239 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
4640     old grid files, moved CPP_EEMACROS.h to pkg/exch2
4641 dimitri 1.238 o added useSingleCPUIO flag to monitor.F and mon_out.F
4642 dimitri 1.241 o added temporary hack for sea-ice dynamics on the cube:
4643     metric terms are ignored and it is assumed that
4644     there is no sea-ice on cube faces 1, 2, 4, and 5.
4645 dimitri 1.238
4646 jmc 1.1203 checkpoint52f_post (2004/01/09)
4647 afe 1.236 o added exch2 cube routines to pkg/exch2
4648     o modified hs94.cs-32x32x5 to use it
4649     o added new grid files to hs94.cs-32x32x5
4650 jmc 1.1203 checkpoint52f_pre (2004/01/07)
4651 dimitri 1.228
4652 jmc 1.1203 checkpoint52e_post (2004/01/07)
4653 jmc 1.234 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
4654     for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
4655 jmc 1.235 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
4656     to work with implicit vertical advection and AB ;
4657     o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
4658     o update output (gad_calc_rhs.F changes affect truncation error) of exp:
4659     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
4660 jmc 1.1203 checkpoint52e_pre (2004/01/02)
4661 jmc 1.233
4662     o fix bug in impldiff when Nr=1 or Nr=2.
4663 jmc 1.232 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
4664     o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
4665 jmc 1.229 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
4666     ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
4667 dimitri 1.228 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
4668 dimitri 1.231 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
4669     o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
4670 jmc 1.220
4671 jmc 1.1203 checkpoint52d_post (2003/12/16)
4672 adcroft 1.230 o re-tiled many expts to allow comparison in multi-processor mode
4673     - updated output accordingly
4674     - changed hs94.128x64x5 to use intial T from file rather than use the
4675     random number generator
4676 molod 1.227 o add infrastructure in model routines for fizhi and gridalt packages
4677 jmc 1.220 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
4678 dimitri 1.222 o changes to permit hi-res, cubed-sphere, configuration
4679     - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
4680     - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
4681     - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
4682     of surface winds for the cube
4683     (A verification experiment, based on global_ocean.cs32x15, but with
4684     pkg/seaice turned on and with on-the-fly interpolation from the NCEP
4685     Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
4686     complete with example surface forcing files and matlab scripts to look
4687     at the output and compare it with that of global_ocean.cs32x15.)
4688 jmc 1.223 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
4689     but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
4690     to conform to the common rule.
4691 jmc 1.224 o check-in the first version of the coupler + interfaces for multi-components
4692     set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
4693     - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
4694     - atmosphere: use pkg aim_v23 ; no sea-ice for now.
4695     - ocean and atmos. share the same horizontal grid (no interpolation).
4696     - exchanges between component and coupler is done in forward_step
4697 jmc 1.225 o new verification experiment, cpl_aim+ocn:
4698     coupled ocean - AIM atmosphere on cs32 grid.
4699 jmc 1.217
4700 jmc 1.1203 checkpoint52d_pre (2003/12/06)
4701 jmc 1.217 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
4702 jmc 1.218 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
4703 heimbach 1.213
4704 jmc 1.1203 checkpoint52c_post (2003/11/25)
4705 heimbach 1.213 o Fixing OPTIONS files for use of exf:
4706     - ALLOW_ECCO not needed
4707     - ECCO_CPPOPTIONS.h should not be included from
4708     EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
4709     as has been the case in the past
4710     - All cal/exf related options are currently set in
4711     single header file. Should remain so until we
4712     agree on a consistent new policy.
4713 heimbach 1.214 o Removed all CPP options for cal package.
4714     cal has no more CPP options.
4715 heimbach 1.215 o modified STOREs in GAD_ADVECTION
4716     o corrected key comp. for passkey
4717 heimbach 1.210
4718 jmc 1.1203 checkpoint52b_post (2003/11/23)
4719 jmc 1.212 o new version: "thsice" of thermodynamic sea-ice pkg:
4720     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
4721     - modify fluxes but do not change theta directly;
4722     - light cleaning of bulk_force pkg (still needed with thsice).
4723     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
4724     + output_thsice.txt to test thsice & bulk_force pkgs.
4725     o put back grid & coriolis monitor output.
4726 jmc 1.1203 checkpoint52b_pre (2003/11/23)
4727 jmc 1.211
4728     o call "do_the_model_io" at the beginning (=> dump initial state)
4729     o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
4730 heimbach 1.210 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
4731     (need info on NUMBER_OF_PTRACERS)
4732     o missing PTRACERS headers in some routines
4733     o default tamc.h in pkg/autodiff supposed to crash
4734     to ensure proper customization
4735 dimitri 1.206
4736 jmc 1.1203 checkpoint52a_post (2003/11/17)
4737 jmc 1.208 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
4738 dimitri 1.207 - moved surfaceTendencyTice from pkg/seaice to main code
4739 jmc 1.208 - subroutine FREEZE_SURFACE now limits only surface temperature
4740     and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
4741     => new output.txt for global_ocean.cs32x15 & global_with_exf
4742     - keep the old version of FREEZE for backward compatibility;
4743     global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
4744 heimbach 1.209 - corresponding modifs for TAF directives
4745 dimitri 1.207 o added surface flux output variables to TIMEAVE_STATVARS
4746     o time-averaged output for pkg/ptracers
4747 heimbach 1.209 o fix problem with ECCO-related divided adjoint
4748     snapshot file was missing some ad-variables,
4749     but no warning issued by TAF
4750 dimitri 1.206
4751 jmc 1.1203 checkpoint52a_pre (2003/11/12)
4752 dimitri 1.206 o some bug fixes for #undef REAL4_IS_SLOW
4753 heimbach 1.205
4754     checkpoint52 = ecco_c52_e35
4755     o after testing adjoints of checkpoint51u_post
4756 edhill 1.203
4757 jmc 1.1203 checkpoint51u_post (2003/11/06)
4758 heimbach 1.204 o this is the post-merge tag of the ecco-branch
4759     (needs another clean checkout and re-testing)
4760     o various natl_box_adjoint configs and results
4761     but no input fields
4762     o obcs adjoint not yet merged!
4763     o adding ECCO global 1x1 and 2x2 degree configs
4764     o updated/extended some store directives for seaice
4765     o pkg/ecco now containes ecco-specific part of cost function
4766     o top level routines the_main_loop, forward_step
4767     supersede those in model/src/
4768     previous input data.cost now in data.ecco
4769     (new namelist ecco_cost_nml)
4770     o in ctrl/ cleaned some cross-dependencies and updated CPP options
4771    
4772 jmc 1.1203 checkpoint51t_post (2003/11/04)
4773 heimbach 1.204 o this is the pre-merge tag of the ecco-branch
4774    
4775 jmc 1.1203 checkpoint51s_post (2003/11/04)
4776 edhill 1.203 o cleanup: removed various obsolete #define-s
4777 heimbach 1.204 o pkg/grdchk
4778     - renamed 'ph-grd 3' to 'grad-res'
4779     - merged from ecco-branch
4780     (remaining bug fixes for obcs gradient checks)
4781     - additional high-precision output for testreport
4782     (grep for 'precision_grdchk_result')
4783 edhill 1.202
4784 jmc 1.1203 checkpoint51r_post (2003/11/03)
4785 edhill 1.202 o cleaned up or removed CPP_OPTIONS.h files
4786     o updated results for some of the tests to reflect the new
4787     optfiles (-ieee: -O0 instead of -O3)
4788 heimbach 1.201
4789 jmc 1.1203 checkpoint51q_post (2003/10/30)
4790 heimbach 1.201 o cd_code:
4791     - moved cd_scheme.F -> cd_code_scheme.F
4792     - separate read_checkpoint from cd_code_ini_vars.F
4793     - separated cd_code part from write_checkpoint
4794     - updated AD_SOURCE, generated .flow
4795     - added CD_CODE_VARS.h to the_main_loop
4796     - Moving cd_code specific store dir.s to pkg/cd_code
4797     o ctrl package totally restructured
4798     - pack/unpack now optional and decoupled from
4799     xx_/adxx_ I/O
4800     - ctrl_pack/unpack cleaned
4801     (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
4802     - confined inclusion of AD_CONFIG.h to where necessary.
4803     o genmake2: changed AD dependencies from SRCFILES to AD_FILES
4804 edhill 1.198
4805 jmc 1.1203 checkpoint51p_post (2003/10/30)
4806 edhill 1.198 o create initial cd_code package
4807 edhill 1.199 - WARNING: the initialization of fields within packages
4808     is broken because INI_FIELDS (where READ_CHECKPOINT is
4809     called) is called *before* PACKAGES_INIT_VARIABLES.
4810     This seems to be backwards since
4811     1) its important to initially zero the entire field including
4812     the "halo" region
4813     2) zeroing needs to be done *before* reading pickup info
4814     and the pickup call might or might not happen in any
4815     particular run
4816     - this needs an overhaul for R2
4817 edhill 1.198 o cleanup verification/*/code/GMREDI_OPTIONS.h
4818     o cleanup testreport
4819 heimbach 1.196
4820 jmc 1.1203 checkpoint51o_post (2003/10/27)
4821 heimbach 1.196 o bringing AD-related verif's up to date with genmake2
4822     - carbon/
4823     - global_ocean.90x40x15/
4824     - hs.94.1x64x5/
4825     - (front_relax/ )
4826     o (more) consistent directory structure for AD-related verif.'s
4827     o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
4828     o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
4829     o bug fix in find_alpha.F for MDJWF:
4830     - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
4831     change rho -> rho-rhoConst
4832     - replace call find_rho to find_rhonum
4833     o initialisation of rFlx extended to full array (required by TAF)
4834     and shifted to thermodynamics
4835     o removed PTRACERS.h in ptracers routine
4836     o added surfacetendencyPtr to S/R parameter list pracers_forcing
4837     o Correcting initialisations for fVerU, fVerV.
4838     o helping TAF to recognize dependency on kUp for
4839     fVerU, fVerV
4840     o Replacing delZ by delR in pkg/ctrl/
4841 jmc 1.1203 checkpoint51o_pre (2003/10/24)
4842 dimitri 1.192
4843 edhill 1.195 o undid all of cp51 pending some cleanups and discussion
4844 heimbach 1.197 o added the [#include "AD_CONFIG.h"] statement to all files that need
4845     it for adjoint/tl #defines
4846     o re-worked the build logic in genmake2 to support AD_CONFIG.h
4847     o removed tools/genmake since it no longer works
4848 dimitri 1.194
4849 jmc 1.1203 checkpoint51n_post (2003/10/23)
4850 dimitri 1.194 o modifications to make FREEZE flux visible to pkg/kpp
4851     - moved surfaceTendencyTice from pkg/seaice to main code
4852     - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
4853     - subroutine FREEZE now limits only surface temperature
4854     (this means new output.txt for global_ocean.90x40x15,
4855     global_ocean.cs32x15, and global_with_exf)
4856     o added surface flux output variables to TIMEAVE_STATVARS
4857    
4858 jmc 1.1203 checkpoint51n_pre (2003/10/23)
4859 dimitri 1.192 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
4860 edhill 1.193 o added [#include "AD_CONFIG.h"] to all files that use the following
4861     defines:
4862     - ALLOW_ADJOINT_RUN
4863     - ALLOW_TANGENTLINEAR_RUN
4864     - ALLOW_ECCO_OPTIMIZATION
4865 edhill 1.190
4866 jmc 1.1203 checkpoint51m_post (2003/10/21)
4867 edhill 1.190 o incorporating changes to get TAMC/TAF working in genmake2
4868     - added new TAMC/TAF targets to the Makefile
4869     - various cleanups related to package handling
4870 edhill 1.191 - these changes should have no impact on the forward model
4871 dimitri 1.189
4872 jmc 1.1203 checkpoint51l_post (2003/10/20)
4873 dimitri 1.189 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
4874     - faster algorithm for cal_addtime.F
4875     - higher precision arithmetic, where needed
4876     - pkg/exf *startdate variables changed from calendar date to
4877     model integration time
4878    
4879 jmc 1.1203 checkpoint51l_pre (2003/10/17)
4880 jmc 1.188 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
4881     o enable to apply restoring on S & T only in a latitude band.
4882     o update output (external_forcing_surf modif. change truncation errors)
4883     global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
4884 edhill 1.186
4885 jmc 1.1203 checkpoint51k_post (2003/10/16)
4886 jmc 1.187 o change default to: useNHMTerms=.FALSE.
4887     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
4888     adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
4889     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
4890     exp1, ideal_2D_oce
4891     - change data file of oceanic exp (leave the results unchanged for now)
4892     exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
4893     o set gravitySign automatically according to the vertical coordinate used
4894     (and change sign: back to "logical" value: +1 when R increases downward)
4895 edhill 1.186 o added an include barrier to the default CPP_OPTIONS.h and
4896     removed the #include "PACKAGES_CONFIG.h" from it
4897 jmc 1.187 o fix a bug in mom_fluxform (from chk51j_post)
4898 heimbach 1.185
4899 jmc 1.1203 checkpoint51j_post (2003/10/10)
4900 heimbach 1.185 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
4901     o adjusted some flow directives (dynamics, thermodynamics)
4902     o added cubed-sphere case to test cost function
4903     o heckpoint_lev?_directives.h now include
4904     pkg-specific directives, whenever those are enabled.
4905     o Moving pkg-specific flow directives to corresponding pkg
4906     Moving pkg-specific differentiation list to corresponding pkg
4907     Moving pkg-specific checkpoint-lev storing to corresponding pkg
4908     ---> conventions are
4909     - pkg_ad.flow
4910     - pkg_ad_diff.list
4911     - pkg_ad_check_lev?_dir.h
4912 stephd 1.181
4913 jmc 1.1203 checkpoint51i_post (2003/10/09)
4914 edhill 1.184 o merge of the branch-genmake2
4915     - knowingly breaks the older genmake
4916     - automatic generation of all ALLOW_${PKG_NAME} defines
4917     - new testreport supersedes older testscript
4918     o large number of package inclusion and header cleanups
4919 jmc 1.1203 checkpoint51i_pre (2003/10/08)
4920 edhill 1.184
4921 edhill 1.183 o new output for adjoin of global ocean vector invariant
4922     o fix for checkpoint of thermodynamic seaice and bulk_force
4923     o Steph gchem various cleanups
4924    
4925 stephd 1.181 checkpoint 51h_pre
4926 edhill 1.183 o fixed some single quotes
4927 stephd 1.181 o modify gchem pkg to be more versatile
4928     o modifications to clean up dic pkg
4929     o add pkg/cfc
4930 heimbach 1.182
4931 jmc 1.1203 checkpoint51g_post (2003/10/02)
4932 heimbach 1.182 o provide links for ARPACK and ADM*TLM
4933     o start removing verification/vero/
4934     o update AD-related stuff
4935     (in particular some IF-statements in model/src/ routines)
4936     o adding to verification/global_ocean.90x40x15/ adjoint of
4937     vector invariant setup
4938 dimitri 1.177
4939 jmc 1.1203 checkpoint51f_post (2003/10/02)
4940 jmc 1.179 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
4941 dimitri 1.178 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
4942 dimitri 1.177 of tracer Green's fucntions for ocean inversion project.
4943 dimitri 1.175
4944 jmc 1.1203 checkpoint51f_pre (2003/08/07)
4945 dimitri 1.175 o Added on-the-fly spatial interpolation capability
4946     "USE_EXF_INTERPOLATION" to pkg/exf.
4947 dimitri 1.176 - This is a temporary Cartesian-grid hack until
4948 dimitri 1.175 the super-duper ESMF coupler becomes available.
4949 dimitri 1.176 - See verification/global_with_exf/README for usage example.
4950     - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
4951     flags and modified pkg/seaice accordingly.
4952 dimitri 1.175 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
4953     and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
4954     non-local transport term.
4955 heimbach 1.172
4956 jmc 1.1203 checkpoint51e_post (2003/08/03)
4957 jmc 1.174 o pkg/mom_vecinv:
4958     - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
4959     - add time-ave diagnostic of vorticity advection.
4960     o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
4961     o atmospheric geopotential: - include water vapor effect;
4962     - use p^kappa in p* scaling.
4963 jmc 1.173 o land pkg: read initial state from files.
4964     o AIM : add stratospheric drag in the upper level
4965    
4966 jmc 1.1203 checkpoint51d_post (2003/07/18)
4967 jmc 1.173 o change function ILNBLNK (=> last non-blank char.) to return zero
4968     (instead of the string length) when the string. char is empty
4969 jmc 1.171 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
4970 heimbach 1.172 o modif's to restore TAMC compatibility
4971     - avoid "_d" constructs in PARAMETER declarations
4972     - avoid interrupting lines by comment lines
4973     o Use cluster local disks for purely local I/O
4974     vs. globally visible disks needed for ctrl stuff
4975     (merged from ecco-branch)
4976     - new active_file_loc... and mdsio_..._loc routines
4977     - affected packages: autodiff, ctrl, grdchk, mdsio
4978 heimbach 1.169
4979 jmc 1.1203 checkpoint51c_post (2003/07/08)
4980 heimbach 1.170 o introducing integer flag debugLevel
4981     - debLevZero: suppress all output
4982     - debLevA: standard
4983     - debLevB: equivalent to current debugMode=.TRUE.
4984     o introducing pathname variable mdsioLocalDir for mdsio
4985     that can be specified at runtime
4986     (relevant for cluster I/O to local disk)
4987     `
4988 heimbach 1.169 >>>checkpoint51b_post
4989     adjoint of ptracers
4990     o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
4991     o extended state in checkpoint_lev?, etc.
4992     o alternative ctrl/cost with tr1 or ptracer
4993     o new comlev1_bibj_ptracers
4994     o new ptracers.flow
4995     o made ptracers_forcing same as external_forcing_s
4996     o added verification for adjoint with ptracers
4997     - adm. grdchk fail so far
4998     - tlm. grdchk OK
4999     - checked tapelev/comlev recomputations: OK
5000     <<<checkpoint51b_pre
5001 stephd 1.168
5002 jmc 1.1203 checkpoint51a_post (2003/06/25)
5003 stephd 1.168 o added code for biogeochemistry package
5004     - new pkgs: dic, gchem
5005     - new subroutine in ptracers
5006     o modify code for biogeo packages
5007     - in model/src and pkg/ptracers
5008 heimbach 1.166
5009 jmc 1.1203 checkpoint51 (2003/06/24)
5010 heimbach 1.166 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
5011     - autodiff, ctrl, exf, grdchk, seaice
5012     kept separate packages
5013     - cost, ecco, obcs
5014 heimbach 1.167 o updating verification/internal_wave, verification/lab_sea
5015     (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
5016 heimbach 1.165
5017 jmc 1.1203 checkpoint50i_post (2003/06/23)
5018 heimbach 1.165 o Preparing next differentiable checkpoint and sync
5019     of MAIN vs. ecco-branch
5020     - 1st step: this one is differentiable
5021     - 2nd step: next(! not this) checkpoint will have updated packages
5022     from ecco-branch)
5023 jmc 1.161
5024 jmc 1.1203 checkpoint50h_post (2003/06/20)
5025 jmc 1.163 o new package "land": provide surface BC for AIM.
5026     o pkg/ptracers: apply exchange to all tracers after reading a pickup.
5027 jmc 1.161 o AIM: use true log-P extrapolation for near surface temp (= as in
5028     F.Molteni paper) ; update aim.5l_cs output.
5029 adcroft 1.162 o New variable in PARM03 for more flexible pickups
5030 heimbach 1.164 o somewhat cleaned package initialisation sequence for
5031     ctrl/ cost/ ecco/ in packages_... routines
5032 dimitri 1.160
5033 jmc 1.1203 checkpoint50g_post (2003/05/23)
5034 dimitri 1.160 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
5035     - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
5036     - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
5037     made the default because of faster convergence than ADI
5038 heimbach 1.159
5039 jmc 1.1203 checkpoint50f_post (2003/05/23)
5040 heimbach 1.159 o exf totally restructured
5041     - replaced all exf_set_ routines by one generic exf_set_gen.F
5042     and made sure it's still differentiable
5043     - split exf_getffields.F into new exf_bulkformulae.F
5044     - exf_inscal_/exf_outscal_ suffixes consistent with field names
5045     - updated adjoint/makefile and relevant verif. accordingly
5046 adcroft 1.156
5047 jmc 1.1203 checkpoint50f_pre (2003/05/23)
5048 jmc 1.157 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
5049     + change Evap over land. (update aim.5l_cs output)
5050 adcroft 1.156 o added missing .cvsignores and made uniform across expts
5051     o changed configuration of tidal_basin_2d expt
5052     o added pkg/debug functions for tracing code in fatal crashes
5053     o tidied pkg/monitor to use MONITOR_OPTIONS.h
5054     o new fn in pkg/monitor to stop model if solution grows too big
5055     o removed lots of single quotes from comments
5056    
5057 jmc 1.1203 checkpoint50e_post (2003/05/14)
5058 mlosch 1.155 o make KPP work with PTRACERS
5059     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
5060     nearly a copy of kpp_transport_s
5061     - there is no analogue to SurfaceTendencyS, so I have to use
5062     gPtr(of the surface layer) instead
5063     o add a new platform SunFire+mpi (SunFire 15000) to genmake
5064 jmc 1.1203 checkpoint50e_pre (2003/05/13)
5065 mlosch 1.155
5066 jmc 1.1203 checkpoint50d_post (2003/05/13)
5067 mlosch 1.154 o change kpp output from multiple-record state files to single-record state
5068     files analogous to write_state.F
5069     o reduce the output frequency of cg3d-related stuff to the monitor frequency,
5070     analogous to the cg2d-related output.
5071 mlosch 1.155 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
5072     so that writing to internal file fn (with length 512) fails.
5073 jmc 1.1203 checkpoint50d_pre (2003/05/12)
5074 jmc 1.151
5075 jmc 1.1203 checkpoint50c_post (2003/05/12)
5076 jmc 1.153 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
5077 jmc 1.152 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
5078 jmc 1.151 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
5079     o bug fixed in convective adjustment diagnostic (multi-tile set-up).
5080     o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
5081 dimitri 1.150
5082 jmc 1.1203 checkpoint50c_pre (2003/04/30)
5083 dimitri 1.150 Merging from release1_p13:
5084     o bug fix for pkg/seaice dynamic solver
5085     o Added SEAICE_initialHEFF to pkg/seaice
5086 jmc 1.149
5087 jmc 1.1203 checkpoint50b_post (2003/04/17)
5088 jmc 1.149 o store u*,v* in gU,V instead of in guNm1,gvNm1
5089     o in order to put the momForcing out of the Adams-Bashforth:
5090     move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
5091     to timestep.F
5092     o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
5093     o re-generate output for highly sensitive test-exp:
5094     global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
5095 heimbach 1.146
5096 jmc 1.1203 checkpoint50b_pre (2003/04/17)
5097 jmc 1.147 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
5098 heimbach 1.146 o corrected CPP option mismatch in exf_Bulk... functions for case
5099     #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
5100 heimbach 1.145
5101 jmc 1.1203 checkpoint50a_post (2003/03/21)
5102 heimbach 1.145 o Bug fix for merging between c50 and KPP.
5103     ikey was passed from thermodynamics to kpp_calc via
5104     common block rather than being recomputed in kpp_calc,
5105     in contradiction with new key itdkey.
5106     New key ikppkey created, and tamc.h headers updated.
5107 heimbach 1.143
5108 jmc 1.1203 checkpoint50 (2003/03/08)
5109 heimbach 1.144 - 2nd step of merge with ecco-branch:
5110     merge changes in ecco-branch back into main trunk
5111     - bug fix in find_alpha
5112     - more storing in gmredi_calc_tensor.F, kpp_routines.F
5113     - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
5114     - merged some sliced AD support routines
5115    
5116 jmc 1.1203 checkpoint49 (2003/03/06)
5117 heimbach 1.143 merged from ecco-branch:
5118     o exf:
5119     - Enable initialisation of forcing fields to constant
5120     (runtime) values.
5121     - in exf_getffields.F
5122     Reduce i-/j-loop to interior domain, discarding overlaps.
5123     That also fixes wrong TAF-key computations for key_1, key_2
5124     with bulf formulae.
5125     - exf_init.F modify #ifdef for exf_init_evap
5126     - exf_getffieldrec.F, ctrl_getrec.F
5127     The following INT-usages are not safe:
5128     fldsecs = int(fldsecs/fldperiod)*fldperiod
5129     fldcount = int(fldsecs/fldperiod) + 1
5130     and were modified.
5131     o autodiff: checkpoint_lev...
5132     - updated storing for bulk formulae (some arrays were missing)
5133     - added state for seaice package
5134     - synchronized with main branch
5135     o DIVA:
5136     Modif.s in
5137 heimbach 1.144 - the_main_loop.F
5138     - the_model_main.F
5139 heimbach 1.143 and added cost_final_restore.F cost_final_store.F
5140     o With these changes, it is possible to fully separate
5141     the first forward run to compute the cost function (mdthe_main_loop)
5142     and adjoint runs over individual DIVA intervals (adthe_main_loop)
5143     into separate model executions.
5144     This enables better tuning of DIVA to given queue sizes.
5145     o Loss of cost function value in consecutive DIVA runs is
5146     fixed by storing to 'costfinal' file.
5147     o Appropriate call of ctrl_unpack/_pack,grdchk_main at
5148     beginning/end of adjoint integration is accounted for.
5149     The current changes apply to TAF-1.4.26.
5150     TAF has one remaining bug, requiring one manual change
5151     (see MITgcm manual).
5152     o cal: synchronized between MAIN and ecco-branch
5153 heimbach 1.141
5154 jmc 1.1203 checkpoint48i_post (2003/03/05)
5155 heimbach 1.141 o Changes to restore differentiability of code w.r.t. previous tag
5156     (mostly adding new routines to make list and replacing
5157     pressure by totPhiHyd).
5158     o Updated and merged grdchk package
5159     - has both ADM and TLM checks
5160     - works for single- and multi-proc.
5161     - output cleaned
5162     - worked successfully for parallel DIVA
5163     o genmake:
5164     - Adding -platform=SP4
5165     - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
5166     o Modif. for DIVA:
5167     ctrl_unpack should not be called in intermediate DIVA interval.
5168     (similar thing would apply for active files such as
5169     tbar, sbar, psbar, which should not be reinitialised;
5170     only relevant for ecco-branch)
5171 dimitri 1.136
5172 jmc 1.1203 checkpoint48h_post (2003/02/28)
5173 jmc 1.137 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
5174 dimitri 1.136 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
5175     o Added SEAICE_initialHEFF to pkg/seaice
5176 dimitri 1.139 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
5177 jmc 1.135
5178 jmc 1.1203 checkpoint48g_post (2003/02/18)
5179 jmc 1.135 --- EOS:
5180     o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
5181     store total Potential in totPhyHyd for diagnostics & EOS.
5182     o fix restart and overlap Pb when using Z-coord and EOS funct. of P
5183     --- Pressure/geopotential gradient:
5184     o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
5185     o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
5186     ( changes results of global_ocean_pressure )
5187     o NLFS + z-coord.: add eta*Rho' contribution.
5188     o accurate phiHyd when using interface-W at the middle between 2 centers
5189     ( changes results of ideal_2D_oce )
5190     o includes r* 2nd term in potential gradient.
5191 dimitri 1.134
5192 jmc 1.1203 checkpoint48f_post (2003/02/18)
5193 dimitri 1.134 Merging from release1_p12:
5194     o Modifications for using pkg/exf with pkg/seaice
5195     - improved description of the various forcing configurations
5196     - added basic radiation bulk formulae to pkg/exf
5197     - units/sign fix for evap computation in exf_getffields.F
5198     - updated verification/global_with_exf/results/output.txt
5199     o Added pkg/sbo for computing IERS Special Bureau for the Oceans
5200     (SBO) core products, including oceanic mass, center-of-mass,
5201     angular, and bottom pressure (see pkg/sbo/README.sbo).
5202     o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
5203     to avoid negative values in shallow regions.
5204     - updated verification/natl_box/results/output.txt
5205     - updated verification/lab_sea/results/output.txt
5206     o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
5207     o Added useSingleCpuIO option (see PARAMS.h).
5208     o Updated useSingleCpuIO option in mdsio_writefield.F to
5209     work with multi-field files, e.g., for single-file pickup.
5210     o pkg/seaice:
5211     - bug fix in growth.F: QNET for no shortwave case
5212     - added HeffFile for specifying initial sea-ice thickness
5213     - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
5214     o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
5215     kpp_transport_t.F, forward_step.F, and the_main_loop.F
5216     o pkg/seaice:
5217     - adjoint-friendly modifications
5218     - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
5219 jmc 1.131
5220 jmc 1.1203 checkpoint48e_post (2003/02/12)
5221 jmc 1.131 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
5222 jmc 1.132 o dynamics: change definition of computational domain & adapt mom_fluxform
5223     accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
5224     o following exp works with Olx=Oly=2 (and pass through checkbounds option):
5225     adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
5226 jmc 1.133 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
5227 jmc 1.132 global_ocean.90x40x15 global_with_exf global_ocean_pressure
5228     inverted_barometer solid-body.cs-32x32x1
5229     (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
5230 jmc 1.130
5231 jmc 1.1203 checkpoint48d_post (2003/02/09)
5232 jmc 1.130 o in preparation for r*:
5233     a) use pre-computed gradient of hydrostatic potential:
5234     changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
5235     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
5236     => affects results of glob_oce_pressure (different truncation error)
5237     update output.txt of ideal_2D_oce & global_ocean_pressure
5238 jmc 1.129
5239 jmc 1.1203 checkpoint48d_pre (2003/02/08)
5240 jmc 1.129 o in preparation for r*:
5241     new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
5242     pass the 2 comp. of the grad. as arguments to momentum S/R.
5243     but for the moment, only used if it does not change the results.
5244     o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
5245 jmc 1.126
5246 jmc 1.1203 checkpoint48c_post (2003/02/06)
5247 heimbach 1.128 Modifications in treatment of initial flux forcing controls
5248     to avoid extra storing of flux fields.
5249    
5250 jmc 1.1203 checkpoint48c_pre (2003/01/21)
5251 adcroft 1.127 o Added tidal_basin_2d experiment (currently 1D!)
5252 jmc 1.126 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
5253 jmc 1.124
5254 jmc 1.1203 checkpoint48b_post (2003/01/27)
5255 jmc 1.124 o r* coordinate added in #ifdef NONLIN_FRSURF block.
5256     (modification to pressure gradient not yet implemented)
5257     o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
5258     (for U & V) that are used for vertical advection of momentum.
5259 jmc 1.123
5260 jmc 1.1203 checkpoint48a_post (2003/01/24)
5261 jmc 1.123 o In preparation for r*, use temp. array to compute vertical transport
5262     in flux-form momentum pkg. => change results of few test-exp.
5263     Update output of: exp4, exp5, front_relax, global_ocean_pressure,
5264     lab_sea, natl_box & plume_on_slope
5265 jmc 1.122
5266 jmc 1.1203 checkpoint48 (2003/01/23)
5267 jmc 1.122 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
5268 heimbach 1.121
5269 jmc 1.1203 checkpoint47j_post (2003/01/21)
5270 jmc 1.120 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
5271 heimbach 1.121 o moved adexch from forward_step to addummy_in_stepping
5272     o added exch in ctrl_map_...
5273     o aveFreq.=0. at end of cost_final to avoid overwrite in
5274     reverse checkpointing loop
5275     o Yet more changes in gmredi:
5276     * adgmredi_calc_tensor
5277     avoiding all recomputation of gmredi_slope_limit
5278     * adgmredi_x/y/rtransport
5279     added flag for excessive storing to avoid recomp. of
5280     u/v/rtans, dTdx/y/z
5281     -> this is not really necessary and very memory-consuming
5282     * adgmredi_slope_psi:
5283     consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
5284     * gmredi_slope_limit
5285     re-activated full calculation of taperfct for case 'ac02'
5286     o updating verification/ adjoints of carbon, global_ocean.90x40x15
5287 heimbach 1.116
5288 jmc 1.1203 checkpoint47i_post (2003/01/13)
5289 jmc 1.119 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
5290     o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
5291     default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
5292     o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
5293     o gmredi: fix few bugs.
5294    
5295 adcroft 1.118 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
5296 heimbach 1.116 This will be a good checkpoint to plug into the ecco-branch.
5297     o few modif.'s to get latest version adjointed
5298     (mainly kick out code in ini_linear_phisurf)
5299     o modif's to run adjoint with exactConserv
5300     o case GM_BOLUS_ADVEC should be cleaned
5301     S/R gmredi_slope_psi should be cleaned
5302     o verification/carbon now has exactConserv=.TRUE.
5303 jmc 1.114
5304 jmc 1.1203 checkpoint47g_post (2003/01/10)
5305 jmc 1.114 o time-average AIM output: becomes independent from statvars time-average
5306     (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
5307 heimbach 1.115 o After TAF bug fix:
5308     Tested adjoint of gmredi package.
5309     Tests were done with checkpoint47 rather than with latest
5310     checkpoint47f_post since the latter is broken for the adjoint
5311     verification/carbon/ contains both ADM and TLM gradient checks.
5312     Here they are, before they get changed/lost/stolen.
5313     Mostly modif.'s to fix numerical sensitivities.
5314     Gradient checks OK for
5315     - GM_taper_scheme:
5316     * clipping
5317     * ac02
5318     * linear
5319     * glw91
5320     * dm95
5321     * ldd97
5322     - GMREDI_OPTIONS:
5323     * GM_VISBECK_VARIABLE_K
5324     * GM_NON_UNITY_DIAGONAL
5325     * GM_EXTRA_DIAGONAL
5326     * GM_BOLUS_ADVEC
5327     in conjunction with data.gmredi parameters to be checked in
5328     in a few minutes under verification/carbon/code/
5329 cheisey 1.112
5330 jmc 1.1203 checkpoint47f_post (2002/12/28)
5331 dimitri 1.113 Merging from release1_p10:
5332     o modifications for using pkg/exf with pkg/seaice
5333     - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
5334     and SEAICE_EXTERNAL_FLUXES
5335     - pkg/exf CPP options EXF_READ_EVAP and
5336     EXF_NO_BULK_COMPUTATIONS
5337     - usage examples are Experiments 8 and 9 in
5338     verification/lab_sea/README
5339     - verification/lab_sea default experiment now uses
5340     pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
5341    
5342 jmc 1.1203 checkpoint47e_post (2002/12/27)
5343 cheisey 1.112 o created a tag prior to creating a branch
5344    
5345 jmc 1.1203 checkpoint47d_post (2002/12/16)
5346 mlosch 1.111 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
5347     at the bottom boundary had an erroneous half slip boundary condition
5348     o added bottom drag and no slip boundary condition capabilities to
5349     oceanic pressure coordinates code
5350     o added new verification experiment global_ocean_pressure, this experiment is
5351     also described in the tutorial section of the manual
5352 jmc 1.1203 checkpoint47d_pre (2002/12/16)
5353 cheisey 1.110
5354 jmc 1.1203 checkpoint47c_post (2002/12/16)
5355 cheisey 1.110 o Added a verification experiment for a global cubed-sphere ocean run
5356     - verification/global_ocean.cubed32x32x30
5357     - uses pkg/therm_seaice and pkg/bulk_forcing
5358 jmc 1.109
5359     o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
5360     o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
5361     when using P-coordinate; only implemented for atmospheric config.
5362     o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
5363     NOTES: requires option NONLIN_FRSURF to be "#define".
5364     o update advect_xz/results/output.txt (left from checkpoint44g_post)
5365 dimitri 1.108
5366 jmc 1.1203 checkpoint47b_post (2002/12/05)
5367 dimitri 1.108 Merging from release1_p9:
5368     o pkg/seaice
5369     - removed GOTO's and added taf directives
5370     - double precision constants to reduce the g77 (Linux)
5371     to F77 (SGI) differences reported in release1_p8
5372     o tools/genmake
5373     - added SGI options
5374     o verification/testscript
5375     - updated to that of checkpoint47a_post
5376     o verification/global_ocean.90x40x15/input/eedata
5377     - modified for SGI f77 compatibility
5378     o verification/lab_sea
5379     - added description of sea-ice model
5380     - added missing matlab routines
5381     - added test of thermodynamics parallelization
5382 jmc 1.105
5383 jmc 1.1203 checkpoint47a_post (2002/11/23)
5384 jmc 1.105 o new pkg: aim_v23
5385     = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
5386     for now, keep the same surface forcing as before.
5387     - Part-Cell implemented into AIM; check that Heat & Water are conserved
5388     - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
5389     - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
5390     o add diagnostic of surface correction term in monitor output
5391 jmc 1.106
5392     o bulk_force and therm_seaice
5393 cheisey 1.107 - Two packages: bulk_force (Bulk forcing)
5394     and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
5395     - Earlier integration from Stephaine Dutkiewicz
5396     and Patrick Heimbach.
5397     - Two ifdef statements for compile time,
5398     ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
5399 heimbach 1.104
5400 jmc 1.1203 checkpoint47 (2002/11/15)
5401 heimbach 1.104 differentiable version of checkpoint46n_post
5402     o bug fix in quasihydrostaticterms
5403     o * "clean" adjoint code (in terms of extensive recomputations)
5404     can now be obtained for all GMREDI options (i.e. for
5405     - GM_VISBECK_VARIABLE_K
5406     - GM_NON_UNITY_DIAGONAL
5407     - GM_EXTRA_DIAGONAL
5408     - GM_BOLUS_ADVEC )
5409     * However, wrong gradient check problem remains unsolved.
5410     * New CPP options have been introduced for different
5411     tapering schemes
5412     o external_fields_load now part of differentiation list
5413     o pressure needs multiple storing;
5414     would be nice to have store_pressure at beginning or
5415     end of forward_step, e.g. by having phiHyd global (5-dim.)
5416     (NB: pressure is needed for certain cases in find_rho,
5417     which is also invoked through convective_adjustment).
5418     o recomputations in find_rho for cases
5419     'JMD95'/'UNESCO' or 'MDJWF' are OK.
5420     o #define ATMOSPHERIC_LOADING should be differentiable
5421     o ini_forcing shifted to begining of initialise_varia
5422     o Incorporating QNVS line search routines into MITgcm
5423     (this is separate code, and therefore not under pkg)
5424     lsopt/, optim/
5425     o Updated verification/carbon/
5426     - #define GM_VISBECK_VARIABLE_K
5427     - GM_taper_scheme = 'ldd97'
5428 heimbach 1.103
5429 jmc 1.1203 checkpoint46n_post (2002/11/12)
5430 heimbach 1.103 Merging from release1_p8:
5431     o verification/natl_box:
5432     updating new external_fields_load routine
5433     o New package: pkg/seaice
5434     Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
5435     The sea-ice code is based on Hibler (1979-1980).
5436     Two sea-ice dynamic solvers, ADI and LSR, are included.
5437     In addition to computing prognostic sea-ice variables and diagnosing
5438     the forcing/external data fields that drive the ocean model,
5439     SEAICE_MODEL also sets theta to the freezing point under sea-ice.
5440     The implied surface heat flux is then stored in variable
5441     surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
5442     kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
5443     non-local transport term. Because this call precedes model
5444     thermodynamics, temperature under sea-ice may not be "exactly" at
5445     the freezing point by the time theta is dumped or time-averaged.
5446     N.B.: fairly large differences in accuracy occur across
5447     different platforms/compilers; comparison between
5448     g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
5449     generated output gives:
5450     T S U V
5451     C D M c m s m s m s m s
5452     n p a R g m m e . m m e . m m e . m m e .
5453     f n k u 2 i a a d i a a d i a a d i a a d
5454     g d e n d n x n . n x n . n x n . n x n .
5455    
5456     Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
5457     o GAD:
5458     - generated new common blocks to account for call of
5459     same gad routines with differing traceridentities
5460     (needed to modify tracerIdentity indices in GAD.h)
5461     - generated separate common blocks for case useCubedSphereExchange
5462     (Department of Futurology)
5463     - parameter lists to gmredi_?transport: added tracerIdentity
5464     - added new key indices to tamc.h
5465     o external_fields_load:
5466     - added this routine to TAF list
5467     - needed to make some common blocks global and additional storing
5468     along the same lines as exf package (checkpoint_lev?_directives.h)
5469     o exf:
5470     updated external forcing package
5471     - bug fixes carried over from ecco-branch
5472     (missing OBCS_OPTIONS.h in two routines)
5473     - enable easy to use "no forcing".
5474     - added exf I/O for atmospheric loading
5475     - added exf I/O for runoff data
5476     - transfered scaling between exf <-> MITgcm to exf namelist
5477     o Adding new verification experiment global_with_exf.
5478     This verification experiment is almost identical to the
5479     global_ocean.90x40x15 experiment, except that it uses
5480     the exf (and cal) package instead of the
5481     external_fields_load routine (cf README file).
5482 adcroft 1.94
5483 jmc 1.1203 checkpoint46m_post (2002/11/07)
5484 adcroft 1.101 o modified testscript to return -- when there are no lines of "%MON" output
5485 adcroft 1.100 o added new flag "quasiHydrostatic" for QH mode
5486     and new routine quasihydrostaticterms()
5487 adcroft 1.99 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
5488     New routine: mom_u_coriolis_nh()
5489 adcroft 1.98 o fixed sign of non-hydrostatic metric terms in u and v equations.
5490     Depend on correct sign of gravitySign.
5491 adcroft 1.97 o added work.pc* to .cvsignore in aim directories using ifc
5492 adcroft 1.96 o introduced flag for controllin non-hydrostatic metric terms
5493 adcroft 1.95 o removed gravitySign from PARM04
5494 adcroft 1.94 o switched to g77/ifc from pgf77 in aim experiments
5495 mlosch 1.93
5496 jmc 1.1203 checkpoint46l_post (2002/11/01)
5497 mlosch 1.93 o made convective adjustment work with pressure coordinates:
5498     - changed the direction of k-loop in convective_adjustment.F for the
5499     case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
5500     - adjusted the reference pressure k-index in convective_adjustment.F
5501     - adjusted the convection condition in convect.F (in analogy to
5502     calc_ivdc.F)
5503     - convective_adjustment no longer computes anything on the halos
5504     - removed the warnings about negative salinity from find_rho.F and
5505     find_alpha.F; instead the new routine look_for_neg_salinity, called
5506     at the beginning of find_rho, find_alpha, and find_beta, does a
5507     check of the entire slice, if CPP-option
5508     CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
5509 jmc 1.1203 checkpoint46l_pre (2002/10/23)
5510 mlosch 1.91
5511 jmc 1.1203 checkpoint46k_post (2002/10/23)
5512 mlosch 1.91 o fixed the verification/global_ocean.90x40x15 experiment:
5513     - new bathymetry (the world according to A., JMC, and M.)
5514     - new initial fields and forcing fields (*.bin files)
5515     - new POLY3.COEFFS (for the next release one should switch to a full
5516     equation of state: JMD95P or MDJWF)
5517     - fixed several errors and redundancies in the data file
5518     - experiment uses looped cells
5519     - added matlab directory with diagnostic scripts for plotting of output
5520 jmc 1.90
5521     o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
5522     - read AIM physics parameters from a file (data.aimphys)
5523     - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
5524 jmc 1.89
5525 jmc 1.1203 checkpoint46j_post (2002/10/07)
5526 jmc 1.89 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
5527     o move wVel computation at the end of the time step, in S/R integr_continuity
5528     o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
5529     o update timeave pkg for wVel diagnostic.
5530 jmc 1.1203 checkpoint46j_pre (2002/09/27)
5531 mlosch 1.87
5532 jmc 1.1203 checkpoint46i_post (2002/09/25)
5533 jmc 1.88 o Clean up AIM package (and keep the results unchanged):
5534     include CPP_OPTION and use IMPLICT NONE in all routines ;
5535     declare all the variables _RL ; use _d 0 for all numerical constants.
5536     use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
5537 mlosch 1.87
5538 jmc 1.1203 checkpoint46h_post (2002/09/25)
5539 mlosch 1.87 o cleaned up the use of rhoNil and rhoConst.
5540     - rhoNil should only appear in the LINEAR equation of state, everywhere
5541     else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
5542     and the dynamical equations are all divided by rhoConst
5543     o introduced new parameter rhoConstFresh, a reference density of fresh
5544     water, to remove the fresh water flux's dependence on rhoNil. The default
5545     value is 999.8 kg/m^3
5546     o cleanup up external_forcing.F and external_forcing_surf.F
5547     - can now be used by both OCEANIC and OCEANICP
5548 jmc 1.1203 checkpoint46h_pre (2002/09/18)
5549 mlosch 1.87
5550     Added code to convert surface volume flux (fresh water) into
5551     a mass flux when using P coordinates in the ocean (OCEANICP).
5552     Note: It assumes you have set rho0=rhoConst=density of fresh water.
5553 mlosch 1.86
5554 jmc 1.1203 checkpoint46g_post (2002/09/18)
5555 mlosch 1.86 o Include a new diagnostic variable phiHydLow for the ocean model
5556     - in z-coordinates, it is the bottom pressure anomaly
5557     - in p-coordinates, it is the sea surface elevation
5558     - in both cases, these variable have global drift, reflecting the mass
5559     drift in z-coordinates and the volume drift in p-coordinates
5560     - included time averaging for phiHydLow, be aware of the drift!
5561     o depth-dependent computation of Bo_surf for pressure coordinates
5562     in the ocean (buoyancyRelation='OCEANICP')
5563     - requires a new routine (FIND_RHO_SCALAR) to compute density with only
5564     Theta, Salinity, and Pressure in the parameter list. This routine is
5565     presently contained in find_rho.F. This routine does not give the
5566     correct density for 'POLY3', which would be a z-dependent reference
5567     density.
5568     o cleaned up find_rho
5569     - removed obsolete 'eqn' from the parameter list.
5570     o added two new verification experiments: gop and goz
5571     (4x4 degree global ocean, 15 layers in pressure and height coordinates)
5572 jmc 1.1203 checkpoint46g_pre (2002/09/16)
5573 heimbach 1.85
5574 jmc 1.1203 checkpoint46f_post (2002/09/16)
5575 heimbach 1.85 o Enable tangent linear (forward mode) gradient checks:
5576     - extended active file handling to g_... files
5577     - added TANGENT_SIMULATION to theSimulationMode
5578     - extended grdchk package accordingly
5579     o added tangent linear setup in verification/carbon/code_ftl
5580     o added adjoint setup in verification/front_relax/code_ad
5581 mlosch 1.82
5582 jmc 1.1203 checkpoint46e_post (2002/09/05)
5583 mlosch 1.83 o Added new equation of state -> MDJWF
5584     - EOS of McDougall et al., 2002, JAOT, submitted
5585     - caveat: the equation of state is only valid for a smaller (more
5586     realistic?) range of values than JMD95P/Z and UNESCO
5587     - added masks to the calculation of pressure in store_pressure
5588     - added more check values for density in check_eos (ini_eos.F), some of
5589     the old check values are out of the range of the MDJWF-eos, so don't
5590     expect perfect matches for those
5591 jmc 1.1203 checkpoint46e_pre (2002/08/19)
5592 mlosch 1.83
5593 jmc 1.1203 checkpoint46d_post (2002/08/19)
5594 mlosch 1.82 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
5595     'OCEANICP', also initialised field pressure correctly in ini_eos in the
5596     case of pressure coordinates. eosType='JMD95Z' in
5597     combination with buoyancyRelation='OCEANICP' now causes an error.
5598     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
5599     in find_alpha/beta.
5600 jmc 1.1203 checkpoint46d_pre (2002/08/15)
5601 mlosch 1.82
5602     o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
5603     so that JMD95Z and JMD95P give approptiate static stability in find_rho.
5604 adcroft 1.81
5605 jmc 1.1203 checkpoint46c_post (2002/08/15)
5606 adcroft 1.81 o Changes necessary for ocean in p-coordinates
5607     - Added new buoyancy relation = 'OCEANICP'
5608     - Added new parameters = gravitySign (this used to be contained inside
5609     the factor dRdZ which I added when we first switched to R coordinates).
5610     X GM/Redi is not compatible (yet)
5611     X bottom drag and no-slip need to be debugged.
5612 jmc 1.1203 checkpoint46c_pre (2002/08/07)
5613 mlosch 1.80
5614 jmc 1.1203 checkpoint46b_post (2002/08/07)
5615 mlosch 1.80 o Added new equation of state -> JMD95Z and JMD95P
5616 mlosch 1.83 - EOS of Jackett and McDougall, 1995, JAOT
5617 mlosch 1.80 - moved all EOS parameters into EOS.h
5618     - new routines ini_eos.F, store_pressure.F
5619     o Added UNESCO EOS, but not recommended because it requires
5620     in-situ temperature (see JMD95)
5621     o Modified formatting for knudsen2.f in utils/knudsen2 and added
5622     unesco.f to be used with POLY3
5623 jmc 1.1203 checkpoint46b_pre (2002/07/31)
5624 mlosch 1.79
5625 jmc 1.1203 checkpoint46a_post (2002/07/31)
5626 mlosch 1.79 o Added (atmospheric) pressure loading
5627     - new field in FFIELDS.h, etc...
5628     - new cpp flag ATMOSPHERIC_LOADING
5629     o Changed hFacC to _hFacC in calc_phi_hyd.F
5630     o Added SHORTWAVE_HEATING to some files for consistency
5631 jmc 1.1203 checkpoint46a_pre (2002/07/13)
5632 heimbach 1.78
5633 jmc 1.1203 checkpoint46 (2002/07/13)
5634 heimbach 1.78 further merges from release1_p5
5635     o new ctrl package
5636     - adopted from ECCO environment to enable optimization
5637     - added Eliassen Palm fluxes to controls
5638     o added Eliassen Palm flux controls to gradient check package
5639     o cost package
5640     - Compatible with new ctrl package
5641     - added Eliassen Palm cost hooks
5642     - modif's of existing cost functions
5643     o Adjoint-related bug fixes in kpp:
5644     - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
5645     - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
5646     o autodiff package
5647     - flow directives:
5648     + new for S/R do_the_model_io
5649     + enhanced for S/R checkpoint
5650     + new gmredi.flow
5651     - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
5652     disable adcommon.h/g_common.h by default.
5653     - fixed problem for adjoint of global_max
5654     o modified verification/carbon/
5655     o New setup for adjoint of global_ocean
5656     o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
5657     o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
5658     o incorporated hooks for sponge layer code (external_forcing.F)
5659    
5660 jmc 1.1203 checkpoint45d_post (2002/07/12)
5661 jmc 1.77 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
5662 jmc 1.76 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
5663     (affects plume_on_slope "cg2d" output)
5664 jmc 1.77 o add new parameter deltaTfreesurf for free-surface time stepping
5665     o exchange gT,gS when using staggerTimeStep & GM & Oly<4
5666 jmc 1.75 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
5667 jmc 1.74 o change phiMin in exp1 (to agree with documentation)
5668     o add new flags:
5669     - T,S forcing inside/outside Adams-Bashforth
5670     - turn off temp,salt advection and/or forcing
5671     - for each tracer, define internal flag for multiDimAdvection & A-B
5672     o monitor: change definition of KE to check conservation of Energy
5673 heimbach 1.73
5674 jmc 1.1203 checkpoint45c_post (2002/05/30)
5675 heimbach 1.73 o Removed f90 comments ("!")
5676     o Modified initialisations to enable exf package for MITgcm
5677     (without invoking ECCO_PACKAGE).
5678     o modifications to gradient check package (Martin Losch)
5679     - enable centered differences
5680     - modified format of standard output
5681 heimbach 1.72
5682 jmc 1.1203 checkpoint45b_post (2002/05/30)
5683 heimbach 1.72 o cleaned exchange calls in cg2d
5684     o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
5685     o included CPP option SINGLE_LAYER_MODE in thermodynamics
5686     to configure barotropic setup (Martin Losch)
5687     o moved some initialisations within bi,bj loop in dynamics
5688     (TAF flow dependency)
5689     o in initialise_varia, moved call packages_init_variables
5690     before convective_adjustment_init
5691     (corresponding adjustment of TAF tape initialisation).
5692     o in calc_diffusivity/calc_viscosity extended domain to full overlap.
5693 jmc 1.70
5694 jmc 1.1203 checkpoint45a_post (2002/05/01)
5695 jmc 1.71 o compute Rho over the whole domain (extend iMin,jMin indices)
5696     o specific exchange for X-slice domain (case Ny=1)
5697 jmc 1.70 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
5698     o solve_for_pressure : set cg2d_x to zero where OBCS are applied
5699 jmc 1.67
5700 heimbach 1.69 checkpoint44h_post = checkpoint45
5701     o Fix to restore differentiability:
5702     place at which packages_init_variables is called in
5703     initialise_varia is crucial for reverse control flow.
5704     o modifications in GMRedi to enable stable adjoint
5705     (corresponding modif's in thermodynamics, dynamics)
5706     o added missing hook for sponge layer code in external_forcing
5707     o modified test cost functions
5708     o storing in gad_advection (plus removal of write(0,*)!
5709     o missing headers TR1.h added in convective_adjustment routines
5710     o errorMessageUnit set non-equal zero in eeboot
5711     (conflict on some platforms, e.g. IBM SP3)
5712     o modified carbon verif.
5713    
5714 jmc 1.1203 checkpoint44h_pre (2002/03/14)
5715 jmc 1.68 o vertical grid option: allow to put the Interface at the middle between
5716     2 cell-centers ; replace delZ in pkg/kpp by drF.
5717 jmc 1.67 o GM Advective form: Tracers are advected using the residual transport (=
5718     Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
5719 jmc 1.66
5720 jmc 1.1203 checkpoint44g_post (2002/03/05)
5721 jmc 1.66 o fix surface correction term in multiDimAdvection (affects plume_on_slope
5722     results) ; ifdef missing in thermodynamics.F
5723 adcroft 1.65
5724     checkpoint44f_pre,checkpoint44f_post
5725     o added PTRACERS package
5726     This allows an arbitrary number of passive tracers to be integrated
5727     forward simultaneously with the dynamicaly model.
5728     + Implemented so far:
5729     - basic forward algorithm (time-stepping, advection, diffusion, convection)
5730     - I/O and checkpointing
5731     - GM/Redi *but* using the GM/Redi coefficient of Salt
5732     + Not implemented so far:
5733     - KPP
5734     - OBCS
5735     + No specific example supplied (yet) but global_ocean.90x40x15 has the
5736     necessary data.ptracer file. Simply use -enable=ptracers and uncomment
5737     line in data.pkg.
5738     + This package is disabled by default since it increases storage.
5739    
5740 jmc 1.60
5741 adcroft 1.64 o testscript: added -cleanup option
5742 jmc 1.63 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
5743     b) enable to filter 2D fields.
5744 adcroft 1.62
5745     checkpoint44e_pre,post
5746     o re-wrote convective adjustment to use pre-calculated weights
5747     Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
5748     Adds: model/src/convective_weights.F, convectively_mixtracer.F
5749     Original calls to convect() still in place.
5750 heimbach 1.61
5751     chkpt44d_pre,post
5752     o added missing EXCLUDE_MONITOR flags
5753     o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
5754     (incompatible typ in MIN/MAX expressions caused problems
5755     on IBM SP3)
5756     o in genmake added variable MAKEDEPEND
5757     plus resetting for case SunOS
5758     o added timer_stats.c routine for IBM SP3
5759     o removed variables in dynamics
5760     !!! I forgot to create tag chkpt44d_pre !!!
5761     !!! But chkpt44d_pre = chkpt44c_post !!!
5762 jmc 1.63
5763     o real fresh water flux implemented with non-linear free-surface.
5764 heimbach 1.58
5765 jmc 1.59 chkpt44c_pre,post
5766     o few fix (mask in shap_s2, EmPmR in external_field_load,
5767     USE_NATURAL_BCS in solve_for_P);
5768     o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
5769    
5770 heimbach 1.58 checkpoint44b_pre/_post
5771     o merge of relevant stuff from the ecco-branch:
5772     - genmake: removed $S64 overwrite for case SunOS
5773     - pkg/exf: update and corrections for field swapping and obcs
5774     - pkg/ecco: parameter lists for the_model_main, the_main_loop
5775     harmonized between ECCO and MITgcm
5776     - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
5777     updated checkpointing_lev... lists for obcs
5778     - model/src: minor changes in forward_step, plot_field
5779     added directive for divided adjoint in the_main_loop
5780     - pkg/mdsio: added mdsio_gl_slice
5781 jmc 1.57
5782     o check parameters & config (chkpt44a_pre,post)
5783 jmc 1.56 o OBC and NonLin_FrSurf.
5784    
5785 jmc 1.1203 checkpoint44 (2002/01/18)
5786 jmc 1.54 o fix bug in mom_vi_del2uv
5787 jmc 1.56 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
5788     o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
5789     o update AIM experiments (NCEP input files)
5790     o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
5791 heimbach 1.55 o added some stuff for AD
5792 adcroft 1.53
5793 jmc 1.1203 checkpoint43 (2001/09/28)
5794 adcroft 1.53 o added two new advection tests
5795     o added global 4x4 degree ocean test
5796     o added test of H&S94 with free surface on cube
5797     o some final mods for gradient check, adjoint,...
5798 heimbach 1.52
5799 jmc 1.1203 checkpoint42 (2001/09/27)
5800 heimbach 1.52 Fixed AD-related problems:
5801     o Store directives up-to-date with re-arranged Adams-Bashforth
5802     (mainly thermodynamics.F)
5803     o New store directives for multi-dim. advection schemes
5804     * new CPP flag ALLOW_MULTI_DIM_ADVECTION
5805     * new common block and key passkey
5806     (mainly gad_advection.F)
5807     o Modified store directives for split of dynamics/thermodynamics
5808     for the case ALLOW_KPP
5809     o Cleaned argument list for timestep_tracer.F
5810 adcroft 1.51
5811 jmc 1.1203 checkpoint41 (2001/09/27)
5812 adcroft 1.51 o re-formatted/added comments in prologues of key subroutines
5813     to work with protex
5814 heimbach 1.47
5815 jmc 1.1203 checkpoint40 (2001/09/27)
5816 adcroft 1.50 o moved calc_gs, calc_gt and calc_tr1 back to model/src
5817     o added FLT (floats) package from Arne along with demo. experiment
5818     o re-arranged Adams-Bashforth scheme for tracers to allow easier
5819     implementation of forward-in-time forcing terms
5820     o more mods for non-linear free-surface including new variable
5821     o modified multi-dim method to work on cube
5822     o bug fix in KPP (from DM)
5823    
5824 jmc 1.1203 checkpoint40pre9 (2001/09/27)
5825 adcroft 1.49 o added DST advection schemes
5826     o fix MPI bug on SGI's
5827     o modifications for non-linear free-surface
5828     o fixed conditionals for fixed flow/passive tracer only mode
5829     o added tension/strain form of stress tensor
5830     o changes to commenting of arguments for TAF/TAMC
5831     o added/updated many matlab scripts
5832 adcroft 1.50 o added multi-dimensional advection method for tracers
5833 adcroft 1.49
5834 jmc 1.1203 checkpoint40pre8 (2001/09/05)
5835 heimbach 1.47 o new package rw/
5836     Added method for dumping intermediate local arrays:
5837     mdsio_writetile - same as mdsio_writefield except works from inside
5838     bi,bj loop
5839     mdsio_writelocal - same as mdsio_writetile except works for local
5840     arrays
5841     write_local_r? - higher-level wrapper for mdsio_writelocal
5842     Controlled by diagFreq. Defaults to zero (ie. no dumps)
5843     Example given at end of mom_vecinv.F that dumps some local arrays.
5844     o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
5845     control flux-form versus vector invariant code.
5846     Switch is runtime flag vectorInvariantMomentum (defaults to false)
5847     or genmake -DISABLE ...
5848     o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
5849     (additional storing is now needed for case vecinv;
5850     currently nothing implemented to switch this storing off
5851     in case fluxform is used since no CPP flag available).
5852 heimbach 1.46
5853 jmc 1.1203 checkpoint40pre7 (2001/08/14)
5854 heimbach 1.46 o bug fix in dynamics.F
5855     calc_viscosity called before k=1,Nr loop.
5856     o added some #ifdef's ALLOW_PASSIVE_TRACER
5857     o cleaned initialisations in ctrl_map_ini
5858     related to TAF
5859 heimbach 1.45
5860 jmc 1.1203 checkpoint40pre6 (2001/08/13)
5861 heimbach 1.45 o split dynamics into thermodynamics & dynamics
5862     o corresponding split of calc_diffusivity into
5863     calc_diffusivity, calc_viscosity
5864     (kpp_calc_diff, kpp_calc_visc).
5865     o Added diffkr, kapgm to control variables
5866     o bug fix in gmredi_slope_limit for ldd97
5867 adcroft 1.44
5868 jmc 1.1203 checkpoint40pre5 (2001/07/31)
5869 adcroft 1.44 o proper initialization of Adams-Bashforth time stepping
5870     + uses forward step for very first step of model (iter=0)
5871     o re-generated *all* output since almost all output is modified by this
5872     change (sorry but we've been putting this one off for about 2 years)
5873     + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
5874     *not* regenerated since they are already out of date and I don't
5875     want to create the impression that they are suddenly working.
5876     o removed KAP stuff for DEC's
5877     o modified/added many .cvsignore files in */code and */input
5878     o added new expt "solid-body.cs-32x32x1"
5879     + this uses an alternative form of ini_curvilinear_grid.F which
5880     is not necessarily any better than the current one...
5881 heimbach 1.43
5882 jmc 1.1203 checkpoint40pre4 (2001/07/30)
5883 heimbach 1.43 o added re-initialisations of utrans,vtrans,rtrans in
5884     calc_common_factors which are crucial for TAF.
5885     o extended iMin,jMin range for calc_common_factors,
5886     calc_diffusivity
5887     o added option ALLOW_PASSIVE_TRACER
5888     o a few minor updates and fixes
5889    
5890 jmc 1.1203 checkpoint40pre3 (2001/07/13)
5891 heimbach 1.42 o created calc_gtr1.F for gad package
5892     o split the_main_loop and re-introduced forward_step
5893     o some recomputations of nIter0 for TAMC
5894    
5895 jmc 1.1203 checkpoint40pre2 (2001/07/13)
5896 heimbach 1.41 o Updated to latest branch of AJA, JMC
5897     o Added gradient check package
5898     o Added routines for passive tracer handling
5899     o Added carbon sequestration sensitivity experiment
5900    
5901 jmc 1.1203 checkpoint39 (2001/05/14)
5902 heimbach 1.39 o Modifications and fixes to support TAMC
5903     (mainly missing or wrong directives)
5904     o Corrected common blocks when fooling TAMC to produce adjoint I/O
5905     in addummy_in_stepping
5906     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
5907     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
5908     o Included following packages:
5909     cal: calendar
5910     exf: external forcing
5911     ecco: essential routines to control use of cal, exf
5912     (NB: this is not the full ECCO environment)
5913 heimbach 1.40 o disabled some packages by default in genmake
5914 heimbach 1.39
5915 jmc 1.1203 checkpoint38 (2001/04/10)
5916 heimbach 1.38 o see notes_c37_adj.txt
5917     o corrected wrong layer index in external_forcing_t
5918     o replaced the_main_loop/forward_step by the_main_loop
5919     o removed forceoutput from write_state
5920     (replaced criteria for initial/final state)
5921     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
5922 jmc 1.36
5923 jmc 1.1203 checkpoint37 (2001/03/13)
5924 jmc 1.37 o mdsio.F routine split and packaged in pkg/mdsio
5925     (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
5926     used unless genmake -disable=mdsio)
5927     o allow a more precise surface-geopotential gradient for the atmosphere
5928     taking into account the change in space of Alpha (=1/rho) at the surface.
5929     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
5930     (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
5931     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
5932     Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
5933     [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
5934     o Time-Average diagnostics defined as a pseudo package "timeave".
5935     o pickup files : old pickup (before c35) did not work with new code (c35
5936     and after) unless activating 2 commented lines in initialise-varia.
5937     o Non-Hydrostatic pickup file Pb fixed.
5938     o bug with Rigid-lid version (since c35) fixed.
5939    
5940 jmc 1.1203 checkpoint36 (2001/02/20)
5941 jmc 1.37 o implement Crank-Nickelson barotropic time-stepping
5942 jmc 1.36 o recover Time-Average diagnostics
5943     o fix Pb in checkpoint (PR#19)
5944     o AIM become a standard package ; clean unused CPP_kees
5945 jmc 1.35
5946 jmc 1.1203 checkpoint35 (2001/02/08)
5947 jmc 1.35 o subtantial rewrite of dynamics.f
5948     o allows staggered time-stepping
5949     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
5950     o added bottom drag (linear + quadratic)
5951 heimbach 1.33
5952 jmc 1.1203 checkpoint34 (2001/01/30)
5953 heimbach 1.33 o Modified exchange routines for correct reverse simulation.
5954     o Added verification output to comply with bug fix in impldiff.F
5955     as of c33 (exp2, natl_box).
5956     o Corrected store directives in dynamics.F
5957     o Corrected array boundaries in impldiff.F
5958     o Corrected array dimensions in gmredi.
5959     Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
5960 heimbach 1.34 o Added routine GLOBAL_SUM_INT to global_sum.F
5961 heimbach 1.33 o Added mdsio_gl.F for ECCO purposes.
5962 adcroft 1.32
5963 jmc 1.1203 checkpoint33 (2000/11/30)
5964 adcroft 1.32 o Fixed bug in lower BC in impldiff.F
5965     o Fixed confusion about units of forcing arrays in FFIELDS.h
5966     namely Fu,Fv,Qnet,Qsw,EmPmR:
5967     - Removed verification/natl_box/code/external_fields_scale.F
5968     (did not differ from that in model/src)
5969     - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
5970     (see FFIELDS.h for description)
5971     - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
5972     kpp_calc.F and kpp_transport_t.F
5973     - Removed model/src/external_fields_scale.F and calls to it
5974     - verification/natl_box uses flux data with "atmospheric" sign so
5975     a special version of external_fields_load.F is used to
5976     change the data as it's read in. This way, the arrays
5977     have the right units and signs at all times tha a user could
5978     possibly use them.
5979     o Corrected genmake to delete a temporary file during configuration
5980 heimbach 1.31
5981 jmc 1.1203 checkpoint32 (2000/11/13)
5982 heimbach 1.31 o Scaling of forcing fields moved from external_forcing.F to
5983     external_fields_scale.F, called directly after loading fields.
5984     o Surface relaxation terms added to surface tendency fields in
5985     extra subroutine.
5986     o impldiff.F changed to avoid storing by TAMC of huge intermediate
5987     fields.
5988     o Changes in GMRedi to comply with packaging structure.
5989     o Modifications and bug fixes in KPP package.
5990     o Verification experiment for KPP added (verification/nat_box/)
5991 heimbach 1.30
5992 jmc 1.1203 checkpoint31 (2000/09/11)
5993 heimbach 1.30 o Packages interface brought in line with defined standard
5994     -> new routines packages_...F
5995     -> changes in initialise_fixed.F, initialise_varia.F
5996     -> enables initialisation interface for ECCO package
5997     o Rescaling of external forcing fields immediately after read
5998     (removed from external_forcing.F)
5999     -> new: surface_fields_scale.F
6000     -> affects ini_foorcing.F, external_fields_load.F
6001     o Computation of surface tendencies before tendency updates.
6002     -> new: external_forcing_surf.F
6003     o Change of variable names useGMRedi, useKPP, useECCO
6004     o Further changes in dynamics.F, impldiff.F for TAMC
6005     o Tested for experiments 0, 2, 4.
6006     - not yet tested for GMRedi.
6007     - not yet tested for KPP.
6008 adcroft 1.29
6009 jmc 1.1203 checkpoint30 (2000/07/13)
6010 adcroft 1.29 o Updates for OBCs
6011     o New experiment for test OBCs (internal_wave)
6012     o New output.txt in verification/exp4/results/
6013     o Updates for KPP: calculation of viscosity corrected, new variables
6014     kpp_dumpFreq and kpp_taveFreq
6015     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
6016     and entry for T90 in genmake
6017 adcroft 1.28
6018 jmc 1.1203 checkpoint29 (2000/06/21)
6019 adcroft 1.28 o packaged KPP and GM/Redi
6020 heimbach 1.27
6021 jmc 1.1203 checkpoint28 (2000/06/09)
6022 heimbach 1.27 o Corrected initialization of hFacMin for difference vertical coordinates
6023     o Modified calculation of partial cell thickness to more robust algorithm
6024     o config_summary.F: replaced write_1D_... by write_0D_...
6025     read_write.F: added subroutines write_0D_...
6026     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
6027     included some initialisations required for TAMC.
6028     o routine calc_isoslopes: modified sqrt computation to make it
6029     differentiable for zero argument.
6030     o routines dynamics, impldiff:
6031     included store directives and tape key computations required for TAMC.
6032     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
6033 adcroft 1.26
6034 jmc 1.1203 checkpoint27 (2000/04/10)
6035 adcroft 1.26 o fixed calc_isoslopes() to so that cancellation of terms in tensor
6036     formulation works properly with variable resolution.
6037     o restructured the calling tree between the_model_main() and dynamics()
6038     o split initialise() into initialise_fixed() and initialise_varia()
6039     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
6040     in new routine ini_psurf()
6041 adcroft 1.25
6042 jmc 1.1203 checkpoint26 (2000/04/05)
6043 adcroft 1.25 o moved some #ifdef in optional routines to encompass everything
6044     except the argument declarations. This was using up some memory.
6045     o fixed macros like _ADT to work with both versions of Linux cpp
6046     o cleaned up some unused and uninitialized variables
6047     (helps when debugging with strict compile options)
6048     o split up CPP_EEOPTIONS.h into options and macros
6049     (macros are now in eesupp/inc/CPP_EEMACROS.h)
6050     o patch for 2 processor JAM mode
6051 adcroft 1.24
6052 jmc 1.1203 checkpoint25 (2000/03/15)
6053 adcroft 1.24 o updates for OBCs and NH
6054     o dramatically reduced memory usage
6055     o added "JAM" routines for use on Artic network
6056     o parameterization of convection by implicit vertical diffusion
6057     o added a diagnostic of convective index
6058     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
6059     (this is was partly for OBCs and NH but also in anticipation of
6060     an explicit free-surface option)
6061     o initial state input files for U and V
6062 adcroft 1.23
6063 jmc 1.1203 checkpoint24 (1999/08/02)
6064 adcroft 1.23 o Removed some spurious "REAL"s
6065     o Updated KPP to latest version from JPL
6066     o Added a COS(latitude) in horizontal viscosity
6067 adcroft 1.22
6068 jmc 1.1203 checkpoint23 (1999/05/26)
6069 adcroft 1.22 o Added del^4 diffusion for salt and temperature
6070     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
6071 adcroft 1.21
6072 jmc 1.1203 checkpoint22 (1999/05/18)
6073 adcroft 1.21 o Made many small changes: implicit none, format(i5), etc...
6074     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
6075 adcroft 1.20
6076 jmc 1.1203 checkpoint21 (1999/05/18)
6077 adcroft 1.20 o Introduced new I/O package that supports direct-access records (mdsio.F)
6078     o Split-up mid-level I/O routines
6079     o Updated input data for experiments 0,1,2,4 and 5
6080     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
6081 adcroft 1.18
6082 jmc 1.1203 checkpoint20 (1999/03/22)
6083 adcroft 1.19 o Tidied up open-boundaries some more
6084     o Added non-hydrostatic code
6085     o Fixed some input data
6086     o Modified MPI start-up to work in "coupled" context.
6087    
6088 jmc 1.1203 checkpoint19 (1998/12/15)
6089 adcroft 1.18 o Tidied up directory structure for verification experiments.
6090     o Added new code for open boundaries.
6091     o Corrected advective terms near boundaries.
6092     o Added CPP flag for "old UV" geometry and corrected spherical geometry.
6093     o Implemented free-slip/no-slip BCs and del^4 dissipation.
6094 adcroft 1.19 o Split default parameters out of ini_parms.F into set_defaults.F.
6095 cnh 1.17
6096 jmc 1.1203 checkpoint18 (1998/11/30)
6097 cnh 1.17 o Further changes for optional code generation with
6098     CPP - ugh!
6099 cnh 1.16
6100 jmc 1.1203 checkpoint17 (1998/11/03)
6101 cnh 1.16 o Beginning to incorporating modularity
6102     for supporting atmos. and ocean configs.
6103     o Small changes for TAMC complinace
6104     o New ultra simple test case. Barotropic box
6105     configuration "exp0".
6106 cnh 1.15
6107 jmc 1.1203 checkpoint16 (1998/10/28)
6108 cnh 1.15 o Minor changes to exchange routines to support
6109     accumulation in reverse mode. Adjoint of an
6110     assignment is an addition.
6111     o Changes to support compilation by TAMC (LR(1)
6112     syntax) and by g77 under Linux ( 72 character
6113     limit ).
6114 cnh 1.14
6115 jmc 1.1203 checkpoint15 (1998/09/29)
6116 cnh 1.14 Rewrote exchange routines to allow
6117     o General tile <-> tile connectivity.
6118     o TAMC reverse mode flag ( is this really needed? )
6119     o Variable width overlap and exchange region widths.
6120     o Hooks for sharing data via DMA, Arctic, Memory Channel,
6121     shmput/shmget, VIA, SYSV shmem and every other cool
6122     communication method.
6123 cnh 1.13
6124 jmc 1.1203 checkpoint14 (1998/09/09)
6125 cnh 1.13 Consistent isomorphism chages made. These allow dynamical core
6126     to support both pressure and meters as a vertical coordinate.
6127 cnh 1.12
6128 jmc 1.1203 checkpoint13 (1998/07/17)
6129 cnh 1.12 Release which corrects global_max problem and a couple
6130     of KGM time-averaging diagnostic errors. Also contains
6131     a double-gyre experiment setup as well as the baseline
6132     4 degree global template. The double gyre template is
6133     organised to allow it to be applied automatically to
6134     the baseline configuration.
6135 adcroft 1.11
6136     branch-point-rdot
6137     A few tidy-ups have been made bt the real point of this
6138     check-point (excuse the pun) is to allow a branch to be
6139     made for the purposes of adding the rDot alterations.
6140     I don't want to commit the rDot to the main-trunk until
6141     we've actually tested it...
6142 cnh 1.10
6143 jmc 1.1203 checkpoint12 (1998/07/08)
6144 cnh 1.10 Tidy up and added generic genmake script (formerly
6145     configure script).
6146     Released to testers.
6147 adcroft 1.9
6148 jmc 1.1203 checkpoint11 (1998/07/02)
6149 adcroft 1.9 Re-arranged initialise() and introduced ini_vertical_grid()
6150     and ini_masks_etc().
6151 adcroft 1.8
6152 jmc 1.1203 checkpoint10 (1998/07/01)
6153 adcroft 1.8 Introduced the configure script.
6154     Separated out the diags package.
6155     Added template for writing time-averages of tile/intermediate quantities.
6156     Updated SIZE.h in exp2 and made the data big-endian.
6157 adcroft 1.7
6158 jmc 1.1203 checkpoint9 (1998/06/22)
6159 adcroft 1.7 MPI fix. Filename changes (meta/data). salbin*y stuff.
6160     General tidy-up.
6161     SST.bin SSS.bin added to verification/exp2
6162 adcroft 1.6
6163 jmc 1.1203 checkpoint8 (1998/06/22)
6164 adcroft 1.6 Inludes time-dependant forcing and time-averaging.
6165     Works at 4x4 and 2.8125x2.8125 global
6166    
6167     checkpoint7-4degree-ref
6168     Branch from checkpoint7. Released for application to
6169     global modeling and general modeling - process studies, regional
6170     model etc..
6171     Configured for verification/exp2 - 4 degree global, two process.
6172 cnh 1.5
6173 jmc 1.1203 checkpoint7 (1998/06/15)
6174 cnh 1.5 Created by cnh
6175     Simple 4 degree global simulation
6176     configuration.
6177     Includes climatological wind,
6178     hydrography, bathymetry etc
6179     Does not include Heat Flux and E-P
6180 cnh 1.4
6181 jmc 1.1203 checkpoint6 (1998/06/08)
6182 cnh 1.4 Created by cnh
6183     merged checkpoint5 with CD and
6184     spherical polar code.
6185     Still some problems with GM Redi
6186     abd full topography.
6187 cnh 1.3
6188 jmc 1.1203 checkpoint5 (1998/06/08)
6189 cnh 1.3 Created by AJA
6190     contains updates to GM Redi
6191     and reordered timestepping loop
6192     for Implicit Diffusion.
6193 cnh 1.2
6194 jmc 1.1203 checkpoint4 (1998/05/30)
6195 cnh 1.2 Created by cnh
6196     Contains memory saving macros ( _rdxc etc..) for when
6197     grid variations are limited.
6198     Contains polynomial coeffs for EOS and knudsen program
6199     for generation.
6200    
6201 jmc 1.1203 checkpoint3 (1998/05/26)
6202 cnh 1.1 Created by cnh
6203     Added extra flags for runtime options
6204     Added this file
6205     Added implicit free-surface
6206     Added pre-conditioner
6207     Put compare01 into repository ( compare01/... )
6208     Put data and eedata into repository ( verification/exp1 )
6209    
6210     checkpoint2
6211     Created by AJA
6212     Added GM/Redi
6213    
6214     checkpoint1
6215     Created by AJA
6216     Restructured kloop in dynamics.F
6217     Added non-linear EOS
6218    
6219 cnh 1.2 baseline
6220     Original checked in code
6221 cnh 1.1

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