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Revision 1.1369 - (show annotations) (download)
Mon Jan 24 14:35:07 2011 UTC (13 years, 2 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint62r
Changes since 1.1368: +2 -1 lines
checkpoint62r tag

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

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