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Revision 1.1610 - (show annotations) (download)
Mon Mar 5 16:23:23 2012 UTC (12 years, 2 months ago) by jmc
Branch: MAIN
Changes since 1.1609: +10 -6 lines
document changes in pkg/seaice/dynsolver.F

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1609 2012/03/05 15:34:58 gforget Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 o pkg/seaice :
8 - add missing initialisation of COR_ICE array in dynsolver.F
9 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
10 compiled either way, and is tested in all exps (multidim was only tested
11 in lab_sea ad before).
12 - cosmetic change to prepare for future addition of ITD. no change to results.
13 no defaults change.
14 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
15 - by lack of adequate verification experiments, I further used custom versions
16 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
17 should be correct.
18 - avoid recomputations in ad.
19 o array initialisation in adjoint mode:
20 1) pkg/mom_common/mom_calc_ke.F:
21 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
22 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
23 part this initialisation is gone, resulting in Floating Point Exception
24 (caught by open64 compiler with debug option).
25 2) model/src/convective_weights.F
26 set output convectCount over the full array range (instead of doing
27 an update): this fix a similar issue when called within recomputation (adjoint)
28 which could by-pass the initialisation (normally done in the caller S/R).
29 o pkg/seaice:
30 - final version of turbulent flux params, as agreed at MIT ice meet:
31 SEAICE_mcPheePiston (default is ~ 0.000875)
32 SEAICE_mcPheeTaper (default is 0.)
33 SEAICE_frazilFrac (defualt is 1.)
34 SEAICE_mcPheeStepFunc (default is false)
35 - changes results at trunction error level
36 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
37 o added pkg/frazil:
38 - see frazil_description.tex for details
39 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
40 o pkg/shelfice/shelfice_thermodynamics.F
41 - fix exponents for velocity dependent exchange coefficients: change
42 from 2/3(=0) to 0.66666666666666667
43 - move computation of velocity dependent exchange coefficients into
44 separate loop, so that it applies to both thermodynamics
45 - move some divisions by constants out of loops
46
47 checkpoint63j (2012/02/16)
48 o pkg/seaice:
49 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
50 - SItracer: added run time params, and allow coupling to ocn salinity.
51 o pkg/seaice: remove (almost) all divisions by constants within loops
52 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
53 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
54 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
55 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
56 o pkg/seaice :
57 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
58 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
59 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
60 - add permanent SItflux diag that corresponds to TFLUX but includes
61 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
62 - allow activation/testing of a fix for suspected missing term in
63 ocn-ice heat budget (to be confirmed). To test this, you want to
64 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
65 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
66 - no change in results, fwd or ad.
67 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
68 - switch to variable freezing point.
69 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
70 - bug fix : the sublimation term that was missing is now activated.
71 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
72 - bug fix : flooding sign term for SIsal0.NE.0.
73 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
74 o pkg/seaice:
75 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
76 is now the default, and the old default constant freezing point is recovered
77 with SEAICE_tempFrz0 = -1.96,
78 SEAICE_dTempFrz_dS = 0.,
79 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
80 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
81 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
82 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
83 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
84 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
85 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
86 seaice_growth r149 for legacy branch (no results change).
87 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
88 from I. Fenty).
89 - results did not change except for global_ocean.cs32x15, mostly due to the
90 switch to variable freezing point (see above item for detail).
91 o pkg/thsice:
92 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
93 seawater freezing in thsice_calc_thickn (not used).
94 o pkg/seaice: turbulent flux term specification via run time params.
95 - replace CPP switches with run time switches to facilitate testing
96 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
97 GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
98 - added runtime parameter : SEAICEturbFluxFormula
99 - move Mcphee constants to SEAICE_PARAMS.h
100 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
101 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
102 remove seaice_summary call (moved to seaice_init_fixed)
103 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
104 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
105 - seaice_summary.F : add missing report of read turbulent flux term set up
106 and SITRACER.
107 - seaice_check.F : check range; inform and stop if retired CPPs are used
108 (incl. SEAICE_AGE).
109 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
110 CPP switch, same computation as before for the different options.
111 - change results at the truncation level.
112 o pkg/seaice:
113 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
114 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
115 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
116 - update verification/*/input*/data.seaice:
117 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
118 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
119 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
120 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
121 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
122 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
123 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
124 difference in results only due to machine truncation.
125 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
126 MaykutPolySatVap; keep MIN_LWDOWN.
127 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
128 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
129 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
130 o pkg/salt_plume:
131 - isolate saltPlumeFlux array exch into a specific S/R called from
132 do_oceanic_phys.F
133 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
134 o verification:
135 - move untested set-up to MITgcm_contrib/verification_other.
136 o pkg/seaice:
137 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
138 o pkg/seaice:
139 - seaice_solve4temp.F (keeping results unchanged):
140 * add 2 future run-time params to select which saturation vapor pressure
141 formula is used and how post-iteration fluxes are set.
142 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
143 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
144 the linearized expression to stay consistent with tsurf finding.
145 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
146 can be < 0.
147 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
148 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
149 conductive heat flux F_c , and add it explicitly when updating tsurf as
150 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
151 so that now F_ia has a consistent meaning through the entire routine.
152 This causes differences at truncation level: update output of fwd exp.
153 global_ocean.cs32x15.seaice.
154 o pkg/seaice:
155 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
156 of arrays, sign/direction of fluxes; no effect on results.
157 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
158 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
159 note: this should have been done before changing celsius2K default.
160 - to keep results unchanged, add back old value of celsius2K in verification
161 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
162 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
163 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
164 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
165 freezing temp is consistent with value in seaice_growth.F ; this causes
166 differences at machine truncation level: update lab_sea AD output (3/4).
167 o pkg/seaice:
168 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
169 and climsst/sss even when using seaice (to prevent calculation that might
170 use SST on land); does not affect any verification exp.
171 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
172 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
173 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
174 over land (non-legacy code)
175 o vectorize salt_plume package:
176 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
177 - this code computes plumebk everywhere (also over land), thus requires
178 code to avoid divisions by zero and catch the case of kLev=Nr.
179 - efficiency of salt_plume_frac is still sub-optimal
180 o tools (genmake2):
181 - fix makefile NAME specification (option: -makefile NAME) by adding
182 "-f $MAKEFILE" in few places where it was missing including makedepend
183 command (contribution from Paul).
184
185 checkpoint63i (2012/01/24)
186 o model/src:
187 - add factorized versions of some EOS code to find_rho.F,
188 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
189 o model/src:
190 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
191 - change default celsius2K from 273.16 to 273.15
192 - to keep results unchanged, add back old value of celsius2K in verification
193 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
194 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
195 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
196 to make TAF generate vectorizable code
197 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
198 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
199 have flags that do this more efficiently.
200 o pkg/diagnostics/diagstats_calc.F
201 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
202 o pkg/obcs (with exch2):
203 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
204 and remove code (in obcs_readparms.F) which was based on EXCH of indices
205 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
206 o pkg/exf and seaice exp:
207 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
208 so that switching off area & heff advection flags does not affect results.
209 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
210 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
211 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
212 results of verification experiments: 1D_ocean_ice_column(fwd),
213 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
214 and offline_exf_seaice (all 4).
215 o pkg/seaice:
216 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
217 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
218 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
219 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
220 not multi-dim advection;
221 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
222 SHORTWAVE_HEATING #undef.
223 o optim: make Makefile more robust (?)
224 o pkg/obcs:
225 * fix treatment of obcs_read_pickup for TAF
226 o pkg/shelfice:
227 * add missing initialisation of num_shifwflx
228 * new adjoint verification exp. for isomip
229 * change Prandtl and Schmidt numbers from generic formulations
230 (in terms of model diffus. and visc.) to separate runtime
231 parameters, with Holland and Jenkins (1999) default values.
232 o pkg/exf (interpolation):
233 - extended input field (2 rows) near the N & S poles:
234 * fill in with the symetric value (when even Nb of data in longitude)
235 * add average value at the poles only for scalar quantities ; for vector
236 component interpolation, skip the averaging and keep duplicated values,
237 unless the 2 components have same location (uvInterp=T) in which case
238 interpolate the 2 components together using S/R EXF_INTERP_UV.
239 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
240 together: this allows to account properly for local orientation when
241 averaging at N & S pole.
242 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
243 exf-interpolation near N & S poles. Undef by default.
244 - add debug check/print on 1rst iter if debugLevel >=2.
245 o pkg/exf:
246 - change masking flags definition (no longer "parameter"), put them in
247 common block and set them in S/R EXF_INIT_FIXED.
248 - change recognized masking flag from s,u,v to c,w,s since the mask
249 to use (maskC,W,S) depends on position on model grid and has little to
250 do with scalar/vector difference; fix masking if using P-coordinates.
251 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
252 and update results of exp. global_with_exf (x2).
253 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
254 o pkg/obcs
255 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
256 o pkg/exf (interpolation):
257 - assume periodicity in X only if input field cover full longitude range.
258 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
259 and should vectorise).
260 - fix input lat of the 2 added row (in case we provide N.pole data).
261
262 checkpoint63h (2011/12/30)
263 o pkg/seaice:
264 - change declaration of UVM from _RL to _RS in order to get B-grid
265 uIce,vIce monitor when _RS = real*4
266 o pkg/offline:
267 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
268 - compute vertical velocity if not read from file (switch on exactConserv
269 & staggerTimeStep);
270 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
271 o verification:
272 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
273 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
274 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
275 - update output of exp. global_ocean.cs32x15.viscA4 after changing
276 grid-file angles (used here for coriolis-3d);
277 - remove (or gzip) few files not needed to run fizhi-cs experiments.
278 o pkg/exf (vector interpolation):
279 - rotate vector component toward local grid-axis orientation using grid-angles
280 (stored in GRID.h) instead of locally computed rotation angle; keep old code
281 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
282 o pkg/seaice:
283 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
284 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
285 o pkg/PKG_OPTIONS.h files:
286 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
287 outside of the #ifdef ALLOW_THISPKG / #endif block.
288 - update verification/*/code/PKG_OPTIONS.h files.
289 o add a verification experiment (offline_exf_seaice/input.seaice) that test
290 the B-grid LSOR solver
291 o pkg/seaice: sort out emissivity and long wave radiation step 2:
292 - add emissivity for snow and ice as new run-time parameters
293 (unfortunately) that default to the corresponding exf values; this
294 changes results in most verification experiments so that for backward
295 compatibility these parameter have to be set explicitly to inconsistent
296 values (ugly);
297 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
298 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
299 until we agree how to handle this bug properly
300 o pkg/exf (interpolation):
301 - add a set of run-time param ({inputfield}_interpMethod), one for
302 each interpolated input field, to select the interpolation method
303 with a value of zero switching off the interpolation;
304 - print interpolation parameters to standard output;
305 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
306 (to use instead runoff_interpMethod=0 in data.exf).
307 - simplify default setting of interpolation parameters (for all fields,
308 set position to match model grid cell-center position, leading to trivial
309 interpolation in case of regular Lat-Lon grid) and fix for the case of
310 non-uniform delY.
311 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
312 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
313 this factor is absolutely required, because the lw exitance (= out-going
314 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
315 where the reflectivity rho = 1-emissivity for conservation reasons. Once
316 this is established, we can remove the CPP-Flag (if we want to).
317 o pkg/seaice:
318 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
319 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
320 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
321 what the name implies (and not emissivity*BoltzmannConstant), this means
322 the old default value of 5.5e-8 now means
323 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
324 S/R exf_readparms
325 - FV-discretization of the B-grid LSOR solver, turn on with
326 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
327 of the calling routine dynsolver, so that B and C-grid code look a
328 little more alike.
329 - fix index bugs in ostres.F (B-grid code)
330 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
331 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
332 default for SEAICE_emissivity, if useEXF; requires setting a wrong
333 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
334 backward compatiblity
335 o model/src: use sigmaR in calc_ivdc
336
337 checkpoint63g (2011/12/16)
338 o pkg/seaice/seaice_growth.F:
339 fix heat conservation of the coupled ocean-seaice system.
340 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
341 solid vs liquid water treatment is resolved via QNET.
342 o pkg/seaice/seaice_growth.F:
343 add missing term for sublimation in saltFlux, which was breaking conservation.
344 o pkg/seaice/seaice_model.F:
345 Remove this patholigical case treatment in evolution branch,
346 where it is un-necessary and breaks conservation.
347 Update global_ocean.cs32x15/results accordingly for
348 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
349 o model/src:
350 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
351 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
352 o pkg/obcs:
353 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
354 tendency for temperature and salinity that is then applied to update
355 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
356 horizontal advection and diffusion contributions on the boundary (in
357 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
358 removing the mask in S/R timestep_tracer. The advantage of this approach is
359 that the updated tracer values include contributions from the surface
360 forcing and vertical diffusion.
361 This modification changes exp4.stevens because of vertical diffusion.
362 o model/src:
363 change non-curvilinear grid setting to also work with exch2 + blank tiles:
364 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
365 face dimensions.
366 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
367 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
368 and INI_SPHERICAL_POLAR_GRID.
369 change test-experiment global_ocean.90x40x15:
370 - split the domain in many more tiles (9x4 tiles of 10x10 each);
371 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
372 - update results of both test (std & dwnslp).
373 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
374 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
375 o model/src:
376 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
377 and fix initialisation when using sigma-coords.
378 o model/src:
379 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
380 to their current value at the beginning of forward_step.F": add a new run-time
381 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
382 - set doResetHFactors=T in the following test exp:
383 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
384 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
385 and tutorial_global_oce_in_p (nonLinFS in p)
386 o pkg/ecco
387 - added IES cost term
388 o verification/advect_xz
389 - scale down the depth by 1/100 (from 200 km to just 2.km)
390 - add secondary test using divergent flow, r-star and implicit vertical advection.
391 - add note (check_conserve_TS.txt) and matlab script to check global
392 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
393 o pkg/rbcs:
394 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
395 o pkg/obcs (Stevens BCs):
396 - fix various problems in the phase speed computations of the Stevens
397 boundary conditions:
398 - sign error for western and southern boundaries,
399 - time tendencies were underestimated by factor of dTracerLev and some just
400 zero (for multidim advection schemes) -> now estimate time tendencies
401 from difference between previous (n) time level and the one before (n-1);
402 this requires storing a field per tracer per boundary, also in the pickup
403 files.
404 - replace deltaTmom in cflMer/Zon computation with dTracerLev
405 - set default phase velocity to cflMer/Zon
406 - update verification experiment exp4.stevens
407 o pkg/generic_advdiff (implicit_r):
408 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
409 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
410 - fix implicit vertical diffusion or advection with NonLin FreeSurf
411 (was using current recip_hFacC instead of future recip_hFacC): set future
412 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
413 solver S/R ;
414 - fill diagnostics of vertical advective fluxes (computed from tendency)
415 when using implicit vert. advection;
416 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
417 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
418 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
419 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
420 o pkg/diagnostics:
421 - add diags for T & S tendency which goes through Adams-Bashforth.
422
423 checkpoint63f (2011/11/30)
424 o pkg/obcs/obcs_calc_stevens.F:
425 - join some loops to reduce number of if-statements
426 - fix a bug in code for northern and southern boundaries.
427 o pkg/seaice/seaice_init_varia.F
428 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
429 caused zero ice-velocities for the B-grid code
430 o pkg/seaice/seaice_init_fixed.F
431 - fix a bug in the initialisation of the second metric terms
432 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
433 - this affects all seaice configurations with useCurviLinearGrid = .true.
434 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
435 = .true. (default)
436 - the only verification experiment affected is global_ocean.cs32x15:
437 icedyn, seaice, and seaice_dynmix (AD)
438 o pkg/thsice/thsice_diagnostics_state.F
439 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
440 not contain garbage that can lead to surprises in diagstats_calc.F
441 o model/src:
442 - move bi,bj loops inside INTEGR_CONTINUITY ;
443 - call INTEGR_CONTINUITY directly from forward_step.F
444 (previously called from momentum_correction_step.F)
445 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
446 forward_step.F and pkg/ecco/the_main_loop.F
447 o model/src/do_oceanic_phys.F:
448 - reset addMass to zero only if useICEFRONT ;
449 - separated k-loop for rhoInSitu calculation ;
450 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
451 and at constant T,S (= WdRHOdP);
452 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
453 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
454 transport of locally-referenced potential density);
455 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
456 o gluemnc:
457 - replace ncrcat with ncks when adding variables to *.glob.nc
458 - change the way variables without record dimensions are handled so that
459 files that have variables with and without record variables can be glued:
460 add a record dimension with a new unique name to be able to differentiate
461 between variable with and without a-prior record dimensions. Remove
462 this record dimension before adding the variable to the *.glob.nc file.
463 This procedure automatically works also for grid.*.nc files that do not
464 have any record dimension.
465 o verification/cpl_aim+ocn:
466 - generate new reference output on baudelaire (gfortran, mpich2) (previously
467 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
468 o pkg/obcs/obcs_calc_stevens.F:
469 - add code for northern and southern boundaries.
470 - reorder some loops to save some operations and so that drFBar can be scalar
471 o model/src:
472 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
473 truncation) and add diagnostics for Adams-Bashforth tendency increment.
474 - update test-exp. AD output:
475 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
476 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
477 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
478 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
479 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
480 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
481 tutorial_plume_on_slope.
482 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
483 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
484 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
485 does not even come with an F77 compiler anymore, this should not be
486 a limitation
487
488 checkpoint63e (2011/11/06)
489 o pkg/seaice adjoint of LSR:
490 - substantially rework STORE dirs.
491 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
492 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
493 and only perform SOLV_MAX_FIXED adjoint iters.
494 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
495 always goes to same record, meaning that the last forward field will be
496 the one used in the adjoint - an approximation.
497 - now produces non-zero LSR-related gradients, and acceptable gradients for
498 An's zonal (x-z) test case (to be checked in)
499 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
500 (but these are screwed up by the thermodynamics in the first place);
501 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
502 output_adm.txt also reflects changes to seaice_lsr
503 - global_ocean.cs32x15:
504 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
505 (output_adm.seaice.txt was updated)
506 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
507 (output_adm.seaice_dynmix.txt)
508 o test-exp. exp4+stevens:
509 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
510 o pkg/seaice (lsr solver):
511 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
512 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
513 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
514 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
515 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
516 - compute (with new S/R) and print initial (+ free-driff sol. if available)
517 and final residual of linearised system.
518 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
519 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
520 o pkg/obcs: Stevens BCs (still only for east and west)
521 - fix Stevens BCs by using intermediate velocities of previous
522 time step as "baroclinic" contribution rather velocity of one grid cell
523 inside the boundaries; more consistent but makes the entire treatment
524 more complicated, requires new pickup files and two new S/Rs:
525 obcs_copy_uv_n and obcs_save_uv_n
526 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
527 (undefined by default)
528 - silently move computation of some grid factors into separate loops to
529 save some recomputations
530 - add a hack for non-linear free surface
531 - add a verification experiment to exp4 that tests this code
532 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
533
534 checkpoint63d (2011/10/25)
535 o pkg/obcs + seaice-dynamics:
536 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
537 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
538 values (consistent with an implicit method).
539 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
540 return to older implementation (same results as before); note that none of
541 the "experimental" OBCS_SEAICE options are implemented in the new version.
542 - switch test exp. seaice_obcs to use new version (update output).
543 o pkg/seaice:
544 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
545 - add parenthesis in Water-Ice drag calculations (evp & lsr);
546 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
547 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
548 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
549 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
550 o pkg/layers:
551 - Include potential density as new coordinate (Thanks to David Munday)
552 o pkg/dic:
553 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
554 carbonate computation/output to CALC_PCO2_APPROX
555 o pkg/generic_advdiff
556 - make TAF generate code that vectorizes:
557 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
558 o model/src:
559 - improve vectorization also for adjoint code of
560 solve_tridiagonal and solve_pentadiagonal. As this requires up to
561 5 new 3D-fields, this code is only turned on for the combination of
562 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
563 for singular matrix check (only for TARGET_NEC_SX).
564 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
565 ALLOW_AUTODIFF. This flag now needs to be set outside of
566 solve_tri/pentadiagonal.F
567 o pkg/exf:
568 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
569 optional namelist EXF_NML_OBCS).
570 - add many debug-print (to trace down where pkg/cal error msg comes from)
571 o pkg/mom_vecinv/mom_vi_hdissip.F
572 - rearrange loops so that vectorization is improved and in particular
573 the adjoint routine vectorizes. The code is a little longer now, but I
574 think easier to read.
575 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
576 o pkg/seaice:
577 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
578 o pkg/exch2:
579 - alternative code (without tile x tile matrix) for cumulated (global) sum;
580 used as default; keep using matrix version in adjustment.cs-32x32x1.
581 o tools/build_options:
582 - after merging some MPI and/or multi-threads specific optfiles so that
583 the modified default optfile support both built (using genmake2 -mpi
584 for the MPI built, using genmake2 -omp for OpenMP built),
585 move now obsolete optfiles to tools/build_options/unsupported/
586 (add copy of email sent to support list in doc/optfiles_changes.txt)
587
588 checkpoint63c (2011/09/28)
589 o pkg/ebm:
590 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
591 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
592 o pkg/seaice (SItracer pickup)
593 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
594 To be done:
595 - thorough testing of missing fields in S/R seaice_read_pickup
596 - thorough matching between generic tracers and specific fields used
597 (e.g. volume-weighted age, area-weighted age, salinity, ...)
598 o pkg/grdchk:
599 - all procs calculate and print finite-difference gradient (for testreport)
600 - change description output used by testreport;
601 - AD testing: also compare and report Finite-difference gradient;
602 => update all output_adm*.txt
603 o test exp. global_ocean_ebm:
604 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
605 and turn on exactConserve; update (fwd) output.
606 o pkg/seaice (LSR):
607 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
608 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
609 * identical results with non-CS topology (but save up to half of EXCH calls)
610 * no much changes in cs-32 verification tests since no ice at face edges
611 (differences due to convergence criteria, since nb of iterations changed)
612 * expect some differences on lat-lon-cap grid.
613 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
614 o pkg/exch2:
615 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
616 many tiles); until alternative coding is added, just add a stop.
617 o pkg/kpp:
618 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
619 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
620 o optfiles:
621 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
622 into corresponding standard one, which now support different build:
623 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
624 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
625 o pkg/obcs (seaice):
626 - add missing EXCH for uIce,vIce after applying OBCS;
627 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
628 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
629 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
630 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
631 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
632 and eedata.mth for MPI and mutlti-threaded testing.
633 o pkg/flt:
634 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
635 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
636 - fix pickup and trajectories + profiles output with multi-threads;
637 - add parameter to select group of fields to write along trajectory and
638 profile (default unchanged);
639 - only call PORT_RAND* function when flt_noise <> 0;
640 - add multi-threaded test for verification exp. flt_example.
641 o eesupp/src:
642 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
643 - USE_OMP_THREADING: check that number of threads (from eedata) matches
644 actual number (from env.var. setting).
645 o pkg/ebm:
646 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
647 - add multi-threaded test for verification exp. global_ocean_ebm
648
649 checkpoint63b (2011/08/29)
650 o pkg/ebm:
651 - fix sign of runoff;
652 - update directly forcing fields (Qnet,EmPmR) to use standard
653 external_forcing_surf.F (remove ebm_forcing_surf.F);
654 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
655 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
656 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
657 - update global_ocean_ebm parameters file data and update output (fwd+ad).
658 o verification/matrix_example:
659 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
660 MPI and mutlti-threaded testing.
661 o pkg/matrix:
662 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
663 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
664 - fix for multi-threaded (remove DATA statement);
665 - use standard DIFFERENT_MULTIPLE function;
666 - add MATRIX_OPTIONS.h
667 o verification/matrix_example:
668 To allow to split the domain in several tiles, change the domain size
669 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
670 Western side) of land points.
671 o (*_)write_pickup:
672 - fix few bugs in mypackage_read/write_pickup.F
673 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
674 array of length 1 (was caught by compiler syntax-check).
675 o pkg/diagnostics (velocity potential solver):
676 - fix initialisation of main diagonal matrix (for overlap values)
677 o tools/build_options:
678 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
679 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
680 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
681 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
682 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
683 and use "-devel" testreport option for standard testing on baudelaire.
684 o pkg/grdchk:
685 - Assume that all gradient-check position are within the same tile
686 corresponding to global indices (iGloTile,jGloTile) and that
687 positions (i,j indices or nbeg) are local to this tile;
688 - set tile local-indices and proc. number according to tile global-indices;
689 - remove grdchkwhichproc from namelist (retired param);
690 - send adjoint gradient to all procs so that all procs print it to STDOUT;
691 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
692 o adding package bbl (Bottom Boundary Layer)
693 description in MITgcm/pkg/bbl/bbl_description.tex
694 example/test experiment in MITgcm_contrib/bbl
695 o adjoint verifications
696 - changed 5 experiments to multi-tiles
697 * global_ocean.90x40x15
698 * obcs_ctrl
699 * offline_exf_seaice
700 * tutorial_dic_adjoffline
701 * tutorial_tracer_adjsens
702 changed reference output for those that crossed tile boundaries
703 (changed choices of gradient check positions)
704 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
705 - temporary bug fix in grdchk_loc.F for obcs
706 o genmake2 & testreport
707 - add target "obj" (just for OBJFILES files) to Makefile;
708 - add option to specify FEXTRAFLAGS on command line.
709 o pkg/mypackage:
710 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
711
712 checkpoint63a (2011/08/02)
713 o pkg/diagnostics (velocity potential):
714 - fix velocity-potential calculation when using OBCS: balance net inflow
715 at each level (new S/R OBCS_DIAG_BALANCE).
716 - fix some of the problems with OBCS in stream-function calculation.
717 o pkg/exf/exf_readparms.F
718 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
719 EXF_NML_OBCS) more consistent, so that you need not have these lists
720 in data.exf when they are not used.
721 o optim/optim_readdata.F:
722 - add some output about obcs variables that might help debugging
723 - add a check about nvarlength
724 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
725 o pkg/diagnostics (velocity potential):
726 - fix mask for OBCS (still problems in stream-function with OBCS);
727 - add specific parameter (default = main code CG2D params) for solver;
728 - in case of poor convergence, use solution corresponding to lowest residual.
729 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
730 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
731 and should be avoided where possible.
732 o model/src (rStar):
733 - include r* effect on reference-state (PhiRef) in totPhiHyd
734 (so that it's really the potential anomaly at the cell center);
735 affect solution only if z* with full pressure in EOS.
736 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
737 update output (because of z* in totPhiHyd and viscA4 changes);
738 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
739 @ constant r) until interpolation at constant r is implemented.
740 o pkg/diagnostics
741 - fix RCENTER diagnostics in case cell center is not at interface middle
742 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
743 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
744 that THETA and SALT are "conservative temperature" and "absolute
745 salinity"
746 o pkg/ctrl
747 - fix computation of endrec in s/r ctrl_init_rec
748 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
749 o pkg/seaice/seaice_growth.F
750 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
751 remove then obsolete STORE directives
752 - fix STORE directives for tice and tices, so that only the
753 appropriate part of the fields are stored (and not the entire
754 field); update global_ocean.cs32x15.seaice AD output.
755 - cosmetic changes: adjust CPP flags and indentation for better
756 legibilty
757 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
758 Chris Wilson)
759 o pkg/gmredi:
760 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
761 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
762
763 checkpoint63 (2011/07/11)
764 o pkg/exch2:
765 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
766 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
767 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
768 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
769 o pkg/diagnostics:
770 - deal with pairs of post-processed diags which are computed together; in
771 particular, re-order list of diags within 1 file to save 2nd computation.
772 - add S/R to compute velocity stream-function (called after velocity-potential
773 calculation) from divergence free transport -> new diagnostics "PsiVEL".
774 - add parameter to select grid-point location where PsiVEL == 0.
775 o eesupp/src:
776 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
777 (specific S/R needed with exch2 topology - for now, just print an error msg)
778 o pkg/shelfice
779 - Implement friction velocity-dependent transfer coefficients following
780 Holland and Jenkins, JPO, 1999
781 Original code by M. Losch with small modifs.
782 Enable with CPP option SHI_ALLOW_GAMMAFRICT
783 and runtime flag SHELFICEuseGammaFrict
784 o verification lab_sea & global_ocean.cs32x15:
785 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
786 does not miss some dependencies (but is slower) and also works with many files
787 (default makedepend limitation for AD built).
788 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
789 o pkg/diagnostics:
790 - add run-time parameter "useMissingValue" (def=False) to fill land-point
791 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
792 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
793 - Extend the use of "missing_value" setting from data.diagnostics for the case
794 of counter-diagnostics (where fraction-weight is zero). This applies both to
795 MNC and MDS output files.
796 o pkg/seaice/seaice_growth.F:
797 - add 'a priori' cap of latent heat flux based on actual mass considerations
798 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
799 non-legacy seaice_solve4temp.
800 - add diagnostic of the residual sublimation freshwater flux (the freshwater
801 flux taken from the ocean if the total actual latent heat fluxes exceed
802 the maximum)
803 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
804 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
805 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
806 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
807 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
808 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
809 o verification 1D_ocean_ice_column:
810 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
811 update results
812 o pkg/diagnostics:
813 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
814 which are not filled-up but computed from other diags ; In this case, the mate
815 diag points to the primary (filled-up) diag to used for post processing.
816 - Update Velocity-potential computation using post-processed diag framework.
817 ==> Change the ordering of fields and time-periods in MDS output file
818 when using periodic averaging: now writes one time record with the full set
819 of fields for this time period, then the next time reccord (it used to be
820 one field with the full set of time records then the next field).
821 Note: this is now similar to NetCDF (MNC) output file. <==
822
823 checkpoint62z (2011/06/21)
824 o adjoint monitor:
825 - Add adjoint monitor output for packages exf, seaice
826 and update relevant testreport output
827 o pkg/seaice:
828 - re-order diags inits so that they appear in order in available_diagnostics.log
829 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
830 area/heff/hsnow preceeding thermodynamic growth/melt.
831 - modified diag: SIdA; output actual effect, as the description states.
832 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
833 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
834 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
835 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
836 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
837 - added diagnostics for seaice generic tracers (SItr*).
838 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
839 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
840 I. Fenty: 18-Jun-2011:
841 Minor changes to seaice package:
842 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
843 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
844 - Differentiated "regularization variables" from "floor variables"
845 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
846 * hiceMin became SEAICE_hice_reg (old hiceMin)
847 (with _reg meaning regularization variable)
848 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
849 so as to ensure energy conservation when going between phases
850 - A22 was not used anywhere
851 2) Changed regularization procedure for heffActual and hsnowActual to ensure
852 well-boundedness and smooth adjoint in seaice_growth.F
853 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
854 because the old regularization always set heffActual >= 0.05 cm
855 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
856 on AREA when HEFF > 0.
857 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
858 requiring that DISABLE_AREA_FLOOR *not* be defined
859 Affected verifications:
860 - 1D_ocean_ice_column (output.txt output_adm.txt)
861 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
862 o pkg/diagnostics:
863 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
864 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
865 (was _RL, now integer) with option = 0 to retrieve all levels.
866 - add pieces of code to compute velocity potential at each level (new diagnostics
867 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
868 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
869 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
870 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
871 and in diagnostics_fract_fill.F (do not need a valid pointer for the
872 diagnostics counter-mate); check that definition of counter-diagnostic
873 includes a valid counter-mate (in diagnostics_set_levels.F).
874 o model/src (rStar):
875 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
876 affect solution only if z* with full pressure in EOS;
877 update output of test-exp global_ocean.90x40x15.
878 o pkg/seaice:
879 - introduce siEps=1e-5 parameter
880 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
881 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
882 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
883 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
884 as well as ice cover age and ridging index (attached to AREA).
885 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
886 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
887 Up to SItrMaxNum=3 tracers can be used simultaneously.
888 o pkg/salt_plume:
889 -introduce SPsalFRAC run time parameter that sets the fraction of the
890 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
891 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
892 o model debug options:
893 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
894 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
895 - Refine debug-msg printing selection (3 new levels):
896 debugMode : controls printing of debug messages (sequence of S/R calls).
897 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
898 debLevZero = 0 ; /* level of disabled aux. msg printing */
899 debLevA = 1 ; /* level of minimum aux. msg printing */
900 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
901 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
902 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
903 debLevE = 5 ; /* level of extensive debug printing */
904 New debugLevel default: with default debugMode value (=F),
905 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
906 and if debugMode=T, default debugLevel = 4 (debLevD).
907 Relation with previous settings:
908 debLevB (=2) corresponds to former debLevA (=1)
909 debLevD (=4) corresponds to former debLevB (=2)
910 Note:
911 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
912 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
913 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
914 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
915 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
916 o pkg/obcs:
917 - change OBCSfixTopo default from True to False (should not change the results);
918 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
919 o pkg/thsice:
920 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
921 2nd layer seaice sublimation (unlikely to happen)
922 - use Interior mask for OBCS in thsice_advection.F (similar to what is
923 done in gad_advection & seaice_advection).
924 o adjoint:
925 bug fix spotted by Gael Forget:
926 seaice_advection and thsice_advection still had
927 legacy CPP options to avoid CS corner updates for adjoint
928 o pkg/seaice:
929 => Change some of the defaults (2011/05/29):
930 - change SEAICEuseFluxForm default (from False to True)
931 - change DIFF1 default (from 0.004 m/s to 0. m/s)
932 And print warnings if DIFF1 is not set in data.seaice and centered
933 avection scheme is used without any diffusion.
934 also:
935 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
936 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
937 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
938 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
939 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
940 update results of test exp.:
941 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
942 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
943 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
944 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
945 seaice_obcs: output (SEAICEuseFluxForm=T)
946 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
947 for standard fwd & AD lab_sea tests (to keep the same output).
948 o pkg/seaice/seaice_growth.F:
949 - use Ian Fenty's capping formulas for actual ice
950 thickness thoughout EVOLUTION branch.
951 - put treatment pathological case #2) in CPP brackets
952 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
953 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
954 o pkg/seaice:
955 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
956 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
957 also pass fac as a param, which can be 1. (to update the tendency
958 field) or the time step (to update the field itself).
959 - seaice_advdiff.F: for multidim, call seaice_diffusion with
960 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
961 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
962 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
963 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
964 o pkg/seaice:
965 diffusion with centered advection scheme (diffus.F & advect.F):
966 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
967 to just compute the laplacian of input-field.
968 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
969 - fix flux-form version in diffus.F to conserve tracer.
970 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
971 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
972
973 checkpoint62y (2011/05/26)
974 o pkg/seaice:
975 - seaice_growth.F : in EVOLUTION branch, always include
976 a_QSWbyATM_cover in qnet (as it should be).
977 - verification/global_ocean.cs32x15 : update results accordingly
978 (output.seaice.txt output_adm.seaice.txt).
979 o pkg/seaice + obcs:
980 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
981 equivalent of assuming no tracer gradient outside the OB region.
982 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
983 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
984 after changes above);
985 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
986 only at OB location (instead of over a band of OLx width).
987 o pkg/seaice:
988 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
989 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
990 o pkg/obcs:
991 - split header file "OBCS.h" into 4 separated files:
992 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
993 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
994 (contain no conditional statement which depends on OBCS options).
995 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
996 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
997 o ctrl, cost, grdchk & autodiff pkgs:
998 - make options file more standard (like other {PKG}_OPTIONS.h file but
999 with AD_CONFIG.h); clean-up some of the included header files.
1000 o pkg/obcs:
1001 - do not mask tracer when applying OB (tracer == 0 could generate problems)
1002 - apply tracer OB values to tracer field only at OB location (instead of
1003 over a band of OLx width)
1004 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
1005 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
1006 obcs_apply_tloc.F & obcs_apply_sloc.F
1007 o obcs in model/src:
1008 - call OBCS_APPLY_W only if NonHydrostatic.
1009 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
1010 - reset dEtaHdt and wVel to zero outside OB interior region ;
1011 - leave tracer unchanged outside OB interior region: This has no effect
1012 on the solution but just to prevent unrealistic tracer value outside OB.
1013 - zero out velocity outside OB interior region: This has no effect on
1014 the solution but just to prevent unrealistic velocity outside OB.
1015 o obcs and non-lin free-surf:
1016 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
1017 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
1018 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
1019 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
1020 update results of test-exp. exp4(nlfs).
1021 o exp4 (nlfs) test-exp:
1022 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
1023 with NonLin-FreeSurf); update output.nlfs.txt
1024 o obcs and 2d/3d solver norm:
1025 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1026 and outside OB interior region (will allow to place OB further inside the
1027 domain). Depending on the domain, can affects cg2d-Norm (previous
1028 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1029 and cg3d-Norm (previous Norm was computed before canceling OB terms),
1030 e.g. in tutorial_plume_on_slope.
1031 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
1032 o pkg rbcs:
1033 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
1034 - add capability to apply relaxation to horizontal velocity uVel & vVel.
1035 o pkg/grdchk: add gradient check for control variable xx_shifwflx
1036 o pkg/shelfice/shelfice_init_fixed.F
1037 fix CPP-flag combinations
1038 o pkg/seaice: Merge iceage code of Pierre Rampal
1039 * update/change/correct ice age calculations
1040 * add age updates for pathological cases
1041 Probably needs more testing...
1042
1043 checkpoint62x (2011/05/13)
1044 o pkg/mom_vecinv:
1045 high-order vorticity scheme: use interior masks (maskInW & S)
1046 to zero-out (outside OB) gradient of vorticity.
1047 o verification exp.:
1048 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1049 hs94.128x64x5 and seaice_obcs ; update results.
1050 o pkg/obcs:
1051 fix bug in OBeta for YZ sections in obcs_exf_load.F
1052 o pkg/ctrl, pkg/shelfice, and optim:
1053 - add new control variable xx_shifwflx (fresh water flux underneath ice
1054 shelves). This is almost as tedious as obcs-ctrl, because the
1055 variables needs its own mask.
1056 - add a cost function term that penalizes the deviation of xx_shifwflx
1057 from the first guess (zero) in analogy to other control variables
1058 o pkg/shelfice:
1059 - start basic adjoint
1060 o pkg/ctrl:
1061 - remove extra 2D field "for good measure" when initializing in
1062 ctrl_set_globfld_[xy/xz/yz].F
1063 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1064 - improve error messages in ctrl_set_unpack_*
1065 o OBC implementation in momentum:
1066 use interior masks (maskInC,W & S) in momentum S/R:
1067 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1068 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1069 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1070 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1071 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1072 (and also with Leith/Smagorinsky harmonic-viscosity).
1073 Update output of experiment dome and exp4 (+nlfs).
1074 o exp4 test-exp:
1075 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1076 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1077 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1078 time-varying OB at Western-side for wVel (NonHyd); update output.
1079 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1080 and biharmonic-viscosity ; also use prescribed time varying OB.
1081 o pkg/obcs:
1082 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1083 o model/src:
1084 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1085 - initialise startTime & nIter0 with unlikely values: allows to set one
1086 from the other without ambiguity.
1087 o seaice_obcs test-exp.:
1088 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1089 o pkg/obcs:
1090 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1091 no longer needed with maskInC,W,S in pkg/generic_advdiff.
1092 o pkg/seaice:
1093 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
1094 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
1095 - fixed bug in the initialization of sea ice salinity variable HSALT
1096 in seaice_init_varia.F (removed dependence on ICE2WATR)
1097 o fizhi-cs test exp.:
1098 switch reference output convention for these 2 non-standard test-exp,
1099 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
1100 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
1101 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
1102 o model/inc:
1103 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
1104 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
1105 o pkg/seaice:
1106 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
1107 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
1108 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
1109 and initial HSALT
1110
1111 checkpoint62w (2011/04/26)
1112 o pkg/mom_fluxform:
1113 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
1114 - use parameter "sideDragFactor" in no-slip BC side-drag part.
1115 - update output of exp. global_ocean.90x40x15
1116 o pkg/mom_vecinv:
1117 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1118 o update seaice exp.:
1119 use more consistent parameter values (remove "backward compatability only":
1120 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
1121 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
1122 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
1123 o update test-exp global_ocean.90x40x15:
1124 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
1125 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
1126 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
1127 o turn on zStar & viscA4 in standard set-up (dir input/)
1128 and update output files: output.txt & output.dwnslp.txt
1129 o new AD-test experiment: obcs_ctrl
1130 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
1131 o pkg/dic:
1132 fix two bugs in handling water vapour pressure in carbonate chemistry
1133 and air-sea fluxes. Found by Val Bennington and Galen McKinley
1134 (add DIC Option = WATERVAP_BUG to recover old results)
1135 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
1136 o adding allowInteriorFreezing option to check for water below freezing point
1137 at depth and bring the negative heat anomaly to the surface level
1138 o pkgs _fields_load:
1139 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1140 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1141 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1142 rbcs to get interpolation weights and time reccord number.
1143 - fix multi-threading in aim_fields_load.F
1144 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1145 o external_fields_load:
1146 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1147 interpolation weights) to use in a periodic time-series ; do not divide by
1148 time-step to convert to integer:
1149 - this fixes case where externForcingPeriod is not multiple of time-step
1150 (Thanks to Christopher L. Wolfe)
1151 - this fixes case where externForcingPeriod is an odd multiple of time-step
1152 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1153 store index of time-record which is currently loaded:
1154 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1155 - needed for the adjoint but not yet used because of extensive recomputations;
1156 (to be fixed soon)
1157
1158 checkpoint62v (2011/04/02)
1159 o verification/1D_ocean_ice_column added to test Ian Fenty's
1160 pkg/seaice_growth.F modifications for improving sea ice code differentiability
1161 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1162 (new velocity statistics after changing maskInW & maskInS definition)
1163 o pkg/generic_advdiff with OBCS:
1164 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1165 equivalent to assumption of no tracer gradient outside the OB region.
1166 This will affect the results if using obcs+biharmonic diffusion.
1167 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1168 o pkg/obcs:
1169 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1170 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1171 in Interior region. No impact on solution but affects Velocity monitor stats.
1172 o pkg/ptracers (adjoint)
1173 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1174 tape file for each tracer
1175 o model/inc/src and pkg/autodiff: add parameters that allow to turn
1176 of parts of the adjoint code at run time. For now, there are only
1177 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1178 parameters are set in data.pkg.
1179 This is the lazy coward's version of doing this, but still useful for
1180 debugging. In order to do it right, everything needs to be moved to
1181 pkg/autodiff.
1182 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1183 the end; this fixes the adjoint balancing code for open boundaries.
1184 o pkg/ctrl:
1185 - change behavior of xx_${varname}period to be analogous to exf-conventions:
1186 xx_${varname}period = 0., means time-independent control part
1187 xx_${varname}period = -12., means one-year-periodic monthly control part
1188 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1189 clean up ctrl_init a little, remove unused variables
1190 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1191 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1192
1193 checkpoint62u (2011/03/15)
1194 o model/src:
1195 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1196 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1197 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1198 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1199 o pkg/ctrl/obcs/ecco:
1200 - remove obsolete, unused, and partially broken code:
1201 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1202 ALLOW_CTRL_OBCS_BALANCE
1203 - put a stop statement into ecco/cost_obcsvol.F, but also add
1204 cost_obcsvol to ecco_ad_diff.list
1205 o pkg/ecco: fix counting cost function contributions for obcs (code
1206 by Matt M.) and diffkr for diagnostics
1207 o pkg/ecco, pkg/ctrl, pkg/grdchk:
1208 add cost penalty terms for initial uvel, vvel, eta controls
1209 and I/O for prior error files
1210 o pkg/mdsio:
1211 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1212 (new argument) to check for tiled file in mdsioLocalDir : this fix the
1213 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1214 o pkg/ctrl:
1215 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1216 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1217 unused and superfluous variables
1218 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1219 o pkg/ecco
1220 - enable adjoint of Stevens OB
1221 o pkg/ctrl/ecco/grdchk:
1222 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1223 Fortunately, we do not have any tests for the numerous cpp-flagged
1224 option of "obcs as control parameters" so we will never know
1225 if this is an improvement (but at least now things compile).
1226 - remove an obsolete initialization from ecco_cost_init_barfiles.F
1227 - fix some problems within never used ifdefs to make the code compile
1228 o pkg/obcs:
1229 - Refine Interior mask definition to work with more complex OB (e.g.
1230 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
1231 read in Interior mask from file. Check if Interior mask is consistent
1232 with OB list of indices.
1233 o pkg/seaice
1234 - beginning code for a seaice tracer package,
1235 but currently only used for seaice age: SEAICE_AGE
1236 SEAICE_num = 4
1237 iTracer = 1: area-weighted ice age
1238 = 2: volume-weighted ice age
1239 = 3, 4: template for one-year vs. multi-year ice
1240 data.seaice has new namelist SEAICE_PARM03 for arrays related to
1241 SEAICE_num
1242
1243 checkpoint62t (2011/03/05)
1244 o pkg/obcs:
1245 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
1246 then normal component. This ensures that the normal component is set
1247 correctly even when it conficts with tangential setting from an other OB.
1248 Affects results of test-experiment seaice_obcs: update the output.txt
1249 o pkg/obcs:
1250 - add code to monitor statistics of dynamical fields at OB.
1251 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
1252 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
1253 - change default: balance the Net inflow through all OB (instead of balancing
1254 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
1255 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
1256 to match Nortern OB inflow (OBCS_balanceFacN=0).
1257 o pkg/seaice:
1258 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
1259 o pkg/seaice (seaice_growth v 1.113):
1260 - reverting seaice_growth to v 1.111 in order to have code with exact bit
1261 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
1262 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
1263 runtime flag SEAICEareaFormula is kept but is inactive
1264 o model/src:
1265 - add new param to scale curvilinear grid distance and area when using
1266 a different sphere radius from the grid-files.
1267 - test/check multi-threads EXCH applied to local variable (cg2d_x)
1268 o adjoint:
1269 - enable adjoint of Stevens OB
1270 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
1271 (a bit delicate because of potentially modified adj. common block structure;
1272 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
1273
1274 checkpoint62s (2011/02/15)
1275 o pkg/seaice (seaice_growth v 1.112):
1276 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
1277 computing the ice cover tendency from effective thickness tendencies. Include
1278 Ian Fenty's formula.
1279 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
1280 SEAICEareaFormula.
1281 - simplify notations for the various d_HEFF/d_AREA terms.
1282 o pkg/gmredi:
1283 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
1284 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
1285 add a verification test-run (front_relax.bvp) to test GM_useBVP.
1286 o pkg/seaice (seaice_growth v 1.111):
1287 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
1288 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
1289 also melt ice.
1290 o pkg/seaice:
1291 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
1292 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
1293 o pkg/cheapaml:
1294 - from Nico Wienders: New version of this package.
1295 o pkg/flt:
1296 - add CPP options to prevent floats to re-enter the opposite side of
1297 a periodic domain (default: keep periodicity)
1298 o pkg/gmredi:
1299 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
1300 (needed for multi-dim advection).
1301 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
1302 o model/src:
1303 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
1304 o tutorial_tracer_adjsens
1305 - extend to NLFS and replace maskC by hFacC
1306 (change reference output accordingly)
1307
1308 checkpoint62r (2011/01/24)
1309 o testreport:
1310 - add option -deloutp (-do) to remove output file after successful run
1311 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
1312 extract exact list of procs from this file ; adjust COMMAND by
1313 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
1314 o pkg/ecco: replace old ineffective way of penalizing deviations from
1315 first guess (of obcs) with code by Matt Mazloff
1316 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
1317 exf/cal
1318 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
1319 and handle case of obcs?period == 0
1320 Not affected by these changes: There is still an inconsistency in
1321 the computation of start/endrec for the obcs variables for ALLOW_CAL
1322 defined (see comment by Menemenlis, 7-Mar-2003)
1323 - make S/R ctrl_get_gen_rec return something meaningful even if
1324 ALLOW_CAL is not defined
1325 - ctrl_getobcs?: simplify code so that it does not need to use
1326 S/R exf_swapfields
1327 o testreport:
1328 allow to test MPI with different number of processors for each experiment:
1329 create file "SIZE.h.mpi" in each build dir.
1330 Note: update of "-command" argument not yet implemented.
1331 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
1332 alleviate the need for additional 3D tapes when using
1333 the non-inear free surface in the adjoint. This is done
1334 by adding an 'update' of hfacc etc. to their current
1335 value at the beginning of forward_step.F.
1336 o pkg/seaice
1337 seaice_lsr: move stress-divergence computations out of outer pseudo-
1338 timestepping loop
1339 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
1340 up, so that the calls of the ctrl_* subroutines are really at the end
1341 of the routine.
1342 o pkg/gmredi:
1343 allow to specify a 2-D horizontal map and a 1-D vertical profil
1344 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
1345 o pkg/seaice:
1346 move lsr iterations from seaice_dynsolver to seaice_lsr.
1347 o pkg/seaice:
1348 reduce memory footprint of seaice mutldim advection tapes,
1349 by using a 2D tape independent of the generic_advdiff ones,
1350 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
1351
1352 checkpoint62q (2010/12/29)
1353 o model/src:
1354 - check horizontal grid-spacing for unset or zero/negative values.
1355 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
1356 o pkg/flt:
1357 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
1358 - precision of input and output files set according to readBinaryPrec
1359 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
1360 - initial float position from tiled file was not converted to index space
1361 (looks like a bug): fixed to make it similar to initial pos. global file.
1362 o global_ocean.cs32x15:
1363 change SIZE.h of AD set-up to get same tiling as with MPI.
1364 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
1365 o model/src:
1366 add flag to control printing of domain fields (bathymetry, hFac ...) in
1367 ini_mask_etc (call to plot_fieds_xy*).
1368 o pkg/thsice:
1369 if useEXF, some forcing fields are not valid in overlap: fixed by computing
1370 over the interior only + apply EXCH at the end (like with SEAICE advection).
1371 o pkg/mdsio:
1372 - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
1373 to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
1374 - change barrier call for safe multi-threads access to 3-D shared buffer.
1375 - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
1376 - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
1377 remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
1378 o pkg/flt:
1379 - add fourth-order Runge-Kutta integration
1380 - add basic exch2 support (only 1 facet supported so far!)
1381 o pkg/mdsio+rw:
1382 new S/R to read local (or tile independent) vector (read counterpart of
1383 mds_writevec_loc, and front-end write_glvec_rl/rs).
1384 o global_ocean.cs32x15: additional input_ad.seaice experiment
1385 that uses pkg/seaice rather than pkg/thsice.
1386 (using multidim advection for seaice)
1387 o towards more F95 syntax for array specification in namelist:
1388 - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
1389 of all verification experiments.
1390 e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
1391 was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
1392 - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
1393 o global_ocean.cs32x15: additional input.seaice experiment
1394 that uses pkg/seaice rather than pkg/thsice.
1395
1396 checkpoint62p (2010/12/17)
1397 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
1398 to THSICE_SIZE.h to avoid conflict with pkg/seaice.
1399 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
1400 allow for use of multim. advection in seaice adjoint.
1401 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
1402 - first attempt to close budgets by taking into account the freshwater
1403 flux implied by the sublimation of snow and ice. So far only the
1404 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
1405 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
1406 o eesupp/src:
1407 new S/R with new option (NML_EXTENDED_F77) to change array specification
1408 from F95 standard to commonly accepted extended F77 form.
1409 This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
1410 and to revert back to the original syntax (with -DNML_EXTENDED_F77)
1411 for less tolerant f77 compiler (e.g., pgf77, g77).
1412 o globalFiles:
1413 commented out in parameter file "data" since it's not safe with MPI
1414 (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
1415 in this case); no longer commented out in restart test (tst_2+2).
1416 o add adTapeDir to specify a special directory where adjoint tapes are
1417 written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
1418 and cannot be used together with mdsioLocalDir.
1419 o nesting pkgs:
1420 - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
1421 - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1422 - add parameter files + utils dir + output from short run on beagle.
1423 o pkg/seaice:
1424 fix seaice_growth.F store directives; update results of exp. lab_sea.ad
1425 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
1426 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
1427
1428 checkpoint62o (2010/11/25)
1429 o pkg/exf:
1430 - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
1431 o pkg/seaice:
1432 - seaice_ocean_stress: split a loop for better vectorization of the
1433 adjoint code
1434 - seaice_growth.F: fix bug in conservation of freshwater connected to
1435 capping of heff, put contribution into d_HEFFbyNEG
1436 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
1437 by something more sensible (parameters that are what their name implies)
1438 - change some defaults, so that by default exf-parameters are used for
1439 things like rhoAir, cpAir,latent/sensible heat parameters, in order
1440 to reproduce the old results, many data.seaice now contain funny values
1441 for cpAir and latent heat of sublimation
1442 o packages_readparms.F: move exf_readparms up in line so that
1443 exf-parameters are visible for other packages (e.g. seaice)
1444 o debugMode & debugLevel=2:
1445 - differentiate between debugMode & debugLevel=2:
1446 debugMode: controls printing of debug messages (sequence of S/R calls).
1447 debugLevel: controls printing of algorithm intermediate results and stats.
1448 - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
1449 => allows to print debug-stats without all sequence of call messages.
1450 - switch control of debug print from debugLevel to debugMode in many S/R.
1451 o pkg/obcs (obcs-sponge):
1452 fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
1453 call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
1454 o pkg/generic_advdiff:
1455 - record overlap minimum size for each advection scheme;
1456 - refine criteria on overlap minimum size;
1457 - check and stop (in gad_check) if overlap size is too small.
1458 o pkg/obcs:
1459 - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
1460 once, in ptracers_implicit.F)
1461 - with seaice: remove test on empty file name in obcs_apply_seaice (always
1462 apply OB values when tile has OB)
1463 o model/src, coriolis setting:
1464 - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
1465 useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
1466 files (selectCoriMap=3) with any grid.
1467 - add parameter "fPrime" for constant second Coriolis coeff (default=0).
1468 o pkg/seaice/seaice_growth.F:
1469 a few cosmetic changes that reduce the number of lines of code
1470 o pkg/obcs: add boundary conditions following Stevens (1990)
1471 - the code follows old MOM/NAOSIM code
1472 - so far it is only implemented for the eastern and western boundaries
1473 and NOT for pTracers
1474 o pkg/rbcs:
1475 - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
1476 beginning of the first rbcs forcing period.
1477 - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
1478 offline package, i.e., one file per time, labeled by iteration number;
1479 deltaTrbcs sets the timestep with which the data was generated;
1480 rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
1481 - rbcsForcingCycle=0 makes forcing non-cyclic.
1482 - make arithmetic safe for negative times and odd forcing periods.
1483
1484 checkpoint62n (2010/11/09)
1485 o pkg/seaice:
1486 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
1487 o pkg/obcs:
1488 New S/R to copy tracer value from the OB location to narrow band region
1489 (width = same as overlap) beyond the OB: preserve OB value (needed for
1490 high-order scheme) which were overwritten by EXCH call if in overlap
1491 region. Applied to theta, salt, ptracer and advected seaice variables.
1492 With seaice: use maskInC in similar way as in gad_advection.F,
1493 in seaice_advection.F and advect.F.
1494 Update output of experiment seaice_obcs and change exp4 to test OBCS with
1495 4th order Adv.Scheme. for pasive salt and ptracer.
1496 o tools/genmake2:
1497 - when looking for an optfile (not specified), only search for Fortran compiler
1498 (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
1499 - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
1500 (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
1501 - set default for CPP to "cpp -traditional -P" (was the case without specifying
1502 an optfile, but otherwise default was just "cpp".
1503 - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
1504 - when "CC" is not set in the optfile, look for possible C compiler
1505 (instead of just setting CC=cc)
1506 - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
1507 => add a ".F" to ".o" rule for source files with no "#include" (such as
1508 port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
1509 - move gfortran before g77 in list of possible Fortran compiler (consistent
1510 with reference compiler switch from g77 to gfortran)
1511 o pkg/seaice:
1512 o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
1513 seaice_check that stops the model, when the CPP flag is used.
1514 o seaice_growth.F: make capping of ice volume conserving by returning the
1515 capped ice as freshwater to EmPmR. This does not change the verification
1516 experiments but will change runs where the capping is acutally active
1517 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
1518 (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
1519 global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
1520 lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
1521 o tools/genmake2:
1522 - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
1523 - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
1524 - clean previous genmake log files before anything else.
1525 - change Makefile to remove testreport log files (*.tr_log) and genmake log
1526 files only with "CLEAN" target (instead of "Clean");
1527 o pkg/generic_advdiff:
1528 Change OBCS in multiDim advection (gad_advection.F):
1529 Use maskInC to prevent intermediate update of tracer-field in OB regions,
1530 thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
1531 which were applying future time-step OB values.
1532 This way, all explicit calculations use current-time-step OB values
1533 (simpler and more consistent).
1534 Affects results when set-up uses time-varying OBC and multi-dim advection;
1535 update output of experiment seaice_obcs.
1536 o pkg/seaice:
1537 move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
1538 this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
1539 SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
1540 Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
1541 but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
1542 unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
1543 o pkg aim (2010/10/26):
1544 - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
1545 formulation with obliquity, eccentricity, ... as run-time parameters,
1546 - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
1547 upward shortwave radition at the surface (all-sky and clear-sky).
1548 o pkg/obcs:
1549 - writing sections with globalFiles=T does not work: switch to tiled-files
1550 when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
1551 - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
1552 - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
1553
1554 checkpoint62m (2010/10/21)
1555 o pkg/seaice: vectorize seaice_solve4temp.F
1556 - move iterations loops outside of i/j-loops
1557 - requires 2D arrays for TB and effConduct
1558 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
1559 modified in this routine
1560 - a little bit of clean up, adjusting indentation, etc.
1561 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
1562 performance and '**TWO' by '**2' (because TWO is a float),
1563 replaced ONE, ZERO
1564 o eesupp/src:
1565 fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
1566 o pkg/seaice/seaice_growth.F
1567 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
1568 merging process. The merged routine has two branches, and one activates the 'evolution'
1569 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
1570 In summary, here is what the '10/10 revision' did consist of
1571 part 1: seaice_growth.F revisions 1.71 to 1.75
1572 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
1573 The emphasis here was on improving readability (e.g. by trying to use meaningful
1574 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
1575 part 1.5:
1576 - revising the lab_sea experiment to make it a more useful (i.e. stable
1577 and representative of an actual model run). This was done by generating a
1578 (winter) pickup to start from, switching back the main experiment dynamic
1579 solver from evp to lsr, having one of the experiments use the free drift solution.
1580 part 2: seaice_growth.F revisions 1.76 to 1.85
1581 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
1582 - Sorting out the various fields units and sign (set early on and reset at the end)
1583 to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
1584 fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
1585 - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
1586 and simplifying logical expressions to further improve readibility.
1587 part 3: seaice_growth.F revisions 1.86 to 1.89
1588 - Re-organize the blocks of code more logically.
1589 - Merging the '_if.F' pieces that add something new.
1590 o pkg/thsice:
1591 - vectorize thsice_solve4temp and thsice_get_exf.
1592 Problem: thsice_solve4temp has an unvectorizable statement that
1593 might also be problematic for TAF
1594 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
1595 does not change the verifcation experiment, but will change all
1596 experiments that have this flag undefined (not tested in verification);
1597 a little reorganization to save a few 2D fields and recomputations
1598 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
1599 - 2nd step: fix some store dirs
1600 o seems to work somewhat, i.e. using ifort but not g77
1601 o likely cause are incomplete init. or recomputation
1602 o start verification/global_ocean.cs32x15/input_ad.thsice
1603 o pkg/obcs: add support for exch2
1604 - the position of the boundary and prescribed values are specified using
1605 a global domain with exch2 facets stacked
1606 - in x for N,S boundaries (like W2_mapIO=-1)
1607 - in y for E,W boundaries (so E,W boundaries do not overlap)
1608 o pkg/mdsio: add support for writing global sections with exch2
1609 file layout is as for obcs described above:
1610 - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
1611 - for y-z sections, facets are stacked in y
1612 o pkg/thsice:
1613 - change a few routines for better vectorization: thsice_albedo.F,
1614 thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
1615 not affected, but in particular the latter routine has changed
1616 dramatically (not necessarily easier to read now).
1617 - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
1618 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
1619 o verification/lab_sea:
1620 - overhaul of the forward model experiments. The main motivation
1621 for this revision is that lab_sea has proven quite fragile (when
1622 changing the sea-ice code, and switching platforms) to a point
1623 when failures were very hard to attribute to specific code problems.
1624 - the suspected reason for this fragility is noise amplification by evp so,
1625 to start with, we decided to replace evp with lsr in the main experiment.
1626 - the input.lsr experiment thus became obsolete and was removed.
1627 - it was replaced with the input.fd experiment that uses an
1628 analytical "free drift" solution as the ice velocity field.
1629 - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
1630 will hopefully allow us to discriminate problems due to dynamic solvers
1631 from problems due to the thermodynamic code. input.salt_plume (lsr) allows
1632 us to test additional options, along with the salt plume package.
1633 - Finally a pickup was generated (at the end of a one year run) to
1634 make the tests more representative of an actual model run. Previously
1635 the tests starting point was a 1m thickness of ice everywhere.
1636 o pkg/seaice:
1637 - introducing S\R seaice_freedrift.F that compute the
1638 analytical solution to an approximate ice momentum
1639 equation (i.e. the simple stress/coriolis balance).
1640 - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
1641 of the free drift velocity field, and enable its use.
1642 To actually use the free drift solution as the model ice
1643 velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
1644 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
1645
1646 checkpoint62l (2010/10/04)
1647 o pkg/seaice:
1648 -fix the USE_ORIGINAL_SBI version (for variable freezing point);
1649 -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
1650 version (with USE_ORIGINAL_SBI undef);
1651 o add hooks for new packages OASIS, the package will follow
1652 (hooks exclude the seaice pkg for now)
1653 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
1654 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
1655 rather than mdsio_readvector.F/mdsio_writevector.F, within
1656 adread_adwrite.F to read/write adjoint-related tapes to disk.
1657 o eesupp and pkg/mdsio: ALLOW_WHIO
1658 Option to write/read 2D fields to files including tiles halos.
1659 The main purpose is for adjoint related "tape I/O".
1660 The secondary purpose is for debugging phases.
1661 A word on those rather specifically intended purposes.
1662 The code was meant to be stripped down to the bare minimum.
1663 Typically, there is a unique and basic mapping to the global
1664 buffer (tile by tile, then proc by proc, then level by level), and
1665 byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
1666 meant to generate user friendly outputs of various shapes and forms.
1667 Rather it is intended, for the knowledgeabale developers,
1668 to be largely independent of the many mdsio options, to allow
1669 outputs of tiles+halos in debugging phases and in adjoint runs,
1670 and to allow some flexibility in tuning (adoint) I/O depending on each
1671 file system behavior. With regard to tuning, most of the potential knobs
1672 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1673 to specify directories, to specify the typical size of I/O calls, etc.)
1674 are not yet included, and will be added if they prove useful.
1675 o pkg/seaice:
1676 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1677 o pkg/seaice:
1678 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1679 code (seaice_budget_ice_if.F) which enable to recover old standard
1680 code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1681 temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1682 o model/src (rStar):
1683 use simple average (not area weighted) of rStarFac at U,V point when using
1684 vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1685 update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1686
1687 checkpoint62k (2010/09/17)
1688 o adjoint
1689 * changed verification/global_ocean.cs32x15 ; adjoint now tests
1690 Adams-Bashforth 3 + NLFS + RSTAR
1691 * some more modifs required for ECCO-GODAE v4
1692 o pkg/seaice
1693 add SEAICE_AGE_VOL option to use volume instead of area for
1694 integrating SEAICE_AGE
1695 o model/src:
1696 first check-in of sigma & hybrid-sigma coordinate code ; also includes
1697 non-linear free-surface parts ; but pressure-gradient not yet coded.
1698 o pkg/ptracers:
1699 option for ptracer to convert Salt Relax into additional EmP.
1700 tested in exp. global_ocean.90x40x15.dwnslp (update output)
1701
1702 checkpoint62j (2010/08/25)
1703 o pkg/ggl90:
1704 other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
1705 o pkg/dic: car_flux.F, phos_flux.F
1706 - reduce number of exp-calls in order to improve performance
1707 - clean up a little (replace fields by their macros, etc., fix
1708 typo in CPP-flag)
1709 o pkg/ggl90: minor changes
1710 - GGL90diffKrS was removed --> always use GGL90diffKr
1711 - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1712 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1713 (commented out for now)
1714 - change in max/min operations to ensure that smoothing is ok
1715 - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1716 - always use diffKrNrT as background profile (i.e. never use diffKr field)
1717 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1718 o pkg/dic:
1719 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1720 vectorization
1721 - small bug fix in insol for the unlikely case of a cartesian grid
1722 - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1723 + now vectorize, which also removes adjoint recomputations;
1724 + replace integer maksp1 by _RL maskp1
1725 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1726
1727 checkpoint62i (2010/07/21)
1728 o pkg/flt:
1729 - with OBCS: stop floats which enter the OB region
1730 o model/src:
1731 - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1732 for implicit vertical advection.
1733 o pkg/seaice:
1734 - account for melting in seaice age evolution.
1735 - remove double counting of seaice ridging effect on seaice age.
1736
1737 checkpoint62h (2010/06/18)
1738 o pkg/exch2:
1739 - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1740 o tools/genmake2
1741 - remove "-pdefault" option: redundant with the use of "packages.conf";
1742 - remove file pkg/pkg_default : set the default as a pkg group
1743 ("default_pkg_list") defined in pkg/pkg_groups;
1744 - fix for case pkg/pkg_depend is missing (was hanging before);
1745 - add option "-pgroups" to specify a different pkg_groups than the default.
1746 o verification/adjustment.cs-32x32x1:
1747 add a "minimal" set-up test (code_min & input_min) which only compiles
1748 eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1749 o tools/genmake2
1750 - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1751 - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1752 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1753 files are nearly the same anyway.
1754 Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1755 - redefinition of tau(i,i) (by a factor of ustar)
1756 - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1757 - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1758 - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1759 - replace
1760 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1761 shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1762 by
1763 shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1764 (changes results)
1765 -> exf_bulkformulae v1.22,
1766 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1767 (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1768 output.txt 1.63
1769 offline_exf_seaice: output.seaicetd.txt 1.7
1770 seaice_obcs: output.txt 1.10)
1771 Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1772 -> exf_bulkformulae v1.23,
1773 unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1774 and global_ocean.cs32x15.icedyn (only 11 matching digits)
1775 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1776 o adjoint of exch-1:
1777 - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1778 (note: was already like this when using EXCH-2) and remove flow dir
1779 and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1780 - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1781 - update pkg/exch2 diff list.
1782
1783 checkpoint62g (2010/05/19)
1784 o eesupp/src (exch-1):
1785 - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1786 and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1787 (renamed to exch1_*rx_cube.F).
1788 - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1789 to call new exch1 S/R ; update Makefile and .cvsignore.
1790 - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1791 exch2_xy_rx later)
1792 Note: after updating your code, need to run "make clean" in eesupp/src
1793 o test experiment bottom_ctrl_5x5:
1794 new output_adm.txt with fewer grdchk & less monitor output.
1795 o model/src:
1796 remove the call to ini_cori in initialise_varia.F (just keep the usual one
1797 in initialise_fixed.F). More consistent with coriolis & horizontal grid
1798 beeing treated in the same way (ini_grid is not called a 2nd time).
1799 o pkg/exf:
1800 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1801 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1802 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1803 - cosmetic changes to exf_bulkformulae.F to make it look more like
1804 exf_bulk_largeyeager04.F
1805 o eesupp/src (exch-1):
1806 - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1807 - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1808 array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1809 (even without using MPI).
1810 - Message mode: move RecvAck setting (indicator of buffer being ready)
1811 from send_put to recv_get S/R (was useless before, but not sure if
1812 it's much more useful now);
1813 - Switch the order of sync: MPI-proc 1rst and then threads;
1814 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1815 - fix AD code for communication mode ='get' (but not used).
1816 o model/src:
1817 initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1818 not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1819 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1820 o pkg/ctrl: require a specific set of control variables and exf-flags for
1821 adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1822 o model/src:
1823 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1824 1rst forward sweep, to avoid over-writing output files during recomputations
1825 recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1826 b) 2nd version:
1827 - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1828 - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1829 writePickupAtEnd) + seaice & ptracers output;
1830 - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1831 o model/src:
1832 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1833 o pkg/exch2:
1834 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1835 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1836 o pkg/autodiff & exch2:
1837 process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1838 (for now, only if ALLOW_EXCH2 is defined).
1839 o pkg/autodiff:
1840 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1841 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1842 + clean-up comments (_RS is not always real*4)
1843 - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1844 - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1845 was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1846 o testreport (AD-tests):
1847 no longer link files from dir "../input" (1rst link files from
1848 "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1849
1850 checkpoint62f (2010/04/29)
1851 o model/src/the_main_loop.F:
1852 adjust store directives for seaice evp and multicategory according to
1853 pkg/ecco/the_main_loop.F
1854 o adjoint:
1855 global_sum_ad was incomplete (noted many times by many people ;)
1856 nice description by Jean U. as follows:
1857 * allreduce(var) in global_sum.F can be interpreted as
1858 reduce(sum) followed by broadcast of sum.
1859 * The adjoint of that is
1860 sum(adjoint) followed by broadcast(summed adjoint value)
1861 or in other words, allreduce(sum, adjoint vars)
1862 We were missing the sum(adjoint)!
1863 Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1864 (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1865 The fix should produce 16-digit accuracy between
1866 single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1867 multi-CPU single-tile (e.g. nSx=1, nPx-2)
1868 We'll probably change this yet again shortly
1869 o eesupp/src:
1870 - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1871 o pkg/icefront
1872 - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1873 specification of addmass array based on a 2D field, which is added
1874 at bottommost wet level at each horizontal location.
1875 o model/src:
1876 horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1877 layout; (not always compatible with delX,delY setting; commented out for now).
1878 o pkg/exch2:
1879 change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1880 (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1881
1882 checkpoint62e (2010/04/15)
1883 o pkg/obcs:
1884 - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1885 o pkg/dic:
1886 -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1887 (note: not presently tested in any forward verification exp.)
1888 update tutorial_global_oce_biogeo AD output file.
1889 o pkg/exf:
1890 - account for the variation of albedo as a function of zenith angle
1891 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1892 o build_options:
1893 - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1894 o pkg/dic:
1895 change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1896 - use binary pickup file for restart;
1897 - initialise atmos-CO2 box from dic_pCO2 parameter;
1898 - fix multi-threaded.
1899 o pkg/rbcs:
1900 - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1901 change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1902 - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1903 and update output.txt
1904 o pkg/kpp:
1905 - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1906 - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1907 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1908 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1909 - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1910 KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1911 o pkg/offline:
1912 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1913 (bug was added in version 1.10 on 2007-08-23).
1914 o pkg/offline:
1915 - no need to specify periodicExternalForcing, etc ... to use offline pack
1916 - offline input files no longer just single prec --> parameter offlineLoadPrec
1917 o verification/lab_sea:
1918 change AD test to multi-tile setup and update all 4 AD output.
1919 NOTE: while cost function values remain very similar,
1920 gradients are very different, although gradient checks are self-consistent
1921 Should try to get to the bottom of this (cost function summation order?)
1922 o pkg/dic:
1923 in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1924 a weakness of TAF that drops part of double precision in log10 derivative.
1925 <= changes removed since problem has been fixed in current TAF version 1.9.71
1926 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1927 o pkg/ecco:
1928 add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1929 update all 4 lab_sea AD output.
1930
1931 checkpoint62d (2010/03/22)
1932 o build_options:
1933 remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1934 o remove unbalanced quote (single or double) in commented line of source code
1935 (may cause some warning with some preprocessor/makedepend versions).
1936 o pkg/seaice:
1937 fix seaice_model.F for adjoint (gael) and update AD results of experiments
1938 lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1939 o testreport:
1940 add option '-runonly' (short: '-ro') to just do the run part (without make).
1941 o eesupp: remove JAM communication code (obsolete).
1942 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1943 (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1944 to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1945 (update also the output).
1946
1947 checkpoint62c (2010/03/02)
1948 o tools/build_options :
1949 move (some) old optfiles from build_options/ to build_options/unsupported/
1950 o model/src and pkg/exf
1951 surface relaxation -- separating data and data.exf options
1952 The point is to ensure that we specify the surface relaxation
1953 either in data or in data.exf (but not half and half) and to
1954 avoid an accidental relaxation to 0 (which happened if a time
1955 scale was specified but the file name was left empty)
1956 o model/src model/inc and pkg/mom_common
1957 ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1958 => addition to the viscosity field as computed by others schemes
1959 o tools/build_options:
1960 - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1961 but keep the former optfile for few weeks for smooth transition
1962 o pkg/ecco
1963 - allow user defined cost function contributions
1964 CPP: ALLOW_USERCOST_CONTRIBUTION
1965 USAGE: compute contributions in cost_usercost_all.F
1966 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1967 the two options are complementary.
1968 o pkg/smooth
1969 - migration from contrib to the main repository
1970
1971 checkpoint62b (2010/01/26)
1972 o pkg/monitor:
1973 - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1974 (in case someone forgot to update customized pieces of code)
1975 o nonHydrostatic:
1976 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1977 - add a simple 2-D experiment (short_surf_wave) to test it.
1978 o pkg/icefront:
1979 adding the shell of, and the hooks to, a new package that
1980 will model melting and freezing of vertical glacier ice fronts
1981 o momentum:
1982 add diagnostics of momentum tendency from Hydrostatic pressure gradient
1983 (without surf.pressure term: would need a 2nd filling since implicit term).
1984 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1985 two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1986 cannot deal with the former
1987 o cleaning:
1988 - remove all (except OpenAD) old TLM output from results_ad dirs.
1989 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1990 - comment out maskH definition (replaced by maskInC)
1991 o pkg/monitor:
1992 - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1993 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1994
1995 checkpoint62a (2010/01/15)
1996 o model/src:
1997 - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1998 o pkg/diagnostics:
1999 - add optional level number diagnostics (i.e., level number to be define
2000 explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
2001 - strictly check for valid parser-code(10) ;
2002 - check if adding diag to the list from the right place.
2003 o pkg/longstep:
2004 - change parameters and fix tracer conservation with rstar/nonlinear free surface
2005 o diagnostics:
2006 - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
2007 S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
2008 o pkg/diagnostics:
2009 - Add option for writing vertical integral (sum of selected levels) of an output
2010 field instead of writing output field levels. Activate this option on a per
2011 output-file basis, by setting the 2nd character of fileflag to 'I'.
2012 - Add field-specific information relative to level integral in 3rd postion
2013 of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
2014 vertically (x level-thickness x hFac), "r"=same but without hFac.
2015 o do_the_model_io:
2016 - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
2017 in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
2018 writing pickups and stopping.
2019 o pkg/diagnostics (for now, only with mdsio):
2020 - write time information to meta file (and modify accordingly rdmds.m) :
2021 time-averaged diagnostics output: write starting and ending time of the
2022 time-averaging interval ; snap-shot diagnostics output remains unchanged;
2023 o pkg/timeave:
2024 - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
2025 always Nr), now assumed to be equal to number of levels of averaged field;
2026 only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
2027 o pkg/sbo:
2028 - fix ocean bottom pressure global-average & 2-D time-ave output (was
2029 neither initialised nor filled).
2030 - add starting iteration in suffix of global-average output file
2031 (to avoid over-writing the file after a restart)
2032 - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
2033 o time-average:
2034 - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
2035 (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
2036 ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
2037 this fix DIC_COST cumulative-time array (previously: bi,bj,k)
2038 - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
2039 - fix missing accumulation for pkg/opps.
2040 - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
2041 (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
2042 - fix initialisation of time-ave vars and do only full time-step increment
2043 (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
2044 o pkg/layers:
2045 - use standard RW pkg S/R to write the output
2046 and remove local write_fld version (which had a problem).
2047 - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
2048 - fix LAYERS_CALC argument list.
2049 o pkg/timeave:
2050 - store cumulative-time in a simple tiled array (drop the level index)
2051 - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
2052 o pkg/ocn,aim_compon_interf
2053 - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
2054
2055 checkpoint62 (2009/12/23)
2056 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
2057 (was not previously tested in any other exp.)
2058 o pkg/monitor:
2059 - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
2060 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
2061 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
2062 - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
2063 - change del2 calculation.
2064 - use interior masks (instead of maskH, <- to be remove).
2065 - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
2066 o mask & obcs:
2067 - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
2068 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
2069 (called after packages_init_fixed)
2070 o pkg/obcs:
2071 - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
2072 Fixes bug in obcs+exf with nSx*nSy.GT.1
2073 - fix multi-tile handling in obcs balance code
2074 o nonHydrostatic:
2075 - Implement AB-3 for non-hydrostatic vertical momentum ;
2076 (change ordering of var. stored in pickup file when using NH)
2077 - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
2078 - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
2079 (in prep. for new NH free surface form).
2080 o pkg/obcs:
2081 add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
2082 o model/src:
2083 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
2084
2085 checkpoint61z (2009/12/01)
2086 o nonHydrostatic:
2087 Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
2088 a spurious source of energy in simple baroclinic adjusment test case.
2089 Update all non-hydrostatic exp output.
2090 o model/src (3-d solver):
2091 Change again 3-D solver free-surface RHS term when exactConserv=T:
2092 simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
2093 (which was not the case with previous formulation).
2094 To recover previous version, just reset "oldFreeSurfTerm" to previous value.
2095 Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
2096 o nonHydrostatic:
2097 - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
2098 for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
2099 - change 3-D solver to work with r* (for now, only with linear free-surf.)
2100 - add few debug diagnostics (cg3d_x, residual)
2101 o model/src:
2102 fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
2103 update output of exp. global_ocean.cs32x15.viscA4
2104 o update output of exp. global_ocean.cs32x15.icedyn after removing
2105 #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
2106 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2107 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
2108 for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
2109 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
2110 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
2111 runtime flag useSRCGSolver. Modify verification experiment global_with_exf
2112 to test this code
2113 o pkg/cd_code:
2114 Change defaut D-grid time-stepping to get the same for D-grid momentum as for
2115 C-grid momentum. D-grid velocity used to be stepped forward in time with
2116 Adams-Bashforth only on surface pressure term. Tests show that using AB on
2117 D-grid coriolis term improves stability (as expected from CD-scheme paper).
2118 To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
2119 Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
2120 lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
2121 tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
2122 Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
2123 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
2124 o pkg/obcs:
2125 - fix bug in initialisation (broken since Oct 1rst modification)
2126 for useOBCSprescribe without useEXF.
2127
2128 checkpoint61y (2009/11/15)
2129 o pkg/seaice
2130 - change (once again) the discretization for the evp solver: rather than
2131 squaring the averages of strain rates, average the squares to give
2132 a better approximation to VP behavior (in simple test); this breaks
2133 verification experiments that use EVP (lab_sea and lab_sea.hb87)
2134 --> update outputs
2135 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
2136 to improve vectorization of adjoint code on TARGET_NEC_SX
2137 o verification/vermix:
2138 - change vermix to a more "classical" 1d column with high vertical
2139 resolution, seasonal heat flux forcing and constant wind forcing
2140 --> update outputs
2141 o pkg/seaice
2142 - fix diagnostics of principal stress components for EVP
2143 - add optional diagnostics of non-linear convergence for LSOR solver
2144 - make maximum zeta a runtime parameter
2145 o model/src (3-d solver):
2146 Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
2147 which consisted in removing the Surf. Non-Hydrostatic pressure from the
2148 whole column and adding it to Eta (inspired from Casualli, 1999):
2149 Only affects 3-D solver initial guess and only if using ExactConserv,
2150 but tests did show a degradation of solver convergence. For this reason,
2151 decide to disable this piece of code.
2152 to recover previous version, just set zeroPsNH = exactConserv (line 78).
2153 Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
2154 o pkg/ggl90:
2155 - fix previous modif (unfortunatly has not been documented here).
2156 o pkg/seaice/autodiff:
2157 - add CPP flag to include clipping of zeta in EVP code;
2158 although clipping of zeta is not necessary for EVP and not recommended
2159 it was done by default, now clipping is disabled by default
2160 - modify computation and store zetaC/Z in seaice_evp for TAF
2161 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
2162 - change seaice_calc_viscosities/strainrates for better
2163 vectorization after AD by TAF
2164 - rearrange common blocks in SEAICE.h once again for easier dumps of
2165 adjoint output, adjust adcommon.h and g_common.h
2166 - change flux form of default advection scheme for better vectorization
2167 of adjoint code
2168 - modify lab_sea/input.lsr to test the flux form of default advection
2169 scheme
2170 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
2171 transition in checkpoint61r)
2172
2173 checkpoint61x (2009/10/19)
2174 o adjoint: adding two new verification experiments
2175 * tutorial_global_biogeo: an online dic sensitivity experiment
2176 (work with G. Forget)
2177 * tutorial_dic_adjoffline: an offline dic sensitivity experiment
2178 (an update of the Dutkiewicz et al., 2006 paper)
2179 Both use the same CO2FLUX cost function, but different controls
2180 Gradient checks look good, but some recomp. could still be traightened out
2181 Should add xx_dic control variable to test at some point
2182 o model/src:
2183 add run-time parameters to check and/or mask initial Temp & Salt
2184 o pkg/ptracers:
2185 apply zonal filter (if used) to all passive tracers
2186
2187 checkpoint61w (2009/10/12)
2188 o adjoint:
2189 * update and finish work on adjoint of dic package (G. Forget)
2190 * start adjoint of offline package
2191 * bug fix for cube-sphere TLM code (active_file_g.F)
2192 o tutorial_global_oce_optim:
2193 now tested with 4 tiles (change data.grdchk and update output_adm.txt)
2194 and add SIZE.h_mpi for MPI testing
2195 o pkg autodiff
2196 - fix bug in autodiff_restore
2197 - make genmake2 remove comments and empty lines from ad_input_code.f in
2198 order to reduce file size (new script file remove_comments_sed)
2199 o allows to specify vertical profile of vertical viscosity (viscArNr)
2200 o pkg autodiff
2201 autodiff_ini_model_io: comment out writing of grid information to netcdf
2202 files, because at this time the grid fields are a bunch of zeros
2203 (this is analogous to ini_mnc_vars.F)
2204 o pkg seaice/autodiff:
2205 left-over from removing the 3-time-level fields:
2206 - small rearrangement of common blocks (SEAICE.h)
2207 - fix field declaration in order to get meaningful output in
2208 adseaice.*.nc (adcommon.h)
2209 o pkg obcs:
2210 - go through NH code only if nonHydrostatic=T
2211 - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
2212 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
2213 => Update output of experiment seaice_obcs
2214 - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
2215 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
2216 - fix restart for useOBCSprescribe + useEXF
2217 o pkg ctrl
2218 - make obcs as control parameter work also with useSingleCPUio
2219 - replace a few sny and snx by Ny and Nx to be consistent with
2220 ctrl_set_globfld_x/yz.F
2221 o pkg seaice
2222 - re-introduce global field frWtrAtm for the case of
2223 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
2224 - catch the case of an empty filename in seaice_cost_init_fixed.F
2225 o pkg ecco:
2226 - small bug fixes in the_main_loop
2227 . fix order of monitor arguments
2228 . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
2229 . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
2230 that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
2231 - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
2232 imbalance diagnostics for wmean_h/sflux = 0
2233 - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
2234 - catch the case of empty filenames in ecco_cost_init_fixed.F
2235 and ecco_readparms.F
2236 - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
2237 to make this statement meaningfull in ecco_cost_weights.F
2238 o pkg zonal_filt:
2239 - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
2240 - when using rStar, filter uVel*hFacW instead of uVel
2241 (tested without topography: fix a Pb of growing instability with NLFS)
2242 o pkg/aim/thsice:
2243 -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
2244 (works as SST restoring)
2245 o pkg/thsice:
2246 -add specific parameter for salt restoring in slab mixed-layer
2247 (by default equal to the temperature restoring)
2248
2249 checkpoint61v (2009/09/21)
2250 o pkg/kpp:
2251 -add double diffusive contributions as a hack, turned off by default
2252 for now, and the code can be excluded with a CPP-flag
2253 EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
2254 -add a verification experiments to "vermix" to test this code
2255 o pkg/mom_common:
2256 Move computation of length scales to mom_init_fixed.F (avoid recomputation
2257 at each time-steps*levels).
2258 o pkg/layers:
2259 Created a new package for computing volume fluxes in temperature or
2260 [not yet implemented] density layers, e.g. for calculating residual
2261 overturning circulations.
2262 o pkg/diagnostics:
2263 implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
2264 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
2265 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
2266 To avoid mixing type (RS/RL) of input/output array argument,
2267 replace single mixed-type array with a pair from each type (RS/RL).
2268 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
2269 is now implemented for all pkgs (previously only done for the main pickup)
2270
2271 checkpoint61u (2009/08/25)
2272 o pkg/obcs:
2273 - change OB?eta from _RS to _RL and put them into a separate commen block
2274 - add code to read OB?eta from a file via obcs_prescribe_read: the code
2275 compiles and does not destroy any other experiments, the data is read
2276 properly, but the code is not tested in actual applications
2277 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
2278 create a meaningful unit attribute for the time coordinate variable
2279 o pkg/ebm: add plenty of missing "_d 0" ;
2280 update results of experiment global_ocean_ebm (fwd + adjoint tests)
2281 Notes: several pieces of code only works for (very) specific set up
2282 (domain size, lat range, etc ...); should be documented & stop if one
2283 of those assumptions is not meet.
2284 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
2285 update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
2286 and offline_exf_seaice (seaicetd + adjoint).
2287 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
2288 update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
2289 seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
2290 o few changes to pass when compiling with strick checking of arguments
2291 across S/R (allow to find few bugs in S/R calls).
2292 o pkg/seaice:
2293 - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
2294 2d-fields, for slightly better performance
2295
2296 checkpoint61t (2009/07/22)
2297 o pkg/seaice:
2298 - remove unused variables in seaice_evp
2299 - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
2300 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
2301 named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
2302 each processor opens a different file (a fix from Matt).
2303 o cg2d:
2304 use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
2305 this reduces number of EXCH calls by 2 when using exch2.
2306 For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
2307 directives and missing simple EXCH (exch_s3d_rx) adjoint code.
2308 o pkg/thsice:
2309 add code for Near Infra-Red albedo (from Jeff)
2310 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
2311 o ini_model_io:
2312 move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
2313 MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
2314 to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
2315
2316 checkpoint61s (2009/06/30)
2317 o pkg/exch2 (exch2_rxN_cube*):
2318 remove last BARRIER (no need to synchronise after getting data from shared
2319 buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
2320 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
2321 and generate new output (for the 2 tests) using default rotationPeriod.
2322 o pkg/exch2:
2323 - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
2324 (was already the case with AUTODIFF_EXCH2 defined)
2325 - add bj in exch2 arrays and S/R.
2326 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
2327 MLAdjust to exch2 (identical results except with MPI -> truncation diff);
2328 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
2329 - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
2330 GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
2331 - verification experiment natl_box.longstep
2332 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
2333 allow different versions of ifort (8 or 9) and different versions
2334 of mpi (mpich or mpich2) to be used with the same optfile.
2335 requires to load a netcdf module and set MPI_INC_DIR (see comments inside
2336 optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
2337 o pkg/seaice:
2338 fix previous modif (3-level field removed) for old-pickup reading
2339
2340 checkpoint61r (2009/06/25)
2341 o pkg/seaice:
2342 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
2343 1. introduce fields for time step (N-1)
2344 2. do not use levels 2 and 3 anymore (but keep them)
2345 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
2346 includes changes to pkg/thsice/thsice_get_velocity.F,
2347 model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
2348 pkg/obcs/obcs_apply_uvice.F.
2349 - completely remove code for leap-frog time stepping for second order
2350 advection
2351 - adjusted adjoint accordingly;
2352 gradient checks have improved by an order of magnitude!
2353
2354 checkpoint61q (2009/06/22)
2355 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
2356 - the boundary conditions along open boundaries are unclear, because the
2357 associated masks are set to zero and are thus treated as closed when
2358 applying the slip-boundary conditions.
2359 - move initialisation of grid variables from seaice_init_varia to _fixed
2360 o adding doc/diags_changes.txt
2361 o model/src:
2362 do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
2363 to avoid "_diags" naming if no relation to pkg/diagnostics.
2364 ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
2365 file and only call PLOT_FIELD_XYZ if debugMode=T.
2366 remove few PLOT_FIELD_XY calls outside initialisation.
2367 remove few unnecessary BARRIER.
2368 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
2369 of salt_plume package in Southern Ocean
2370 o pkg/thsice:
2371 - fix hOceMxL in overlap (needed for sea-ice advection);
2372 update output of experiment global_ocean.cs32x15.icedyn.
2373 o pkg/seaice:
2374 - make the (placeholder-)tracer IceAge a little more meaningful
2375 by avoiding ridging of age due to convergent ice flow
2376 - add diagnostics for surface temperature, atmospheric and oceanic
2377 heat flux, and atmospheric and oceanic ice growth
2378
2379 checkpoint61p (2009/06/10)
2380 o eesupp (global_max & global_sum):
2381 - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
2382 - remove starting & endding barrier (no longer needed)
2383 o pkg/mdsio, writelocal:
2384 works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
2385 (remove the STOP): uses shared buffer IO to store data from all threads
2386 and then let master-thread write nThreads tiles.
2387 o pkg/mdsio (read/write field):
2388 - tiled IO done in 1 piece (all levels at a time);
2389 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
2390 - multi-threaded: allow to read/write local (non-shared) array
2391 (was already working with singleCpuIO ; now works also without);
2392 => no longer needs barrier call after reading a file (added inside
2393 mds_read/write field).
2394 - move barrier calls outside gather/scatter_2d to mds_read/write_field
2395 o pkg/obcs/exf
2396 - exf_getffieldrec.F: add a few ". _d 0" and
2397 add code to catch the case fldperiod = 0.
2398 - obcs_precribe_read.F: change if statements so that they match
2399 the variable type (_RL)
2400 - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
2401 exf_iprec) as part of namelist EXF_NML_01
2402 o pkg/mdsio:
2403 - read/write tiled (local) files: read/write 1-level tile chunk at a time
2404 (instead of segment of length sNx); expected to speed up tiled IO.
2405 o pkg/exch2:
2406 - take buffer copy from/to array out of S/R exch2_send/recv into new
2407 S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
2408 (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
2409 - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
2410 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
2411 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
2412 including Topology header file (and common blocks).
2413 - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
2414 remove 2nd exch call in exch2_s3d_rx (no longer needed).
2415 - document S/R arg. list (+ update some comments)
2416 o pkg/seaice:
2417 - added SEAICE_CLIM_AIR code, which permits modulation of surface air
2418 temperature and humidity over sea ice based on climatological values.
2419 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
2420 of LSR (this change is expected to change the results slightly because now
2421 it uses slightly difference moduli from the second last LSR solution, but
2422 that is more consistent with the stress computations; this part of the code
2423 is not tested in the verification experiments)
2424 - fix diagnostics for flux of ice in case of B-grid
2425 - turn strain rates eij and press into global fields within global
2426 common block in SEAICE.h for more straighforward diagnostics
2427 - fix diagnostics for principal stress components, press, zeta, eta
2428 to give something meaning full
2429 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
2430 new output (all 4 tests) using default rotationPeriod.
2431 o pkg KPP:
2432 - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
2433 - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
2434 and normal grid from 1 to Nr)
2435 o Fix computations of L4rdt in mom_calc_visc.F
2436 o eesupp:
2437 new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
2438 should be called before a "stop" if we know that all process are going
2439 to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
2440
2441 checkpoint61o (2009/05/26)
2442 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
2443 o model/src/ini_curvilinear_grid.F:
2444 compute angleSin/CosC when they are not read from a file
2445 o pkg/seaice:
2446 add pseudo time stepping for LSOR
2447 o pkg/exch2:
2448 temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
2449 o pkg/seaice:
2450 Adding separate sea ice albedo, drag coefficients, and HO in Southern
2451 Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
2452 o SingleCpuIO:
2453 fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
2454 o pkg/seaice:
2455 put exchanged variable in (local) common block for MPI+Multi-Threads
2456 to work (necessary with exch1, and for now with exch2 too).
2457 o verification: to get more experiments tested with mpi, mth and mpi+mth,
2458 change tiling of:
2459 aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
2460 hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
2461 update output of exp:
2462 exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
2463 tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
2464 + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
2465 (note: output.txt generated on faulks using only 1 tile)
2466 o eesupp & mdsio (SingleCpuIO):
2467 - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
2468 parameter "W2_useE2ioLayOut" (read from file "data.exch2").
2469 Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
2470 - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
2471 - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
2472 gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
2473 o pkg/exch2:
2474 - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
2475 read parameter file "data.exch2" if it exists; otherwise try default regular
2476 cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
2477 - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
2478 with new code (not to be used, just as a backup solution).
2479 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
2480 in utils/exch2/input.
2481
2482 checkpoint61n (2009/05/12)
2483 o eesupp & mdsio (SingleCpuIO):
2484 - move mapping to global io-buffer inside gather_2d/scater_2d: this save
2485 memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
2486 receive real*4 array (instead of real*8) to read/write 32.bit files.
2487 (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
2488 and remove new mapping S/R)
2489 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
2490 - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
2491 xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
2492 when using exch2. Add S/R to map global io-buffer to global model array.
2493 - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
2494
2495 checkpoint61m (2009/04/29)
2496 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
2497 and add 3 other S/R for other types (R4,R8,RS).
2498 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
2499 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
2500 - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
2501 - reduce number of macro definitions (keep only those which are used);
2502 can always call directly the corrresponding S/R if needed.
2503 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
2504 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
2505 Fixed wrong type of arg in:
2506 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
2507 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
2508 To fix: global_sum of var in common block is wrong (multi-threaded) in:
2509 dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
2510 To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
2511 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
2512 "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
2513 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
2514 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
2515 edges are closed (zero depth); might happen with "blank tiles";
2516 for now, disabled if using OBCS.
2517 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
2518 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
2519 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
2520 to reduce length of 1.D array print in STDOUT.
2521 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
2522 + use 48 tiles (16x8): this will allow to test "blank tiles".
2523 o start to test MPI + multi-threaded (change testreport to skip tests
2524 where number of tiles do not match).
2525 o genmake2: add option "-omp" to turn on Open-MP ;
2526 passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
2527 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
2528 and keep the original tile numbering. Note: compatible with old
2529 W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
2530
2531 checkpoint61l (2009/04/07)
2532 o Overlaps had been forgotten in calculating ijk keys : fixed
2533 o fix cyrus makedepend for gcc 4.4
2534 o experiment fizhi-cs-aqualev20:
2535 switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
2536 and generate new output. Note: new output is much closer to the old
2537 one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
2538 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
2539 o pkg/fizhi:
2540 - change to avoid indices going deliberately over array-bounds
2541 - remove unnecessary MPI stuff
2542 - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
2543 - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
2544 does not go over array-bounds and therefore returns reliable output.
2545 - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
2546 this S/R has 4 output arguments, which are used inside "get_alarm";
2547 when it is called with the same variable "ndum" in place of several
2548 output arguments, this produces weird side effect inside "get_alarm"
2549 (e.g., datein=dates(n) is overwritten by timein=times(n) since both
2550 datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
2551 address) and produces error.
2552 o tools/gemake2: (March 27-29 2009)
2553 with option "-mpi": link *_mpi files from "MODS" dir (this is what
2554 testreport does).
2555 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
2556 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
2557 update lab_sea.lsr & lab_sea.salt_plume results
2558 o pkg/seaice:
2559 Major overhaul of the LSOR solver: change discretization from original
2560 finite differences to finite volume. The old routine is still in the
2561 file seaice_lsr.F and can be turned on with the CPP-flag
2562 SEAICE_OLD_AND_BAD_DISCRETIZATION
2563 Along with this change, the discretization of the strain rates is changed.
2564 The same flag turns on the old discretization in seaice_calc_strainrates.F
2565 All verification experiments with seaice are affected (except for
2566 seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
2567 results by setting the above flag.
2568 Further changes involve changes in defaults:
2569 - ALLOW_FLOODING is defined and turned on by default
2570 - SEAICEadvSnow = .true. is now the default
2571 - SEAICEadvSalt = .true. is now the default
2572 - SEAICEadvAge = .true. is now the default
2573 - SEAICE_clipVelocities = .false. is now the default
2574 (as per J. Zhang's recommendation)
2575 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
2576 is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
2577 - seaice_growth: replace computation of UG by a simple copy from wspeed
2578
2579 checkpoint61k (2009/03/18)
2580 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
2581 seaice_lsr: fixed a few metric terms,
2582 affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
2583 add more debugging diagnostics
2584 seaice_evp: removed superfluous many metric terms of FV discretization
2585 of stress divergence
2586 affects lab_sea, lab_sea.hb87
2587 seaice_ocean_stress: removed superfluous many metric terms of FV discretization
2588 of stress divergence for non-evp solver
2589 (this part is not tested anywhere)
2590 seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
2591 they were effectively only half slip
2592 affects lab_sea.hb87
2593 updated all relevant verification experiments (except lab_sea//output_adm.txt
2594 which was left over, but fails at level 7 & 6)
2595
2596 checkpoint61j (2009/03/17)
2597 o pkg/seaice: turn a few hard wired parameters into run time parameters
2598 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
2599 time in seconds as promised by the usints in seaice_monitor and exf_monitor
2600 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
2601 that are not cubed-sphere grids
2602 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
2603 o pkg/ctrl:
2604 fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
2605 o non-hydrostatic (calc_gw.F):
2606 fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
2607 update output of exp. global_ocean.cs32x15.viscA4
2608 o remove backward compatibility for thetaMin,phiMin
2609 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
2610 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
2611 interpolated wind field not only for curvilineargrid=.true., but also
2612 for a rotated grid (rotateGrid=.true.)
2613 o pkg/exf: add capability to bypass interpolation for runoff
2614 by setting yet another CPP-flag
2615 o eesupp/src, B-grid exchange:
2616 add simple (6 tiles, non MPI) CS exch + standard interface S/R.
2617 o autodiff
2618 new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
2619 allows to switch to single-prec common blocks;
2620 corresponding switch occurs in tamc.h, integer isbyte
2621 TAF store directivs "byte" and "kind" seem equivalent;
2622 Most tamc.h have been updated correspondingly.
2623
2624 checkpoint61i (2009/02/13)
2625 o autodiff:
2626 fix autodiff_sore/_restore indices for obcs
2627 (spotted by I. Hoteit, M. Mazloff)
2628 o pkg/autodiff, pkg/ctrl:
2629 Add flag to reduce all tapelev I/O to single-prec.
2630 In data.ctrl set
2631 doSinglePrecTapelev = .TRUE.
2632 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
2633 check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
2634 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
2635 real fresh water flux (not yet)
2636 o pkg/mdsio & rw:
2637 - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
2638 - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
2639 o pkg/flt:
2640 - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
2641 init_fixed & ini_varia.
2642 - clean-up & simplify linear interpolation S/R:
2643 move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
2644 - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
2645 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
2646 - add vert. coordinate & horiz. indices to output files.
2647 - change vertical position in initial condition, from index to depth [m].
2648 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
2649 (easier to get to a curvilinear grid) ; delX,delY no longer used.
2650 o pkg/ggl90: a few modifications:
2651 - fix bottom boundary condition, and interpolation of KappaE
2652 near top and bottom
2653 - use same set of viscosity/diffusivity for TKE/momnetum/tracer
2654 - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
2655 - add a few options for mixing-length upper limit (--> mxlMaxFlag)
2656 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
2657 (maintain temporary backward compatibility, until next checkpoint)
2658
2659 checkpoint61h (2009/01/27)
2660 o pkg/diagnostics with "periodic averaging diagnostics":
2661 fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
2662 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
2663 o pkg/obcs: fix loop ranges for balancing code
2664 o pkg/flt:
2665 - improve criteria for finding which tile owns a float.
2666 - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
2667 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
2668 aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
2669 with ocean biogeo)
2670 o pkg/flt:
2671 - do some cleaning and fix the restart ;
2672 - add output.txt in flt_example/results to get this pkg tested.
2673 o genmake2: add an EXTENDED_SRC option and flag.
2674 for now, cannot be turned on on command line (only through genmake_local)
2675 o pkg/mdsio: read/write vector:
2676 - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
2677 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
2678 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
2679 - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
2680 (drop to 4 digits matching for grad). But this test does not look very
2681 reliable (was already failling on eddy, fc5, at 6.digits). Update output.
2682
2683 checkpoint61g (2008/12/29)
2684 o pkg/flt:
2685 - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
2686 + make OPTIONS file more standard.
2687 - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
2688 - fix _BYTESWAPIO CPP-Flag
2689 - standard reading of file-parameter "data.flt"
2690 - fix argument list of S/R FLT_RESTART
2691 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
2692 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
2693 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
2694 a still unfixed compiler/optimization bug
2695
2696 checkpoint61f (2008/11/21)
2697 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
2698 update results of global_ocean.cs32x15.icedyn test.
2699 o move getcon.F from model/src to pkg/fizhi.
2700 o pkg/exf: add parameter for extrapolation of temp up to the surface
2701 and option to prevent negative evap (in bulk_largeyeager04 only).
2702 o Prather Advection scheme: fix tracer conservation for divergent flow
2703 (e.g., when using NonLin Free-Surface).
2704 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
2705 o gmredi (Visbeck-variable-K):
2706 - add more parameters to Visbeck-variable-K.
2707 - use a 5 points average for dSigmaR in Visbeck-K calculation
2708 (more "homogenous": same stencil and same weights as in dSigmaH)
2709 - update output of ideal_2D_oce experiment.
2710 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
2711 (#undef REAL4_IS_SLOW)
2712 - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
2713 coordinate variable
2714 - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
2715 (surface forcing fields), removes some of the functionality
2716 - model/src/write_grid.F: write _RS variables as RS-netcdf variables
2717 - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
2718 probably not all: copy _RS surface flux fields to RL field before
2719 calling DIAGNOSTICS_FILL
2720 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
2721 real*4 (CALL EXCH_*_RS) versions.
2722 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
2723 (generate new output).
2724
2725 checkpoint61e (2008/10/23)
2726 o gmredi (Visbeck-variable-K):
2727 - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
2728 - change computation of Visbeck-K where Slope > Smax :
2729 now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
2730 previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
2731 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
2732 to be the same as with Z-coord. (i.e., m/s & no-units respectively).
2733 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
2734 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
2735 does not become too large (to avoid precision problems in implicit-diffusion
2736 solver); update ideal_2D_oce output.
2737 o pkg ggl90:
2738 - in ggl90_cal.F: compute only one set of visc/diff, used to
2739 step forward TKE/T/S/momentum
2740 - default value of GGL90viscMax/GGL90diffMax larger and equal (to
2741 have Prandlt =1)
2742 o gmredi (fm07):
2743 - add lower limit on Transition layer thickness + lower limit on 1/lambda
2744 - allow to set few more params from data.gmredi
2745 o pkg ggl90:
2746 - add missing sqrt(2) factor in computation of mixing length
2747 scale in ggl90_calc.F
2748 (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
2749
2750 checkpoint61d (2008/09/25)
2751 o adjoint modifs
2752 - adapt to new field rhoInSitu
2753 - allow to revert from StoreDynVars2D, StoreDynVars3D
2754 to individual fields
2755 (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
2756 o store 3-D (in-situ) density in commom block (DYNVARS.h)
2757 - save 1 rho computation.
2758 - no longer modify T & S inland when using down_slope pkg.
2759 o gad_som : allow to switch to SOM advection for T & S without corresponding
2760 pickup files (using new S/R: MDS_CHECK4FILE).
2761 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
2762 (for useSingleCpuIO to work in multi-threaded)
2763 o pkg/shelfice:
2764 - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
2765 with SHELFICEtopoFile in data.shelfice
2766 - move code for reading ice shelf topography and modifying hFacC into separate
2767 subroutines of the shelfice package
2768 - separate initialisation of "fixed" and "variable" variables
2769 - kTopC is not (yet) replaced by kSurfC, although this is possible
2770 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
2771 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
2772 and rename:
2773 ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
2774 ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
2775 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
2776
2777 checkpoint61c (2008/08/30)
2778 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
2779 to add mass source/sink of fluid in the interior (3-D generalisation
2780 of oceanic real-fresh water flux).
2781 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
2782 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
2783 o new pkg: down_slope
2784 density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
2785 - presently, modify T & S inland (dwnslp_calc_rho.F).
2786 can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
2787 - implementation for ocean in P-coords not tested.
2788 - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
2789 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
2790 (to facilitate conversion of oceanic pkg to p-coordinate).
2791 o change FIND_RHO to FIND_RHO_2D :
2792 pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
2793 o new pkg: cheapaml
2794
2795 checkpoint61b (2008/08/05)
2796 o exch2:
2797 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
2798 - no longer depend on the order sequence (N,S,E,W).
2799 - 3rd exchange no longer needed (tested with 24 tiles).
2800 - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
2801 - exch_UV_A-grid readily available (but not yet tested).
2802 comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
2803 (both are no longer needed) in exch_uv: no effect in forward run; but
2804 get truncation error differences with adjoint exch.
2805 o exch2:
2806 - change index-bounds storage (moved from target to local tile,
2807 more intuitive this way) ; rename/remove some variables.
2808 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
2809
2810 checkpoint61a (2008/07/29)
2811 o exch2/matlab-topology-generator:
2812 fix bug in index bounds for N-S internal exchange (hard to tell if this
2813 had any effect on the solution).
2814 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
2815 is exceeded
2816 o testreport: modify syntax of awk, so that it works also with
2817 awk, and not only with nawk and gawk
2818
2819 checkpoint61 (2008/06/24)
2820 o autodiff
2821 Change default for TAF usage by removing argument '-nonew_arg'
2822 This changes TAF subroutine argument list (ordering of active var.)
2823 Omission of this flag leads to incompatibility w.r.t. TAMC
2824 To restore TAMC-compatibility, need following modifs:
2825 * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
2826 * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
2827 Tested TAF version is 1.9.22
2828 N.B.: exch2 hand-written adjoint code currently not TAMC compatible
2829
2830 checkpoint60 (2008/06/19)
2831 --->>> This is the last checkpoint for which generating the adjoint
2832 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
2833 --->>> by default.
2834 --->>> Future checkpoints will ommit this flag by default.
2835 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
2836 o pkg/grdchk: Add gradient check to etan0 perturbations.
2837 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
2838 o pkg/autodiff: more flexibility in zeroadj.
2839 model/src: modifying do_oceanic_phys.F accordingly.
2840 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
2841 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
2842 special setup of gmredi for which the adjoint is stable
2843 enough for parameter optimization.
2844 o bridging the gap between eddy stress and GM.
2845 -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
2846 along with a change in CPP option (now ALLOW_EDDYPSI).
2847 -> when using GM w/ GM_AdvForm:
2848 The total eddy streamfunction (Psi = eddyPsi + K x Slope)
2849 is applied either in the tracer Eq. or in momentum Eq.
2850 depending on data.gmredi (intro. GM_InMomAsStress).
2851 -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
2852 The key modifications are in model/src/taueddy_external_forcing.F
2853 pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
2854
2855 checkpoint59r (2008/05/29)
2856 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
2857 from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
2858 fix option to read coriolis(@ cell-corner) from files with CS-grid.
2859 o pkg/mnc: add some attributes to standard 1D-coordinate variables
2860 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
2861 mass points, when using mnc for output
2862 - add runtime parameter (missing_value, missing_value_int) to override
2863 default (which is the value of getcon('UNDEF'))
2864 o pkg/mnc: prepare mnc for the actual use of missing values with the
2865 diagnostics package: small fix in mnc_cw_readwrite.template and more
2866 initialisation of never used fields
2867 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
2868 versions
2869 o pkg/thsice/thsice_ini_vars.F added default initial values so that
2870 thermodynamics sea ice solver does not blow up when some initial fields
2871 are missing.
2872 o move from external_forcing_surf.F to ini_forcing.F
2873 the p-coord. hack consisting in using pLoad to set phi0surf ;
2874 update output of tutorial_global_oce_in_p (affected @ truncation level).
2875 o Freshen up a bit hs94.1x64x5, notably:
2876 remove rotationPeriod and tRef=5*0. (adjoint only), and add
2877 exactConserv=.TRUE.
2878 o pkg/generic_advdiff:
2879 change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
2880 applies to files where Temperature & Salinity 2nd Order moments are used.
2881 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
2882 this uses a dynamically allocated internal state data structure
2883 (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
2884 and requires a fortran 90 compiler
2885
2886 checkpoint59q (2008/05/06)
2887 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
2888 (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
2889 o Refresh tutorial_global_oce_biogeo, notably:
2890 - change bathymetry (put back seamounts in ACC, use hFacs)
2891 - change EOS (POLY3 --> JMD95Z)
2892 - use Bryan-Lewis vertical diffusivity
2893 - use multidimensional advection
2894 - remove old virtual virtual in dic pkg, now done through ptracer pkg
2895 - change a couple of parameters in dic pkg
2896 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
2897 o pkg/obcs: change default to OBCSfixTopo = .true.,
2898 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
2899 - replace "debugMode" with "debugLevel .GE. debLevB"
2900 o implementation of TAF directives for gchem,cfc,dic
2901 o remove "exp5" (replaced by tutorial_deep_convection).
2902 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
2903 this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
2904 the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
2905 --> changes results in exp4, seaice_obcs
2906 o tutorial_deep_convection :
2907 update the set-up and increase resolution and domain size ; start
2908 from pseudo initial conditions = output at t=120mn in order to see
2909 something happening when running testreport.
2910 o pkg/seaice: add os7mp as an advection scheme
2911 add check for advection schemes
2912 add a flag for restoring T and S underneath sea ice
2913 o pkg/my82: add netcdf-support and diagnostics
2914 o thsice pkg:
2915 - Now hsMax limits snow height by turning it into ice following
2916 flooding scheme (and now conserving energy)
2917 - Slight rewriting of the formula in thsice_calc_thick.F
2918 - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
2919 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
2920
2921 checkpoint59p (2008/04/10)
2922 o gchem / dic / cfc :
2923 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
2924 - add new parameter files: "data.dic" & "data.cfc" ;
2925 - various re-arrangement in initialisation & header file ;
2926 - fix tutorial_global_oce_biogeo for multi-threaded test.
2927 o pkg/dic: test for "pickup_dic" file when restarting ;
2928 if no pickup-file, can restart with a re-initialised pH (same as it did
2929 before) providing pickupStrictlyMatch is set to False.
2930 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
2931 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
2932 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
2933 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
2934 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
2935 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
2936 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
2937 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
2938 scheme to use for vorticty-term ;
2939 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
2940 (with default selectVortScheme, return to original discretisation)
2941 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
2942 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
2943 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
2944 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
2945 also fix diagnostics VISCAHW & VISCA4W.
2946
2947 checkpoint59o (2008/03/07)
2948 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
2949 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
2950 move a few statemens out the main loop into separate loops
2951 o pkg/shelfice:
2952 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
2953 (kg/m^2/s), does not break tests, because in verification/isomip,
2954 rhoConstFresh=rhoConst (by accident)
2955 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
2956 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
2957 new file model/src/seawater.F, so that they are available for all pkgs.
2958 - convert potential temperature into in-situ temperature. This changes the
2959 isomip tests => update tests
2960 o add a flag writePickupAtEnd (default=true) to be able to suppress
2961 writing a pickup at the last timestep
2962 o tools/mpack-1.6 :
2963 - disable automake (not working) and autoconf (not needed).
2964 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
2965 also cleaner with much less compilation warnings.
2966 o pkg/profiles:
2967 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
2968 (for "less than 32 characters name" compiler requirement)
2969 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
2970 conditions that have a different sampling frequency than S/T/U/V obcs
2971 o pkg/diagnostics (stats-diags):
2972 - fix global Min/Max in case 1 processor get only empty tiles
2973 o genmake2: replace (4 times)
2974 make genmake_tc_1.o >> genmake_warnings 2>&1
2975 with
2976 COMM="$CC $CFLAGS -c genmake_tc_1.c"
2977 echo $COMM >> genmake_warnings
2978 $COMM >> genmake_warnings 2>&1
2979 to make genmake2 always see the value of CC as specified in the optfile.
2980 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
2981 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
2982 - modify verification advect_cs test to test SOM-advection on CS-grid.
2983 o pkg/ctrl:
2984 - Rewrite of ctrl_map_ini_ecco.F,
2985 introducing a generic routine (ctrl_map_ini_gen.F).
2986 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
2987
2988 checkpoint59n (2008/02/09)
2989 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
2990 number in dedicate array "hdiag":
2991 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
2992 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
2993 - many small changes (integer format) for large number of diagnostics
2994 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
2995 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
2996 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
2997 usingSphericalGrid, this allows to define the rotated grid coordinates
2998 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
2999 geographical coordinates according to the inverse of the rotation defined
3000 by the Euler angles, so that Coriolis parameter and online-interpolation by
3001 exf works with the geographical coordinates on XC/YC/XG/YG.
3002 Naturally, this feature does not work with all packages, so some
3003 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
3004 profiles), because there the coordinates are assumed to be regular
3005 spherical grid coordinates.
3006 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
3007 - introduce isopycnal diffusion coefficient control.
3008 o tools/adjoint_options:
3009 - additional control vector components.
3010 o pkg/mnc: have mnc create marginally meaning full coordinate variables
3011 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
3012 o pkg/mypackage:
3013 - add example of read/write pickup for state-var ;
3014 - add entry points to the main code for state-vars diags & write-pickup.
3015 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
3016 transitions for useExfYearlyFields
3017 - add new subroutine that determines the file to read from for
3018 use*YearlyFields = .TRUE. and .FALSE.
3019 - add a verification experiment to global_with_exf that tests
3020 useExfYearlyFields with USE_EXF_INTERPOLATION defined
3021 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
3022 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
3023 subroutines (which could be generated from a template, because they are
3024 almost identical), for now they are included in obcs_prescribe_read.F for
3025 simplicity
3026 o pkg/exf:
3027 - add a little more diagnostic to exf_interp_read (in analogy to
3028 mds_read_field, can be turned off with debugLevel < debugLevA=1)
3029 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
3030 ugly but fast by unrolling short inner loops, inserting a unroll=8
3031 directive in routine lagran, and splitting a loop and making do while the
3032 outermost loop (the latter requires the intoduction of index arrays)
3033 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
3034 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
3035 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
3036 o verification/seaice_obcs: updated for restart test and latest options
3037 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
3038 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
3039 for now this is only available for the C-grid code and also within
3040 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
3041
3042 checkpoint59m (2008/01/14)
3043 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
3044 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
3045 o gad_som : fix flux output (& diagnostics) to have same units as other
3046 advection scheme fluxes (was previously multiplied by deltaT).
3047 o added verification/seaice_obcs both to test seaice open boundaries
3048 and to provide an example matlab scrpt for generating them
3049 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
3050 o pkg/salt_plume: clean up salt_plume_frac.F to
3051 remove redundancy in PlumeMethod 1 and 4
3052 o pkg/kpp: added saltplume diagnostics
3053 o pkg/obcs and pkg/seaice:
3054 - do not set uice and vice to zero when OB*icefile are unspecified
3055 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
3056 - moved seaice tracer obcs after call to seaice_growth
3057 o pkg/salt_plume: added various options for salt plume depth
3058 criterion and for vertical distribution of the salt
3059
3060 checkpoint59l (2007/12/18)
3061 o pkg/ptracers: new version of ptracers pickup:
3062 read meta file and write only fields which are needed to restart.
3063 ( same logic as main pickup file ; also using pickupStrictlyMatch )
3064 o pkg/seaice:
3065 - add timescale for melting due to warm mixed layer as a means of
3066 setting SEAICE_availHeatFrac more conveniently
3067 - add a CPP-flag/runtime parameter check for flooding algorithm
3068 - reformulated availHeat in seaice_growth.F to be independent of AREA
3069 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
3070 unit changes
3071 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
3072 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
3073 SX vector computer.
3074 o pkg/seaice:
3075 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
3076 seaice forcing fields can now be read only through pkg/exf
3077 - removed some unused halos
3078 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
3079 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
3080 or U/VICE from U/VWIND before computing U/VSTRESS
3081
3082 checkpoint59k (2007/11/30)
3083 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
3084 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
3085 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
3086 all experiments pass when compile with un-initialised var. checking option.
3087 o added pkg/salt_plume
3088 o script to test restart (for now, in MITgcm_contrib/jmc_script)
3089 o pkg/seaice: new read/write pickup version.
3090 read meta file and write only fields which are needed to restart.
3091 ( same logic as main pickup file ; also using pickupStrictlyMatch )
3092 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
3093 o lab_sea.hb87: modify the domain & update output.hb87.txt :
3094 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
3095 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
3096 process. Fixed here by closing the domain at the Northern boundary.
3097 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
3098 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
3099 a set of consecutive levels in/from a 3-D array.
3100 o pkg/ptracers:
3101 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
3102 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
3103
3104 checkpoint59j (2007/11/09)
3105 o in pkgs: dic, obcs, offline, rbcs:
3106 standard way to compute coeff. for time interpolation between 2 time reccords
3107 which retains full precision (& make results less dependent on compiler).
3108 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
3109 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
3110 packages instead of reading ice cover and wind speed separately
3111 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
3112 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
3113 to allow to compile customized code before the update)
3114 o cleaning-up:
3115 - fix CPP instruction syntax in pkg/obcs
3116 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
3117 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
3118 - fix some threads issue in IO parts.
3119 o pkg/dic:
3120 - add tons of "_d 0" (--> much better testreports !)
3121 and then update outputs of tutorial_global_oce_biogeo
3122 o pkg/mom_fluxform:
3123 add a special version of momentum advection intended to conserve momentum
3124 next to a bathymetry step or a coastline edge. (default = off = #undef)
3125 o new read/write pickup version:
3126 - for now, only implemented for main (mdsio) pickup file.
3127 - write out only what is needed to restart; merge pickup_nh , pickup_ph
3128 and main pickup together.
3129 - read meta file; read only what is needed to restart; stop if a field
3130 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
3131 if it make sense (even if the restart is not perfect).
3132 - if no meta file, assume that pickup to read corresponds exactly to
3133 a pickup that would currently be written.
3134 - read pickup written in the old format (until checkpoint59i) if it
3135 recognizes an old meta file (no field-list).
3136 - add a meta file in exp. which starts from a pickup: 2 cases:
3137 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
3138 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
3139 b) a meta file describing the content of the associated pickup file
3140 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
3141 o pkg/mdsio & pkg/rw:
3142 - new routine to read a meta file ; new set of routine to read
3143 Multiple-fields file (with meta file).
3144 o added open boundary conditions capability for seaice
3145 HSNOW, HSALT, UICE, and VICE
3146
3147 checkpoint59i (2007/10/21)
3148 o adjoint:
3149 * fix multiDimAdvection adjoint
3150 (partial recomputation problem by TAF for fVerT(:,:,kDown)
3151 and comlev1 size definition (maxpass vs. max. number of tracers)
3152 * verification/global_ocean.90x45x15 adjoint now tests
3153 NLFS and multiDimAdvection using DST3 (=30)
3154 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
3155 o pkg/kpp: add "_d 0" to real constant (if missing);
3156 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
3157 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
3158 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
3159 for internal parameters related to restart process (formerly from PARAMS.h)
3160 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
3161 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
3162 as argument. (only atm2d & obcs write_pickup have not yet been updated)
3163 o pkg/monitor:
3164 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
3165 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
3166 - account for deep Atmosphere factor and density factor (anelastic)
3167 o added open boundary conditions capability for seaice HEFF and AREA
3168 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
3169 thermodynamics
3170 - requires a little reorganization, which affects the testreport results
3171 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
3172 so that now the conservative form is tested
3173 - add a few comments
3174 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
3175 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
3176 o add new diagnostics to seaice: advective, diffusive fluxes (only for
3177 multidim-advection, for scheme 2 they are not filled) and transports,
3178 thermodynamic growth rates
3179 o change units of EmPmR (inside the code, + within coupling interface)
3180 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
3181 Affects results @ truncation level (cg2d match) and update output of
3182 experiments: lab_sea(6), global_ocean.90x40x15(10),
3183 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
3184 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
3185 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
3186 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
3187
3188 checkpoint59h (2007/09/29)
3189 o pkg/exf:
3190 - improve vectorization by moving if-statement out of loops in
3191 exf_mapfields, exf_radiation
3192 - exf_bulkformulae.F: introduce 2D fields and vectorize code
3193 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
3194 o testreport:
3195 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
3196 monitor & update offline_exf_seaice exp. output.
3197 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
3198 o pkg/seaice:
3199 - bug fix in the evp solver: boundary conditions were affected be
3200 masking of zMax/zMin (changes results)
3201 - minor bug fix in boundary conditions in seaice_calc_strainrates
3202 (changes results for no_slip)
3203 - seaice_lsr.F: make interpolation of eta dependent on boundaries
3204 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
3205 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
3206 stress formulation and no-slip boundary conditions
3207 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
3208 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
3209 o pkg/seaice: a first HSALT time stepping equation has been checked in
3210 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
3211 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
3212 without requiring DO-IF statements
3213 o pkg/thsice:
3214 use continuous power-law function for partition of energy between lateral
3215 melting/freezing and thinning/thickening ; old code using step function
3216 still available with #undef THSICE_FRACEN_POWERLAW
3217 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
3218 o testreport: change AD testing : check against results/output_adm.txt
3219 using same scripts as for forward test.
3220
3221 checkpoint59g (2007/09/17)
3222 o adjoint testing: in preparation for changing testreport:
3223 - output format: cost and grad written on separated lines
3224 - ad output results in directory "results" (instead of "results_ad")
3225 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
3226 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
3227 o pkg/ecco: allow user defined cost function contributions
3228 o testreport:
3229 Allow to choose (per experiment) the list of tested output variables
3230 and the main variable (used to issue a pass/FAIL ) ;
3231 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
3232 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
3233 Also modify printing of summary:
3234 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
3235 b) echo the list of tested variables in the individual summary.txt of
3236 each experiment.
3237 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
3238 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
3239 (but still depend on the tile decompostion of the domain).
3240 o pkg/seaice: change a discretization detail to make the B-grid code
3241 "more symmetric". This change is likely to remove all "ridges/leads" that
3242 where quasi-aligned with the grid in B-grid solutions. It may also be
3243 the solution to the stress coupling issues with the B-grid.
3244 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
3245 remove .cvsignore from input dir. (since testreport no longer run here).
3246 o pkg/thsice:
3247 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
3248 - fix reshaping of sea-ice just after advection:
3249 melt all the ice only if ice-volume is too small.
3250 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
3251 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
3252 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
3253 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
3254 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
3255 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
3256 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
3257 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
3258 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
3259 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
3260 -> update output.txt
3261 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
3262 this affects truncation error: -> update output.txt of exp:
3263 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
3264 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
3265
3266 checkpoint59f (2007/08/21)
3267 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
3268 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
3269 a bounded range (in forward mode)
3270 o pkg/ecco, ctrl, autodiff and mom_common:
3271 internal parameter controls, completements of implementations
3272 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
3273 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
3274 (not seem any difference in testing results).
3275 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
3276 at face corners.
3277 o pkg/generic_advdiff:
3278 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
3279 loop range indices for computing vertical advection tendency
3280 and do the calculation in the interior only (no overlap) ;
3281 for now, only implemented for SOM advection (to save CPU time).
3282 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
3283 o exch2 adjoint
3284 First set of changes:
3285 - add exch2 hand-written adjoint templates
3286 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
3287 This will require cleanup in pkg/autodiff/*.F
3288 (changed routines currently kept separate in verif. code/)
3289 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
3290 that used to hide exch2 or cubed-sphere specific code
3291 (commented via 'cph-exch2')
3292 o pkg/seaice
3293 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
3294 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
3295 output of global_ocean.cs32x15.thsice .
3296
3297 checkpoint59e (2007/07/26)
3298 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
3299 for B-grid vector (not yet tested) and C-grid vector (<- only used
3300 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
3301 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
3302 (#ifdef ALLOW_SALT_PLUME)
3303 o gather_2d/scatter_2d: removed halo regions
3304 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
3305 scheme and the corresponding test case (under front_relax dir). For now,
3306 only available with Skew-flux form and not yet tested in realistic set-up.
3307 adjoint: store directives updated, but gradient checks deteriorated,
3308 so maybe GM/Redi adjoint is now broken.
3309 o seaice adjoint
3310 * add AREA, HEFF, HSNOW as control variable
3311 (should not change lab_sea results)
3312 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
3313 o pkg/seaice:
3314 * added computation of saltFlux in seaice_growth;
3315 For time being, sea ice salinity is assumed constant
3316 contribution of snow flooding to freshening of sea ice is neglected.
3317 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
3318 defaults to 0.0 in order to maintain backward compatibility.
3319 Typical values for SEAICE_salinity are 4 to 10 g/kg.
3320 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
3321 * added SEAICE_availHeatFrac, which specifies fraction of surface level
3322 heat content used to melt or grow ice
3323 * commented out cap of HICE: it helps keep ice thinner
3324 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
3325 * applied OBCS T/S mask to HEFFM sea ice mask
3326
3327 checkpoint59d (2007/06/21)
3328 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
3329 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
3330 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
3331 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
3332 and change default value of parameter "GM_Small_Number";
3333 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
3334 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
3335 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
3336 o pkg/ecco: cost function when applying pkg/smooth to controls
3337 o pkg/ctrl: add forcingPrecond run time parameter
3338 o pkg/seaice:
3339 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
3340 - fix bug in metric terms of u-equation in LSR solver (implicit part),
3341 changes verification/lab_sea
3342 - rearrange implicit part of u-equation in LSR solver to make it easier to
3343 read, understand, and debug. This causes changes at the truncation level.
3344 - fix (serious) bug in the boundary conditions (sign error in the implicit
3345 part) of the LSR solver. Changes all LSR results.
3346 - fixed problem with HSNOW initialization to avoid thick snow when AREA
3347 is initilized with small values - does not change lab_sea results.
3348 - added HsnowFile initialization capability
3349 o pkg/smooth: addition to model/src and pkg/ctrl so allow
3350 initialization of pkg/smooth and application to control vector
3351 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
3352 o dependencies: pkg/profiles requires pkg/cal
3353 o pkg/profiles:
3354 - added option ALLOW_PROFILES_GENERICGRID
3355 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
3356 that interpolation information (grid points and coefficients) is provided
3357 within the netcdf input files.
3358 -> sample matlab scripts can be found in MITgcm_contrib/gael
3359 that allow you to prepare netcdf input files.
3360 - also modified: cleaner include statements, cleaner error print statements,
3361 cleaner stops when error, and more tests of the netcdf input files consistency.
3362 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
3363 o pkg/seaice:
3364 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
3365 requires a new routine: seaice_diagnostics_fill.F
3366 - make sure that seaice does not move if not forced (pressure replacement
3367 method, Hibler and Ip, 1995), changes results
3368 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
3369 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
3370 It is turned off by default (=-1.), because it changes the results.
3371 - make it possible to read AREA from a file, too.
3372
3373 checkpoint59c (2007/06/04)
3374 o add S/R and diagnostics for oceanic mixed-layer depth
3375 o move GMRedi call after all vertical mixing schemes (including KPP)
3376 o pkg/thsice:
3377 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
3378 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
3379 o pkg/obcs:
3380 - bug fix for balance code
3381 o pkg/seaice:
3382 - allow values of SEAICE_elasticParm > 1
3383 - add new parameter SEAICE_evpTauRelax as an alternative
3384 to SEAICE_elasticParm
3385 - make lsr boundary conditions free slip (by default), changes result
3386 - add code for no slip boundary conditions for lsr
3387 - set minimum of zeta to zero (and not 4e8) (changes results)
3388 - add a cap on AREA after advecting AREA if seaice_growth is not called
3389 o change calculation of Visbeck K:
3390 - no longer depend on tapering scheme; instead, compute slope (limited
3391 by GM_maxSlope). this is equivalent to what was comuted before with
3392 clipping or linear tappering.
3393 - fix vertical averaging (wrong by 1/2 level)
3394 - leave the old version (but will not be maintained) within
3395 #ifdef OLD_VISBECK_CALC / #endif
3396 - update output of exp. ideal_2D_oce
3397 o change error catch in calc_r_star to improve vectorization
3398 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
3399 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
3400 o adjoint:
3401 Re-organized adjoint checkpointing according to Matt Mazloff
3402 (but with modifs/completions/cleanups)
3403 Storing is now bundled into large arrays to optimized I/O
3404 (and second step in cleanup of the_main_loop)
3405
3406 checkpoint59b (2007/05/16)
3407 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
3408 - export/import (between ocean & coupler) fields needed for ocean DIC.
3409 o pkg/seaice:
3410 - get rid of three more exchanges seaice_calc_viscosities (required
3411 different loop boundaries in seaice_lsr and seaice_ocean_stress)
3412 - bug fix in seaice_ocean_stress (update of lab_sea required)
3413 - reduce loop boundaries to necessary minimum also in seaice_evp
3414 - go back to the old way of computing deltaC/Z as the adjoint likes that
3415 better
3416 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
3417 passive tracer to an Age Tracer) + update output.txt
3418 o pkg/exf:
3419 - implement A-grid / C-grid selection for wind-stress input files.
3420 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
3421 for now, in exf_bulk_largeyeager04.F only :
3422 - change implementation for case where windspeed + 2. components wind-stress
3423 are read-in. AND use rhoConstFresh to convert evap.
3424 o pkg/seaice:
3425 - use correct EXCH_UV for wind-forcing (on A-grid).
3426 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
3427 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
3428 o pkg/exf:
3429 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
3430 EXF_INTERPOLATION:
3431 - merge global_with_exf/code version of exf_interp_read.F
3432 to the main code ;
3433 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
3434 reading the file ; Important: This options needs to be defined to recover
3435 previous code.
3436 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
3437 - no longer loose real*8 precision along the way when using exf_iprec=64.
3438 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
3439 - change discretisation of evp-solver in order to avoid another exchange
3440 (changes lab_sea) and clean up a little
3441 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
3442 help the adjoint (this also changes the results slightly)
3443 - add a few "_d 0" where they had been missing in seaice_evp.F
3444 - cleaning up: remove unused seaice_calc_rhs.F
3445 o pkg/exf: some cleaning-up:
3446 - change various "constants" into runtime parameters
3447 - cleaned-up Large&Yeager04 routine which should eventually
3448 replace exf_bulkformulae.F (changed names of S/R and CPP)
3449 and merged various ALLOW_ATM_WIND options
3450 only used with thsice pkg (in thsice_get_exf.F):
3451 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
3452 which are used when useStabilityFct_overIce=TRUE (= the default)
3453 - change default values of ice & snow emissivity and scale downward LW
3454 by ice & snow emissivity.
3455 o pkg/thsice:
3456 fix few little problems, in thsice_calc_thickn.F:
3457 - growth vertically (and not laterally) if iceFrac == iceMaskMax
3458 - melt only laterally if hIce < hThinIce (as the comments say)
3459 and in thsice_extend.F:
3460 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
3461 - start to form ice as soon as the minimum ice-volume is reachable.
3462 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
3463 and cpl_aim+ocn
3464 o pkg/kpp
3465 - move computation of surface related input fields to KPP into a new
3466 subroutine kpp_forcing_surf.F
3467 - remove wrong (within bi,bj loops) EXCH calls.
3468 - little cleaning (add argument myThid in last position, cvs header ...)
3469 - for now, fix conservation problem by exchanging KPPviscAz (may not
3470 be the best fix)
3471 o pkg/seaice
3472 - check for inconsistent evp parameter/cpp-flag combination
3473 - remove leftover errIO flat for obsolete name list error handling
3474 o OpenAD
3475 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
3476
3477 checkpoint59a (2007/05/01)
3478 o pkg/seaice: some parameter clarifications and a little bit of clean up
3479 o pkg/thsice: rename run-time parameters:
3480 himin -> hIceMin
3481 himin0 -> hThinIce
3482 hihig -> hThickIce
3483 i0 -> i0swFrac
3484 transCoef -> bMeltCoef
3485 frac_energy -> fracMelting
3486 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
3487 with default values (for now) that do not change the results.
3488 remove old version of thsice vars advection in pkg/seaice.
3489 o in FFIELDS.h:
3490 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
3491 - make pLoad & sIceLoad always available (but still only used if
3492 ATMOSPHERIC_LOADING is #define).
3493 o pkg/kpp: replaced _KPP_RL with _RL
3494 o bug fixes for vertical diffusivity computations when both KPP and
3495 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
3496 are no longer updating the vertical diffusivity array
3497 (passed as argument) but are (re-) setting those arrays.
3498 o pkg/seaice: fix bug in evp solver, while doing that
3499 - change (improve?) discretization of stress computations for both
3500 cgrid-lsr and evp solver
3501 - add a new routine to compute strain rates
3502 - the above changes lab_sea results
3503 - add no slip conditions for evp solver (off by default), lsr-version
3504 may follow
3505 - fix exchange for shear at Z-points (does not change lab_sea)
3506 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
3507 (to force the user to pick a time step since there is not "safe" way
3508 of choosing it)
3509 - add principal stress diagnostics
3510 - rearrange fields for evp a little to avoid having to call a: too many
3511 exchanges and b: exchanges for stress trensor components which we do
3512 not have.
3513 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
3514 of evp, complete rewrite for lsr case (latter is does not yet work
3515 in all cases)
3516 o pkg/kpp: add code to have mixing in shelf ice caverns
3517 - add myThid to all kpp routines (long overdue)
3518
3519 checkpoint59 (2007/04/19)
3520 o pkg/exf:
3521 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
3522 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
3523 - move exf header files from lower_case.h to UPPER_CASE.h ;
3524 add missing cvs Header & Name
3525 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
3526 - add namelist param. selectStressGridPosition, exf_monFreq
3527 - retire many _CLIM routines, and remove data.exf_clim
3528 + params moved to data.exf
3529 + climsst, climsss now handled by exf_set_gen, i.e.
3530 climss?period=0 refers to constant field,
3531 climss?period=-12 to monthly forcing
3532 - split up namelists in data.exf
3533 o pkg/seaice:
3534 - remove seaice_exch and seaice_exch_uv
3535 - remove superfluous exchange of theta
3536 - add myThid to seaice_budget_ocean/ice
3537 - add new interface for atmospheric wind forcing (C-grid only)
3538 + new routine
3539 + two new field (taux, tauy for stress over ice)
3540 + removed one global field (DAIRN) for C-grid case only
3541 o pkg/thsise
3542 - 2nd set of modifs for thsice adjoint in conjunction with exf
3543 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
3544
3545 checkpoint58y_post (2007/04/15)
3546 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
3547 vertical diffusivity, similar to that in MOM4; turned on using
3548 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
3549 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
3550 o Added capability for 3D specification of background vertical diffusion
3551 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
3552 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
3553 "data" file that contains the 3D vertical diffusivity coefficients.
3554 o ice dynamics (pkg/seaice) with thsice thermodynamics:
3555 - add code within pkg thsice to advect & diffuse sea-ice fields
3556 similar to (and will replace) what has been added in seaice_advdiff.F,
3557 but: - conserving Mass, Heat & Salt.
3558 - better when using non-linear advection scheme (not yet fully tested)
3559 - can also be used in atmospheric set-up (for now, only the diffusion).
3560
3561 checkpoint58x_post (2007/04/04)
3562 o IO option for global-file compact format:
3563 - add options when generating topology (utils/exch2/matlab-topology-generator)
3564 - add I/O capability (pkg/mdsio).
3565 - adapt utils/matlab/rdmds.m to read this format.
3566 for now long-line format not yet supported by pkg/mdsio (& exch2).
3567 o shelfice: add a few diagnostics
3568
3569 checkpoint58w_post (2007/03/13)
3570 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
3571 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
3572 (and replace horiVertRatio in NH code).
3573 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
3574 and tutorial_plume_on_slope (sensitive to truncation)
3575 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
3576 directly to drive seaice model (C-grid only)
3577 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
3578 - reintroduce computation of wind from stress,
3579 - compute tau (in exf_bulkformulae.F) from windstress averaged to
3580 mass points to avoid tau = 0
3581 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
3582 o rdmnc.m: make it work with "global" files created with gluemnc
3583 o rdmnc.m : some improvements in dealing with singleton dimension
3584 (tested on all testreport mnc output files).
3585 o genmake2: disable pkg/profiles if netcdf test fails.
3586 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
3587 o move call to cal_readparms up to make calendar parameters/variable available
3588 to all packages
3589
3590 checkpoint58v_post (2007/02/08)
3591 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
3592 useDynP_inEos_Zc tested.
3593 o pkg/exf: changes to properly interpolate/mask/scale initial fields
3594 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
3595 and portions thereof. See read_cs.txt for description and examples.
3596 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
3597 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
3598 following the great-circle arc between those 2 points.
3599 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
3600 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
3601 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
3602 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
3603 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
3604 - still needs work (not working with some options ; efficiency to improve)
3605 and serious testing.
3606 - use this scheme for temperature & salinity in 2 advection test exp.:
3607 advect_xy & advect_xz, respectively.
3608
3609 checkpoint58u_post (2007/01/12)
3610 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
3611 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
3612 o testreport: add option "-skipdir" to skip some test.
3613 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
3614 momentum calculation.
3615 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
3616 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
3617 remove checkpoint.F and the_correction_step.F (no longer used);
3618 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
3619 o add option (linFSConserveTr) to correct for tracer source/sink due to
3620 Linear Free surface
3621 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
3622 o pkg/thsice: fix reading mnc-pickups
3623
3624 checkpoint58t_post (2006/12/30)
3625 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
3626 o pkg/mdsio:
3627 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
3628 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
3629 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
3630 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
3631 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
3632 either MDS_READ_FIELD or MDS_WRITE_FIELD )
3633 - new S/R (to replace MDSWRITEMETA), which allows to write more
3634 informations (variable names, time ...) to meta files.
3635 - modify rdmds.m to give back the meta file content.
3636 o pkg/diagnostics: change vertical interpolation to be safer, and more
3637 flexible (define p-levels to interpolate to in data.diagnostics);
3638 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
3639 diagnostic pointer.
3640 o pkg/seaice: more cleaning up of seaice_growth, added many comments
3641 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
3642 o fix multi-category seaice:
3643 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
3644 SEAICE_MULTICATEGORY
3645 - fix short wave heat flux
3646 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
3647 and allow to use EVP solver. Change forward lab_sea: test both EVP
3648 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
3649 o Initial check-in of lab_sea adjoint
3650 (very similar to natl_box_adjoint/code_seaice)
3651 * used C-grid and EVP solver
3652 * used KPP, GM/Redi
3653 * uses inAdExact=.TRUE.
3654 * gradient checks fail for both ADM and TLM
3655 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
3656 f.d. gradients actually seem more problematic than ADM, TLM gradients;
3657 issue is related to forward mismatch between g77 an ifort
3658 o pkg/seaice: overhaul of thermodynamics
3659 - growth.F and groatb.F are replaced by new routine seaice_growth.F
3660 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
3661 - move a few global fields out of SEAICE.h into seaice_growth.F and
3662 make them 2D (FICE/QNETO/ ...)
3663 - remove FO (it is the same as QNETO)
3664 - introduce a few local fields to avoid modifying external fields such
3665 as atemp, etc.
3666
3667 checkpoint58s_post (2006/12/11)
3668 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
3669 changed exf_set_gen.F so that
3670 genperiod=0 means input file is one time-constant field and
3671 genperiod=-12 means input file contains 12 monthly means
3672 o CG2D: use pre-computed solver main-diagonal (stored in common block);
3673 this affects truncation error ; generate new output file for exp. which
3674 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
3675 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
3676 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
3677 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
3678 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
3679 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
3680 o start implementation of deep-atmosphere and anelastic formulation
3681 o verification: remove 2nd copy of input files and use script "prepare_run"
3682 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
3683 o mom_common/vecinv/fluxform: fix a few initialisation isssues
3684 o profiles: fix for multithreaded case
3685
3686 o diagnostics: rename few diags:
3687 s/'PRESSURE'/'RCENTER '/g
3688 s/'TICE '/'oceFreez'/g
3689 s/'TAUX '/'oceTAUX '/g
3690 s/'TAUY '/'oceTAUY '/g
3691 s/'SWFLUX '/'oceQsw '/g
3692 s/DIFx/DFxE/g
3693 s/DIFy/DFyE/g
3694 and add few ocean-forcing diagnostics:
3695 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
3696 o modifications to pkg/seaice/growth.F and budget.F, which change results of
3697 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
3698 as actual snow thickness. It now refers everywhere to effective snow
3699 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
3700
3701 checkpoint58r_post (2006/11/17)
3702 o modifications to pkg/seaice/growth.F, which change results of
3703 lab_sea experiment: fixes pertain to melting snow over open water, to
3704 masking EVAP under sea ice, and to using the correct AREA variable for
3705 computations of EVAP, PRECIP, HSNOW, and GHEFF
3706 o add ability to read bathy, salt, and theta using MNC (off by def)
3707 o add flooding algorithm and advection of HSNOW for pkg/seaice;
3708 both are turned off by default and do no change any results
3709 o seaice advection with pkg/thsice: a step toward the use of non-linear
3710 advection scheme, but #ifdef or commented out for now (requires more EXCH).
3711 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
3712 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
3713 in natl_box (affects results @ truncation level: update output.txt)
3714 o multi-threading and IO:
3715 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
3716 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
3717 (needed to work with SingleCpuIO): tested in all verif. exp.
3718 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
3719 affects the results (but none of the verification test uses this scheme).
3720 o Adding some pkg/diagnostics capability to pkg/seaice
3721 (will certainly be subject to changes)
3722 o ctrl: adding new control variables:
3723 lwflux, lwdown, evap, snowprecip, apressure, runoff
3724
3725 checkpoint58q_post (2006/10/20)
3726 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
3727 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
3728 high_res_cube configuration by 4% on Columbia.
3729 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
3730 add (in global_with_exf/code) a version of EXF_INTERP_READ without
3731 dynamical allocation (seems to work in multi-threaded).
3732 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
3733 single CPU io) so that TAF does not have to see EESUPPORT.h
3734 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
3735
3736 checkpoint58p_post (2006/09/08)
3737 o obcs: stop if obcs is used with useCDscheme = .true.
3738 o shelfice:
3739 - fix a sign error so that no slip at shelfice interface works
3740 - remove stop for combination non-hydrostatic code and shelfice. That does
3741 not mean, that the results are correct, but at least they are numerically
3742 stable
3743 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
3744 o added adjoint exch routined for all exch*3d* routines
3745 and updated flow directives
3746
3747 checkpoint58o_post (2006/08/28)
3748 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
3749 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
3750 o change controling S/R for writing pickup file (new S/R do_write_pickup)
3751 and clean-up reading/writing of pickup files.
3752 o fix local version of read/write pickup (NH part) in rotating_tank/code
3753 o simplify EXCH interface:
3754 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
3755 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
3756 o added the regrid package
3757 o shelfice:
3758 - add a simple boundary layer scheme to reduce noise
3759 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
3760
3761 checkpoint58n_post (2006/08/14)
3762 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
3763 local variable (not in common block).
3764 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
3765 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
3766 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
3767 to work with SingleCpuIO.
3768 o add "_d 0" to real constant of pkg/cfc subroutines ;
3769 update exp. cfc_exemple & tutorial_cfc_offline output files.
3770 o multi-threading and IO:
3771 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
3772 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
3773 - barrier before and after reading.
3774 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
3775 - avoid using MDS_WRITELOCAL for LAND pkg output.
3776 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
3777 common-block variables ; Allows multi-threading with master-thread IO.
3778 o change default MAX_NO_THREADS from 32 to 4 ;
3779 and stop cleanly when MAX_NO_THREADS is too small.
3780 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
3781
3782 checkpoint58m_post (2006/07/17)
3783 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
3784 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
3785 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
3786 keep global_ocean.90x40x15 (for AD testing) with former secondary test
3787 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
3788 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
3789 add MITgcm_tutorials (= code + all the tutorials)
3790 o ecco, option to compute cost for total ssh (mean+anom)
3791 o consistent with addition of ptracer and ssh in pkg/profiles
3792 o profiles: adding ptracer and ssh
3793 o testreport: change multi-test output-file name
3794 (from output.txt.{name} to output.{name}.txt)
3795 o profiles: now ok for mutli-tiles case
3796 o seaice: add 4 parameters for different advection schemes for area,
3797 (effective) seaice thickness, enthalphy, and snow height. Their default
3798 is the standard parameter SEAICEadvScheme
3799 o calc_gw:
3800 - add cosFacU in zonal viscous flux (harmonic.visc.).
3801 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
3802 of tutorial_plume_on_slope.
3803 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
3804 o calc_gw: true flux-form, account for horizontal grid spacing.
3805 update rotating_tank results, but not plume_on_slope (affected at
3806 truncation level, 11 digits).
3807
3808 checkpoint58l_post (2006/07/12)
3809 o calc_gw:
3810 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
3811 - remove side-drag for now (need to fix it); update plume_on_slope results.
3812 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
3813 o commit code to make SST/SSS weights spatially variable
3814 (based on either variable in-situ or variable initial T/S weights)
3815 o pkg/ecco:
3816 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
3817 now based on horizontally varying weights wthetaLev, wsaltLev
3818 * cost_averagesflags now returns year indices in addition to day, month
3819 * sflux balance is performed on annual basis
3820 (sflxumm, sfluxmm2, bal_sfluxmm)
3821 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
3822 including separate counting and multipliers
3823 o pkg/rbcs
3824 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
3825
3826 checkpoint58k_post (2006/07/06)
3827 o testreport:
3828 - always build in dir. "build" (if not there, mkdir build instead of building
3829 & running in input)
3830 - run in dir run (if it exists), in build otherwise.
3831 - call prepare_run (if input/prepare_run exists)
3832 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
3833 o pkg/exf modifications to interpolation and rotation routines for more
3834 reasonable treatment of North Pole singularity: for tracers North Pole
3835 value is set to northernmost zonal-mean value, for zonal velocity it is
3836 set to zero, and for meridional velocity it is set to northernmost value.
3837 o pkg/exf/exf_check_range.F
3838 - add tile index to diagnostics and move stop statement to the very
3839 end of the routine.
3840 o pkg/diagnostics: (diagnostics_main_init.F)
3841 define title of isomorphic variables according to the current config.
3842 o pkg/thsice with pkg/seaice dynamics:
3843 - fix domain of computation (interior only, required for exf) and do exchanges
3844 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
3845 o towards a standard way of dealing with multi-threading in MONITOR
3846 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
3847 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
3848 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
3849 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
3850 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
3851 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
3852 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
3853 o tracer advection:
3854 - clean-up and simplify calc_common_factors.F
3855 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
3856 advection subroutine (but still not used within DST advection S/R)
3857 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
3858
3859 checkpoint58j_post (2006/06/15)
3860 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
3861 from file (collects calls previously in FORWARD_STEP)
3862 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
3863 o adjoint store dir. adjusted accordingly
3864 o genmake2
3865 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
3866
3867 checkpoint58i_post (2006/06/14)
3868 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
3869 on wind stress (SEAICEstressFactor defaults to 1.)
3870 o Total number of Timers is finite (<=40): comment out 2 non-essential one
3871 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
3872 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
3873 on CS-grid: no longer loosing mass.
3874 o exf & curvilinear-grid: no longer modify longitude xC & xG.
3875 o pkg/ggl90: fix sloppy output and fix a bug
3876 o pkg/seaice: added SEAICEuseEVPpickup parameter
3877 - Set to false in order to start EVP solver with
3878 non-EVP pickup files when using SEAICEuseEVP
3879 - fix sign error in diffusion in seaice_calc_rhs
3880
3881 checkpoint58h_post (2006/06/07)
3882 * Modifications for bottom topography control
3883 o replace hFacC by _hFacC at various places
3884 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
3885 o add non-self-adjoint cg2d_nsa
3886 o update autodiff support routines
3887 o re-initialise hfac after ctrl_depth_ini
3888 o works for 5x5 box, doesnt work for global_ocean.90x40x15
3889 * Adding verification for 5x5 box (4-layer) bottom topography control
3890
3891 checkpoint58g_post (2006/06/07)
3892 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
3893 used for mean seasonal cycle, mean diurnal cycle); add an example
3894 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
3895 o pkg/ggl90:
3896 - add parameter (minimum surface kinetic energy)
3897 - fix bug (avoiding division by zero)
3898 o couple pkg/thsice to pkg/seaice:
3899 - modify advection in seaice to accomodate new scalar fields to be advected
3900 - only muliDimAdection scheme work with seaice/thsice
3901 - mapping of thsice-variables to seaice-variables, back and forth
3902 - does not break the verification experiments, but does not give the
3903 desired results either
3904 o pkg/seaice
3905 - make (default) second order advection a bit less confusing?
3906
3907 checkpoint58f_post (2006/06/05)
3908 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
3909 to pkg/seaice):
3910 - new routines thsice_map_exf and thsice_get_exf provide the interface
3911 - add an additional formal parameter to thsice_solve4temp
3912 o pkg/exf:
3913 - add new fields wspeed, snowprecip (to be able to couple to thsice)
3914 - correct Stefan-Boltzmann constant
3915 - new parameter for longwave surface emittance
3916 - separate some stuff from exf_bulkformulae into new routines
3917 exf_radiation, exf_wind
3918 - add new parameters and constants: longwave emissivity for ocean, ice
3919 and snow, evaporation parameters over ice
3920 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
3921 either wind from stress or stress from wind
3922 o pkg/thSIce:
3923 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
3924 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
3925 and THSICE_CALC_THICKN
3926 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
3927 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
3928 to make debugging easier.
3929 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
3930 o pkg/bulk_force:
3931 - clean-up comments and parameters ;
3932 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
3933 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
3934 generate new output for test-experiment: aim.5l_cs.thSI
3935 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
3936 testreport accordingly
3937
3938 checkpoint58e_post (2006/05/17)
3939 o SEAICE_CGRID adjoint done
3940 o R_STAR adjoint implemented.
3941 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
3942 * need to sort out init. of h0facc, etc.
3943 o Make pkg/profile fully independent of ecco,cost, etc. stuff
3944 to be able to use it in pure forward.
3945
3946 checkpoint58d_post (2006/04/21)
3947 o upgrade simple test-experiment to tutorial example:
3948 step.1: duplicate the experiment and (step.2) will remove the old copy.
3949 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
3950 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
3951 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
3952 tutorial_global_oce_biogeo <- copy of dic_example
3953 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
3954 tutorial_plume_on_slope <- copy of plume_on_slope
3955 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
3956 tutorial_global_oce_optim <- empty for now (David ?)
3957 tutorial_global_oce_in_p <- copy of global_ocean_pressure
3958 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
3959 o correct a sign problem in cost_scat.F
3960 o obcs and ptracers: fix boundary conditions for advections schemes
3961 with larger stencil
3962 o thsice adjoint: start
3963 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
3964 completeness
3965 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
3966 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
3967 o ptracers adjoint:
3968 * avoid extensive recomputatations
3969 * fix missing re-init. of gptr (missed by TAF)
3970 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
3971 me to turn off the excessive output to STDOUT that this package produces
3972 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
3973 and add those terms in Vector-Invariant formulation.
3974 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
3975 if the control period (xx_hfluxperiod etc) is 0
3976 o in profiles pkg, clean routines and fix details
3977 o in ecco pkg, reading ssh data:
3978 fix problem in case the model does not start at iter0=0
3979 o fix mnc-pickup/restart for ptracers
3980 o new package prifiles:
3981 code to compute profile-based cost by Gael Forget
3982 (modifs in ecco, ctrl, autodiff)
3983 o Benign bug fix in initialization (spotted by M. Mazloff) of
3984 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
3985
3986 checkpoint58c_post (2006/03/23)
3987 o adjoint: finish NLFS adjoint and provide reference output in
3988 verification/global_ocean.90x40x15/results_ad_nlfs
3989 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
3990 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
3991 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
3992 with SEAICE_CGRID defined.
3993 o move calendarDumps from "data" to "data.cal" and clean-up the code
3994 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
3995 o add useEXF & useCAL flags (for now, set in hard-coded way)
3996 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
3997 (were missing in NH mode, and wrong in quasihydrostatic mode).
3998 waiting for Chris updated version of calc_gw to add those CALLs.
3999 o fix bug in quasihydrostatic S/R ;
4000 add a test for this option: global_ocean.90x40x15.qshyd
4001 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
4002 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
4003 o add on/off flag useOffLine for package OFFLINE
4004 o seaice:
4005 - modify advection so that it works also on the C-grid
4006 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
4007 problem in multi-tile runs with C-grid
4008 - add flags for clipping ice velocities and/or masking solver forcing
4009 - fix drag (ocean on ice) formulation and a bug that caused noise in the
4010 C-grid solver
4011 - added a few comments to seaice_diffusion.F
4012 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
4013 are now exclusive)
4014 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
4015 required re-ordering the code a little:
4016 + make DAIRN global variable (defined in SEAICE)
4017 + move computation of the viscosities eta and zeta into a new separate
4018 routine (because I need to recompute them in seaice_ocean_stress.F)
4019
4020 checkpoint58b_post (2006/03/13)
4021 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
4022 update output.txt of exp. aim.5l_cs.thSI
4023 o various mnc cleanups and improvements:
4024 + shrink lookup tables by factor of ~4
4025 + better error reporting when running out of lookup space
4026 + able to handle longer path/file names (up to 500 chars)
4027 o adjoint:
4028 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
4029 - TBD: "hidden" mom_vecinv recomp. in dynamics
4030 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
4031 (allow to differentiate between forcing components using new integer flags:
4032 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
4033 and add new flag to put Dissipation tendency out of Adams-Bashforth.
4034 o ecco
4035 - enable trend removal from SSH anomaly obs.
4036 o adjoint
4037 - a fix for PmEpR when #undef EXACT_CONSERV
4038 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
4039 - try to fix "hidden" recomp. in forward_step for NLFS
4040 (NLFS seems broken sometimes after I checked it in)
4041 o seaice:
4042 - add c-grid version of the dynamic solver:
4043 + three new routines that are the c-grid substitute lsr, dynsolver
4044 and ostres
4045 + put a few fields that were local to dynsolver into global common
4046 blocks, so that I can move the computation of stresses etc into
4047 seaice_lsr (saves coding but may break the adjoint).
4048 - replace more hardwired parameters by runtime parameters
4049 - add ice masks that mask the rhs of the implicit solvers where there
4050 is no ice (commented out in seaice_dynsolver, because i am not sure
4051 if this works properly), eventually this should replace the clipping
4052 of ice velocities in seaice_dynsolver to +/-40cm/s.
4053 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
4054 include it only where its needed
4055 o move balancing of fluxes before the call of external_forcing_surf
4056 o seaice:
4057 - correct units of turning angles (now they are really in degrees)
4058 - move computation of GWATX/Y out of main routine into dynsolver
4059 - initialize GWATX/Y in seaice_init
4060 o Apply mask on Fresh-Water flux (needed for SSH forcing).
4061 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
4062 o seaice: add runtime flags for turning angles (default to zero)
4063 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
4064 and trend from exf forcing and ctrl control adjustments
4065 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
4066 (since checkpoint57x_post)
4067 o change the default rotation period to 86164.s = the Earth rotation
4068 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
4069 and based on a reference stratification. Tested within hs94.cs-32x32x5.
4070 o seaice advection: add code for choosing between the default (2nd order
4071 central differences) and multiDim advection schemes provided by
4072 pkg/generic_advdiff
4073 o seaice:
4074 - removed all references to SEAICE_GRID.h fields from
4075 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
4076 (cubed-sphere configuration will change a little)
4077 - grid computations in seaice_init are obsolete now.
4078 - cleaned up code a little so that is easier to read (hopefully).
4079 - added new (better?) discretizations of default advection and diffusion
4080 (turn on with SEAICEuseFluxForm)
4081 - replace 1 in 3d global fields by kSurface in growth.F
4082
4083 checkpoint58a_post (2006/02/13)
4084 o seaice:
4085 - bug fix in advect.F
4086 o shelfice:
4087 - separate shelfice load anomaly from pload (breaks with time
4088 dependent forcing), => introduce constant field shelficeLoadAnomaly.
4089 Its default is 0., but it may be computed more cleverly from (unknown)
4090 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
4091 done offline. A good approximation of the pressure load anomaly is
4092 necessary to avoid large initial adjustment processes underneath
4093 deep-reaching shelfice.
4094 - small fix in ISOMIP shelfice_thermodynamics
4095 - add more sophisticated thermodynamics of Hellmer (1989), this is
4096 now the default
4097 - give a few constants more intuitive names
4098 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
4099 if bulk formulae are used in long integration (especially EmPmR). Turn
4100 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
4101 if balancePrintMean, the imbalance that is substracted is printed to
4102 STDOUT.
4103 o fix bug (typo) in obcs_apply_eta.F
4104 o add a new package shelfice which enables us to model the circulation
4105 underneath shelf-ice with draughts of hundreds of meters.
4106 - works
4107 - to do: + include improved thermodynamics
4108 + check whether kSurfC (from model/inc/SURFACE.h) can be used
4109 instead of new field kTopC
4110 + can we use topoFile, Ro_surf and existing code in ini_depth.F
4111 instead of new field R_shelfIce and new code in ini_depth.F
4112 and ini_mask_etc.F?
4113 + adjust vertical mixing schemes?
4114 o seaice pkg:
4115 - add a cpp-flag to include a simple formula for a salinity dependent
4116 freezing point of sea water at the surface
4117 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
4118 meridional stresses are now different (and hopefully correct)
4119 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
4120 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
4121 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
4122 o pkg/diagnostics: add options and parameters for regional-statistics
4123 diagnostics ; define regions by reading a region-mask from a file
4124 (might add other options later)
4125 o pkg/bulk_force:
4126 - add option and parameters to use AIM surface-flux formulae.
4127 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
4128 others forcing fields (defined in PARM05, parameter file "data") are loaded
4129 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
4130 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
4131 - use the right EXCH call for uwind,vwind (to work on CS-grid).
4132 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
4133 and parameters (note: calcWindStress replaces .NOT.readwindstress).
4134 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
4135
4136 checkpoint58 (2006/01/12)
4137 o add "--embed-source" option to genmake2 which, when the supporting
4138 tools can be compiled (as determined by genmake2) will turn on the
4139 embed_files package which then embeds the entire MITgcm source code
4140 (*.[fFhc] + Makefile) used for the build within the executable
4141 - requested by CNH but off by default
4142 - adds a paltry <9MB to the mitgcmuv executable in most cases
4143 - only writes the output when useEMBEDSRC in eedata is true
4144 o clean up 3-dim. relaxation codes:
4145 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
4146 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
4147 * Thanks to Tom Haine for testing!
4148
4149 checkpoint57z_post (2005/12/31)
4150 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
4151 affects output (@ truncation level) of exp. plume_on_slope ; updated.
4152 o fix the pickup behavior for obcs in combination with ptracers
4153 o fix a bug in ptracers_external_fields_load
4154 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
4155 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
4156 o transfered surface NH pressure to eta field (if exactConserv).
4157 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
4158 and update lab_sea output.txt file.
4159 o completing 3-dim. relaxation code: additional term
4160 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
4161 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
4162 * At compile time, in "EXF_OPTIONS.h" set
4163 #define ALLOW_CLIMTEMP_RELAXATION
4164 #define ALLOW_CLIMSALT_RELAXATION
4165 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
4166 tauThetaClimRelax3Dim = 15552000.0,
4167 tauSaltClimRelax3Dim = 15552000.0,
4168 * 3 cases:
4169 1) Use a constant-in-time 3-dim. field
4170 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
4171 3) Real-time relax. to time-evolving prescribed field
4172 o Adding Laplacian-type smoothness constraint on
4173 initial and boundary (forcing) controls (ic, bc)
4174 * enable at compile-time via
4175 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
4176 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
4177 * Absolute scale somewhat unclear so far
4178 * no area weighting was included since no other cost term does so far
4179
4180 checkpoint57y_post (2005/12/08)
4181 First step for a NLFS adjoint
4182 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
4183 o new init. routines for calc_r_star, calc_surf_dr
4184 o still need to deal with ini_masks_etc
4185 o testreport seemed happy
4186 checkpoint57y_pre (2005/12/08)
4187
4188 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
4189 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
4190 o add new offset feature to offline pkg (plus minor cleanup)
4191 o cfc fixes for final year of integration
4192 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
4193 be in GCHEM_OPTIONS).
4194
4195 checkpoint57x_post (2005/12/04)
4196 o fix testreport Pb in multiple test experiment.
4197 o cleanup our namelist syntax in verification:
4198 - make it more F95 standards compliant (some work still needed)
4199 - allows the vast majority of our tests to work with gfortran
4200 o Non-Hydrostatic:
4201 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
4202 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
4203 o Allow to apply AB on T,S rather than on AB(gT,gS):
4204 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
4205 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
4206 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
4207 - need a "clever" read_pickup to restart from the other AB formulation
4208 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
4209 o remove some unused variables (reduces number of compiler warnings)
4210 o adjoint
4211 * Disable useVariableViscosity for adjoint for time being
4212 (there are a number of extensive recomputations)
4213 * Initialize certain variables needed for adjoint
4214
4215 checkpoint57w_post (2005/11/03)
4216 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
4217 fix the singleCpuIO RS version of MDSWRITEFIELD
4218 and add a WARNING if using globalFiles=T with multi-processors.
4219 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
4220 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
4221 o tracer advection scheme:
4222 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
4223 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
4224 was not very convenient).
4225 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
4226 (further tests needed for the implicit DST & Flux-Limiter schemes).
4227 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
4228 and sRef for convenience, handy, when you want to initialize
4229 ptracers in a large domain with a constant non-zero value. Also,
4230 untangle ptracers_init.F a little.
4231
4232 checkpoint57v_post (2005/10/13)
4233 o change dome exp. to use variable viscosity in side-drag terms.
4234 o remove all the files from the cfc_offline test since they are now
4235 incorporated into tutorial_cfc_offline which has been producing
4236 identical results for a few days of testing
4237 o add new parameter: sideDragFactor to enable half-slip-side BC
4238 and change side-drag S/R to use viscosity from mom_calc_visc
4239 (can switch back by setting sideDragFactor=0.); affects results at
4240 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
4241 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
4242 o vorticity & strain are now computed without masking, to account for
4243 no-slip-side BC in variable viscosity calculation ; mask is applied
4244 anyway later on, before computing advection/coriolis terms.
4245 o modify exp4 to test new obcs support for reading from external files
4246 and for passive tracers
4247 o fix behavior of ptracers_monitor when monitor output is written to a
4248 netcdf-file; still not independent of monitor.F (writes in the same
4249 file).
4250 o change default value of tRef (put a uniform, meaningful value for ocean
4251 & atmos) and initialize sRef (was missing, as Martin mentioned).
4252 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
4253 to be proportional to enstrophy dissipation length. Thus,
4254 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
4255 This is now consistent with Smagorinsky and with the manual.
4256
4257 checkpoint57u_post
4258 o OBCS and PTRACERS: add open boundary support for passive tracers
4259 - either use homogenous (pseudo) v.Neumann conditions or prescribe
4260 OB-values from file; this is not different from the way theta and salinity
4261 are treated
4262 - however, Orlanski-radiation conditions are not supported, and the model
4263 will stop if you use pTracers and Orlanski at the same time.
4264 - beefed up the rountine obcs_external_fields_load: now only those open
4265 boundary values are overwritten with values from files for which there
4266 are really files, otherwise the OB-fields remain untouched. This makes
4267 it possible to use different OBs at different ends of the domain (as
4268 with EXF)
4269 o reduce number of exch calls in shap_filt (s2).
4270 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
4271 truncation level) 4/5 MLAdjust test results (11&12 digits match).
4272
4273 checkpoint57t_post (2005/10/03)
4274 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
4275 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
4276 same truncation, independent of the face number: affects affects several
4277 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
4278 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
4279 note that biharmonic viscosity + no-slip was not tested in any experiment.
4280 o fix bug in non-linear free-surf side-drag ; generate new output for
4281 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
4282 o make mnc honor the writeBinaryPrec flag for most kinds of output
4283 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
4284 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
4285 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
4286 o add brackets in multi-terms sum to get same truncation, independent of
4287 the face number (manage to get exactly same value of gU,gV at the cs-edge)
4288 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
4289 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
4290 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
4291 a maximum grid-scale Reynolds number. Also, changes all length calculations
4292 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
4293 Suggested values of viscosity parameters found in mom_calc_visc.
4294 Many new viscosity diagnostics available.
4295
4296 checkpoint57s_post (2005/09/20)
4297 o Add clearing-house for viscosity calculations, mom_calc_visc and
4298 correct numerous bugs in LeithD and Smagorinsky discretizations.
4299 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
4300 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
4301 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
4302 and with Strain-Tension viscous term calculation (mom_hdissip.F).
4303 The Strain-Tension form is now called with useStrainTensonVisc=.true.
4304 ViscAhStrain and viscAhTension are now retired.
4305 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
4306 o In response to JMC's bug report, genmake2 now ignores any soft-links
4307 that it finds in the *current* directory when searching for files.
4308 Soft-links found in any other source directories will still work as
4309 they did before.
4310 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
4311 a C routine to unlimit the stack size
4312 o mnc-ify pkg/aim snapshot vars
4313 o mnc-ify pkg/land as requested by Daniel
4314 o various changes to mnc including:
4315 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
4316 - output can now be grouped so that all files within a group
4317 change the ITER portion of their names in lock-step together
4318 - can now read ("global") PER-FACE (in addition to PER-TILE) files
4319 and works with both EXCH1 and EXCH2 (but needs more testing)
4320 - writing works for all verification test cases w/ g77 on Linux
4321
4322 checkpoint57r_post (2005/09/07)
4323 o make MNC variable initialization happen earlier
4324 o add diagnostics for (almost) each term of the momentum Eq.
4325 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
4326 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
4327 o remove MINIMAL_TAVE_OUTPUT option ;
4328 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
4329 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
4330 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
4331 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
4332 o add time-dependent SST, SSS control
4333 o cost terms in ecco/ modularized (new cost_generic.F)
4334 o cost_averages routines are modularized (new cost_averagesgeneric.F)
4335 o new infrastructure for seaice model vs. obs misfits in seaice/
4336 * driver from the_main_loop.F is seaice_cost_driver.F
4337 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
4338 * gradient check in Exp. 6a of natl_box_adjoint/
4339 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
4340 (see README file)
4341
4342 checkpoint57q_post (2005/08/19)
4343 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
4344 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
4345 - bug was reported by Jean-Michel and Ian Fenty
4346 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
4347 update exp. cpl_aim+ocn output.
4348 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
4349 Needed for high-res. runs with large global files
4350 to be able to limit tapelev size
4351 o Changed some tests for adjoint:
4352 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
4353 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
4354 * global_ocean.90x40x15/ back to default 3-level checkpointing
4355 o Modifications to enable scripted COMMON to MODULE conversion
4356 * verification/OpenAD/code/ has necessary scripts and description;
4357 * converts, compiles and runs successfully;
4358
4359 checkpoint57p_post (2005/08/01)
4360 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
4361 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
4362 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
4363 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
4364 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
4365 (was already the case for dissipation with mom_vecinv,
4366 and also the case for grad.PhiHyd when staggered-timeStep)
4367 This will allow to put dissipation out-off the AB time-stepping.
4368 Unfortunately, affects truncation error. Update output of exp. that "fails"
4369 (cg2d matching number) and leave the others for later: front_relax(10),
4370 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
4371 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
4372
4373 checkpoint57o_post (2005/07/30)
4374 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
4375 (2) its ready to be documented during the 20050801 DocFest
4376 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
4377 for ideal_2D_oce and lab_sea on linux_ia32_g77
4378 o set to #undef CTRL_SET_OLD_MAXCVARS_30
4379 in global1x1_tot/code_seaice_adj to access indices 32, 33
4380 (worth another tag)
4381
4382 checkpoint57n_post (2005/07/29)
4383 o adding precip control xx_precip 32
4384 o adding swflux control xx_swflux 33
4385 o Replacing 10 forcing penalty cost routines by 1 generic.
4386 o Implementing partitioning in time-mean and variable adjustment
4387 for atmos. state.
4388 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
4389 o in natl_box_adjoint:
4390 * updated exp 1 to 10
4391 (but does not have time-mean vs. variable split results yet)
4392 o updated global1x1/*_seaice_adj/
4393 to incorporate latest changes
4394 o enable useSingleCpuIO for mdsio vector routines
4395 (applies in particular to tapelev I/O)
4396 o removed inefficient K-loop in all active_file*control*.F
4397
4398 checkpoint57m_post (2005/07/28)
4399 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
4400 and advect_cs (use EXCH-2 and standard cs-32 grid files).
4401 o pkg/exch2: filling of face-corner halo regions is optional
4402 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
4403
4404 checkpoint57l_post (2005/07/14)
4405 tag before updating tutorials (pre-release-2)
4406 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
4407 for output and interpolation of input fields onto model grid)
4408 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
4409 Affects results of exp. rotating_tank ; update output.txt.
4410 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
4411 and taking the square quantity and/or using a fraction-weight field.
4412 o fix aim_diagnostics_init.F mate numbers.
4413 o add mnc output capability to diagnostics/diagstat and update
4414 our cvsignore files for the ACSII output generated
4415
4416 checkpoint57k_post (2005/07/02)
4417 o lab_sea now uses diagnostics package and provides a suite of
4418 new EXF diagnostics output.
4419
4420 checkpoint57j_post (2005/06/30)
4421 o exf
4422 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
4423 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
4424 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
4425 * extended diagnostics output
4426 - now includes all EXF variables
4427 - hs, hl moved to common block
4428 - separate S/R for diagnostics, called after ctrl vector is added
4429 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
4430 - EXFqnet contains true Qnet (i.e. includes qsw)
4431 * updated verif. lab_sea, global_with_exf
4432 * Rearranging hflux (exf_mapfields -> exf_getforcing)
4433 to ensure that diagnostics sees a true EXFqnet
4434 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
4435 o diagnostics pkg: change pointers so that 1 diagnostic can be used
4436 several times with different frequencies.
4437 o mnc-ify the thsice package as requested by Daniel Enderton
4438 - the monitor--MNC output needs work
4439 - many attributes need to be added (most are currently blank)
4440 o mnc-ify theaim_v23 package as requested by Daniel Enderton
4441 - many attributes need to be added (most are currently blank)
4442 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
4443 o add Sadourny like discretization to the 4th.O vorticity advection scheme
4444 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
4445 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
4446 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
4447 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
4448 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
4449
4450 checkpoint57i_post (2005/06/19)
4451 o Diagnostics package was changed: diagnostic allocation is now deactivated
4452 by setting an empty file name in the namelist (used to be by setting 0 frequency)
4453 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
4454 add 1rst Order upwind vertical Shear.
4455 o add a quick fix for A/B checkpointing in OFFLINE mode
4456 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
4457 end-run around the C/Fortran linking horror in eesup/src/timers.F
4458 o added pkg/runclock: allows user to terminate run based on wall clock
4459 o added non-hydrostatic scaling parameter: nh_am2
4460 o pkg/my82: futile attempt to make results compiler-independent by adding
4461 some "_d 0", etc. no effect.
4462 o for mnc output, fill the 'T' coordinate var with myTime and create a
4463 separate 'iter' variable for iteration count
4464 o pkg/diagnostics:
4465 add new capability: output of Global/Regional & per-level statistics ;
4466 tested against monitor output (including land & thSIce) on various exp.
4467 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
4468
4469 checkpoint57h_done (2005/05/19)
4470 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
4471 data.diagnostics, data.gchem, data.ptracers) is done.
4472
4473 o pkg/diagnostics: prepare for Global/Regional statistics.
4474 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
4475 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
4476 and rename it: DIFFERENT_MULTIPLE
4477
4478 checkpoint57h_post (2005/05/14)
4479 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
4480 o pkg/diagnostics: change output frequency, now in seconds (instead
4481 of Nb of iterations). This requires to change data.diagnostics.
4482 checkpoint57h_pre (2005/05/12)
4483
4484 o in mnc, let the user create the output dir if both mnc_outdir_date
4485 and mnc_outdir_num are false
4486 o add fflags() to pkg/diagnostics which allows one to specify, on a
4487 per-file basis, the file precision [default behavior is unchanged]
4488 o added diagnostics to pkg/kpp, including computation of mixed layer
4489 depth based on a temperature/density criterion
4490 o updated verification/natl_box to test the new pkg/kpp diagnostics
4491 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
4492 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
4493 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
4494 not mnc -- this mistake was found by JMC and is now corrected
4495
4496 checkpoint57g_post (2005/04/15)
4497 o add Adams-Bashforth 3rd Order time stepping:
4498 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
4499 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
4500 checkpoint57g_pre (2005/04/15)
4501
4502 o make lambda[Theta,Salt]ClimRelax spatially varying
4503 (default remains spatially uniform constant based on tau)
4504 o added new control variables
4505 * init. uVel, vVel, etanN
4506 * lambda[Theta,Salt]ClimRelax
4507 o separate masks used for ctrl_pack/unpack 'from write_grid' output
4508 (suggested by G. Forget)
4509
4510 checkpoint57f_post (2005/04/06)
4511 o add parameter "baseTime" = model base time = time at iteration zero
4512 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
4513 account for baseTime shift
4514 o move Coriolis arrays from PARAMS.h to GRID.h
4515 checkpoint57f_pre (2005/04/06)
4516
4517 o mnc-ifying the seaice package
4518 o introduced an alternative length scale calculation for use in the limiting
4519 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
4520 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
4521 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
4522 as well as grad(vort3). Made it compatible with both approximate form
4523 for the cubed sphere and full form of these gradients. Added flag
4524 useFullLeith to select between approximate and full form.
4525 o add "d0" in getcon.F to reduce differences between compilers/platforms
4526 update output.txt of exp. fizhi-gridalt-hs
4527 o change port_rand funtion to allow to set the seed.
4528 o fix obscure MNC bug involving conversion between reals and integers
4529 - it caused no problems with certain (eg. gcc, ifc) compilers but the
4530 new version is now more standards-compliant
4531 o adjoint-related modifications
4532 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
4533 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
4534 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
4535
4536 checkpoint57e_post (2005/02/28)
4537 o Adding eddy stress controls a la Ferreira et al.
4538 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
4539
4540 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
4541 update output.txt of exp. fizhi-gridalt-hs
4542 o add more "Z" dimensions and associated coordinate vars to MNC
4543 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
4544 o parameter calendarDumps: when set, approximate months (30-31 days) and years
4545 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
4546 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
4547 months and years. Requires pkg/cal.
4548 o diagnostics: add pickup functionality
4549 - off by default for backwards compatibility
4550 - current version only uses MDSIO -- MNC will be added
4551 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
4552 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
4553
4554 checkpoint57d_post (2005/02/11)
4555 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
4556 o modify verification/ideal_2D_oce so that it tests the creation of mnc
4557 output from the diagnostics package
4558 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
4559 o make genmake2 more portable by using ".$FS" instead of ".f" for more
4560 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
4561 o add coordinate variables to the MNC output from the diagnostics package
4562 o change MNC-flags default value: true when useMNC=TRUE
4563 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
4564 the ability (off by default) to read the grid information using MNC
4565 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
4566 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
4567 o do snap-shot diagnostics at the middle of the time-interval (instead of
4568 at the end).
4569 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
4570 new test for AIM with thSIce + slab-ocean
4571 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
4572 o move state variable diagnostics to the beginning of the time step ;
4573 (note: still needs some work specially for snap-shot diagnostics)
4574 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
4575
4576 checkpoint57c_post (2005/01/27)
4577 o Change testing option (-ieee) to get closer agreement between g77 & ifort
4578 o generate new output.txt files on faulks with g77 & the new -ieee option
4579 checkpoint57c_pre (2005/01/27)
4580
4581 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
4582 update output.txt of exp. global_ocean.90x40x15
4583 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
4584 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
4585 o add saltFlux(+File) forcing capability with periodicExternalForcing
4586 o allow to use pkg diagnostics for GM-Redi & ThSIce output
4587 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
4588 o improvements for the MNC output from DIAGNOSTICS:
4589 - correct handling of the unlimitied dimension
4590 - all dims now have associated coordinate variables
4591 - variables located at U, V, and Corner ("Z") points are now written
4592 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
4593 *all* data points are output
4594 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
4595 o added pkg/seaice/seaice_monitor.F
4596 o mdsio_readfield.F can now read files visible only to master MPI process.
4597 o pkg/seaice: some test code for ice-modified ocean stress
4598 o exf_getffields interpolation defaults to bilinear for all scalar forcing
4599 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
4600 spurious negative numbers for precipitation and humidity. Will cause
4601 some small numerical differences for integrations using pkg/exf/exf_interp.F.
4602 o pkg/ctrl/
4603 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
4604 May be enabled via doPackDiag
4605 * introduce z-scaling of
4606 + gradient (doZscalePack) and
4607 + control (doZscaleUnpack)
4608 o pkg/mdsio/
4609 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
4610 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
4611
4612 checkpoint57b_post (2004/12/20)
4613 o simplify options in diagnostics_fill arguments (remove weird combinations)
4614 o fix MNC coordinate variables so that they now contain per-face index
4615 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
4616 general, EXCH2 grids are only aligned to a "local" coordinate system
4617 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
4618 o Implement instantaneous output within pkg diagnostics:
4619 setting a negative frequency in data.diagnostics produces
4620 "snap-shot" output (as opposed to time-average if freq > 0)
4621 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
4622 NOTE: change ptracer diagnostics name: use 2 characters to work with
4623 more than 9 tracers. Add also diagnostics of advect & diffus flux.
4624 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
4625 becomes the coordinate variable for the 'T' dimension
4626 o add CF-style coordinate variables to MNC
4627 - just a first cut: numbers are meaningless on the cubesphere and
4628 missing along the T axis but otherwise it works!
4629 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
4630 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
4631 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
4632 this is based directly on what the model compute, so that the content of
4633 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
4634 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
4635 o clean up build options files for SunOS, in particular
4636 - remove -traditional from xmakedepend
4637 - change -xarch=v9 to -xarch=native for f77
4638 - restore use of make (not gmake)
4639 - add CC=gcc if using g77
4640 o changes per discussion of AM, JMC, & EH3 today:
4641 - move redundant "grid" variables out of "state" -- in preparation of
4642 creating proper CF-style coordinate variables and in recognition
4643 that any/all grid variables can be easily copied (eg. w/NCO) from
4644 the grid files into any of the other NetCDF files
4645 - *always* output grid variables with MDSIO (this will eventually be
4646 changed)
4647 - output MNC grid file if useMNC is true
4648 o every instance of _END_MASTER() has been found and replaced with
4649 _END_MASTER( myThid ) in order to satisfy certain picky Sun
4650 preprocessors
4651 o re-arrange diagnostics pkg initialisation:
4652 - allow each package to extend the available diagnostics list
4653 - add some checking and fix small problems (multi-threaded, ...)
4654 - new S/R diagnostics_fill (replace fill_diagnostics):
4655 look through the short list of active diag. (instead of the long list)
4656 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
4657
4658 checkpoint57a_post (2004/12/10)
4659 o this set of changes restores TAMC compatibility
4660 tested for global_ocean.90x40x15 adjoint on trough
4661 (what a pain)
4662
4663 checkpoint57a_pre (2004/12/10)
4664 o some modifs in tools/build_options for sunos
4665 o call ctrl_pack for ctrl at end for optimcycle=0
4666
4667 checkpoint57 (2004/12/09)
4668 o add horizontal bi-harmonic viscosity for vertical velocity
4669 - new parameter viscA4W (defaults to viscA4)
4670 - affects only non-hydrostatic code
4671 - to be done: no-slip lateral boundary conditions
4672 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
4673 o implement Implicit Vertical advection for pTracers
4674 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
4675 (implemented also for implicit vertical diffusion & advection)
4676 o OBCS: extend application of tracer open boundary conditions
4677 to a strip beyond the boundary of width Olx/Oly
4678 o add call monitor to TAF set of required calls (flow directives)
4679 and include in natl_box_adjoint
4680 o untangle a few ifdefs related to cost, ctrl, autodiff
4681 untangel a few ALLOW_ECCO_OPTIMIZATION
4682 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
4683 (theta2, salt2 in ecco_cost_weights)
4684
4685 checkpoint56c_post (2004/12/03)
4686 o OBCS as control variables
4687 - update ctrl_ad_diff.list, obcs_ad_diff.list
4688 - remove balance of obcs controls from default
4689 - fix index bug nobcs in ctrl_init
4690 - fix dummy fields filen in ctrl_pack
4691 - add dummy weights for obcs
4692 o lsopt: comment out fort.94 output
4693 o optim:
4694 - remove unnecessary header files
4695 - adjusted namelists
4696 - add xerbla.F to Makefile
4697 o exf:
4698 - multiple modifications of exf_check_range
4699 - unit change in exf_init_runoff from [m/year] to [m/s]
4700 o mdsio:
4701 - i/o-vector change debugLevel from debLevA to debLevB
4702
4703 checkpoint56b_post (2004/12/01)
4704 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
4705 is called from DO_THE_MODEL_IO
4706 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
4707 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
4708 - clean up PTRACERS_WRITE_TIMEAVE a little
4709 o add another verification experiment that tests both the cfc-pkg and
4710 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
4711 reactive tendencies treated inline with regular timestepping
4712 o testreport previously did a lousy job of comparing small numbers, so
4713 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
4714 implemented in the little c-progam tmp_cmpnum.c which is embedded in
4715 testreport.
4716 o ptracers_monitor: bug fix for MPI
4717
4718 checkpoint56a_post (2004/11/28)
4719 o GCHEM: finish reorganizating the package
4720 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
4721 (introduces another 3D-array for each passive tracer, but only if
4722 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
4723 gchemTendency is not needed because the timestep is done separately)
4724 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
4725 - GCHEM is now---more or less cleanly---separate from PTRACERS
4726 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
4727 so clear to me how that should be done in a general way.
4728 o CFC: improve formatting of output in CFC_ATMOS
4729 o PTRACERS:
4730 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
4731 that ALL experiments with ptracers enable can be checked. This makes
4732 GCHEM_MONITOR obsolete.
4733 - include a runtime parameter PTRACERS_monitorFreq that defaults to
4734 monitorFreq
4735 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
4736 o add PTRACERS (PTR0[1-5]) to testreport output
4737 o exf_check_range:
4738 * default changed to .TRUE.
4739 * will check values for niter0 if debLevA, every timestep if debLevB
4740 * STOP in exf_check_range if 'out of range'
4741 * range chosen generous to allow for potential extema
4742 TBD: a version with stricter range
4743 permitted range would be runtime parameters
4744 o GMredi:
4745 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
4746 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
4747 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
4748 o GCHEM:
4749 - move call to GCHEM_FORCING_SEP, so that it is now called before
4750 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
4751 - introduced a useGCHEM runtime flag and applied it everywhere.
4752 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
4753 this flag is now only visible within GCHEM-pkg routines.
4754 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
4755 be replaced by a 3D array that is computed before thermodynamics; for
4756 this, the tracer ID iTracer had to be included into the parameter list
4757 of ptracers_forcing
4758 - set up forward_step to call gchem_forcing, that will replace
4759 gchem_forcing_int in ptracers_forcing
4760 - cleaning up
4761 o small cleaning of exch2: remove files that are also in eesupp/src
4762
4763 checkpoint56 (2004/11/17)
4764 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
4765 o mnc: cleanup "full" files--fixes out-of-memory problem
4766 o ECCO-GODAE
4767 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
4768 * fully merged and updated from SIO code
4769 windstress sign change affects
4770 - exf_inscal_[u/v]stress
4771 - sign of xx_tau[u/v] adjustments
4772 - signs in cost_scat
4773 * ctrl_get_gen: avoid update of tau[u/v] for first few days
4774 * natl_box_adjoint updated and compressed
4775 * 2-level checkpoint switch added
4776 (tested in EXP. 1 of natl_box_adjoint)
4777 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
4778 o SVD
4779 * first complete, non-hacked version for SVD calculations
4780 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
4781 performed via direct access files admtlm_vector.it????
4782 (via ctrl_[un]pack)
4783 * optimcycle is used for ARPACK iteration counter
4784 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
4785 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
4786 and add linear transforms where necessary
4787 * controls are initial/final SST, SSS (can be extended; need to check
4788 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
4789 o mdsio: filename info to both stderr, stdout
4790 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
4791 from sign change
4792
4793 checkpoint55j_post (2004/11/10)
4794 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
4795 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4796 o add consistent build directories and .cvsignore files to verification
4797 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
4798 o make all subroutines 30 or less characters in length for certain older
4799 compilers to work (a thorough search only turns up two routines in
4800 pkg/ptracers)
4801 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
4802 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4803
4804 checkpoint55i_post (2004/10/28)
4805 o change arrays for total vertical diffusivity (2.D if explicit,
4806 3.D if implicit) ; each ptracer uses its own background value.
4807 o added mnc/NetCDF output capability to ocn_compon_interf
4808 - added bits to verification/cpl_aim+ocn so that it can run on
4809 ITRDA and other clusters without the mpirun "-wd" option
4810 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
4811 configuration
4812 o give MNC the ability to create additional files rather than
4813 exceeding a specified file size limit "MNC_MAX_FILESIZE"
4814 - the default is just less than 2GB which is a practical limit
4815 on many systems
4816 o Compute the non-local term using either KPP vertical diffusivity (=default)
4817 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
4818
4819 checkpoint55h_post (2004/10/20)
4820 o add verification test "vermix"
4821 o remove all the *_ioinc flags and replace with the single global
4822 outputTypesInclusive flag
4823 o allow to set a vertical profile of vertical diffusivity for T & S
4824 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
4825 o useMNC moved from data.mnc to data.pkg
4826
4827 checkpoint55g_post (2004/10/14)
4828 o Renaming carbon AD experiments to comply with testreport conventions
4829 o Updating adjoint of Held-Suarez hs94.1x64x5
4830 o Fixing directives for non-ECCO forward_step, after ECCO directives
4831 have been fixed to avoid recomp. of do_oceanic_phys
4832 Works well for global_ocean.90x40x15,
4833 but recomp. issue remains for carbon
4834 o Updating adjoint output for natl_box_adjoint after
4835 pkg/ecco has been modified (see taga c55d_post)
4836
4837 checkpoint55f_post (2004/10/13)
4838 o rename to timeave_init_fixed
4839
4840 checkpoint55e_post (2004/10/13)
4841 o some delicate re-shuffle of store directives to avoid one
4842 extra call of do_oceanic_physics
4843 affects ecco_the_main_loop.F, do_oceanic_physics.F
4844 checkpoint_lev1_directives.h
4845 o NB: this may break global_ocean adjoint temporarily,
4846 but it is clear how to fix it. Will do later, need this now.
4847
4848 checkpoint55d_post (2004/10/11)
4849 o ECCO specific cost function terms (up-to-date with 1x1 runs)
4850 o ecco_cost_weights is modified to 1x1 runs
4851 o modifs to allow observations to be read in as
4852 single file or yearly files
4853 o enable to read exf forcing fields as either
4854 single file or yearly files (flag useExfYearlyFields)
4855 checkpoint55d_pre (2004/10/08)
4856
4857 o switch between 2-level and 3-level checkpointing
4858 o add ability of MNC to write local and "partial" (eg. 2D slices where
4859 the full 3D field is never actually stored) arrays to NetCDF files
4860 with the correct (that is, the complete multi-dimensional) set of
4861 array indicies
4862 - used in mom_vecinv() to write the diagFreq output
4863 - tested (demonstrated) in verification/aim.5l_cs
4864 o further mnc-ification
4865 - add verification/lab_sea to the list with mnc setups
4866 - fix undefined mnc v-names in cd_code
4867 - add kpp to mnc output (both snapshot and timeave)
4868 o non-hydrostatic code
4869 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
4870 in calc_gw.F
4871 - defaults to viscAh
4872 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
4873 friction or Leith) in non-hydrostatic mode, as long as there is
4874 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
4875 o pkg/cost
4876 extend simple cost functions to treat time mean quantities
4877 (T,U,V) via cost_accumulate_state from cost_tile
4878 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
4879 be 2 times larger than the minimum size the advection scheme requires.
4880 now get a perfect conservation of salt in advect_cs test-exp (updated)
4881 o GGL90 (Gaspar's TKE mixed layer)
4882 - add horizontal diffusion of TKE, requires exchanges in
4883 do_fields_blocking_exchanges, horizontal diffusivity is zero by
4884 default. In OPA there is no horizontal diffusion of TKE but the
4885 mixing coefficients are computed from a horizontal average of TKE of
4886 6 points or so. I think that diffusion has a little more physical
4887 justification.
4888 - clean up ggl90_calc in the hope of reducing memory usage (this hope
4889 was in vain)
4890 - mask tke-variable in ggl90_init
4891 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
4892 o fix biharmonic diffusion on CS-grid.
4893 o more obcs stuff
4894 - added obcs_external_fields_load as an alternative to the EXF-pkg option
4895 for reading boundary values. This routine is called from
4896 obcs_prescribe_read
4897 - updated obcs_check
4898 - changed sponge layer relaxation parameter units for days to seconds
4899 - turned off sponge layer by default
4900 - changed argument list of OBCS_CALC to myTime+deltaTclock
4901 - fixed about 35 bugs in obcs_external_fields_load
4902
4903 checkpoint55c_post (2004/09/23)
4904 o obcs stuff
4905 - new runtime flags useOBCSprescribe, useOBCSbalance
4906 - re-arranged obcs_calc
4907 - moved exf_getobcs to obcs_prescibe_read
4908 obcs_prescibe_read is called after ORLANSKI stuff
4909 and independent of it (executable can contain all).
4910 - updated obcs_check
4911 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
4912 These may be necessary only if tangential velocities are
4913 prescribed at OB, not sure, needs testing.
4914 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
4915 which simplifies the calls and passes the ifc check-bounds test
4916
4917 checkpoint55b_post (2004/09/22)
4918 o add a 2D scalar, Z location, exchange_2 routine.
4919 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
4920 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
4921 affects advect_cs results (for the wrong reason): update output.txt
4922 o use a more standard discretization for biharmonic viscosity ;
4923 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
4924 affects results of dome set-up: update output.txt
4925 o fix gad_advection.F (CubedSphere part), back to version 1.23
4926 o fix bug in mom_vi_del2uv.F (CubedSphere part).
4927
4928 checkpoint55a_post (2004/09/20)
4929 o merged code to
4930 * prescribe/read time-dependent open boundaries
4931 (works in conjunction with exf, cal)
4932 * sponge layer code for open boundaries
4933 * each boundary N/S/E/W now has its own CPP option
4934 (healthy for the adjoint)
4935
4936 checkpoint55 (2004/09/17)
4937 o up-to-date adjoint of previous breaks
4938 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
4939 - global_ocean_ebm: adjoint still needs fix (TLM ok)
4940 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
4941 - carbon: * remove tr1-related adjoint verification
4942 * add ptracer as control variable
4943 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
4944 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
4945
4946 checkpoint54f_post (2004/09/16)
4947 o in verification/carbin/ remove experiment related to
4948 ALLOW_PASSIVE_TRACER (array tr1 etc)
4949 code_ad/ input_ad/ results_ad
4950
4951 o add two new packages
4952 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
4953 + subject to optimization (memory)
4954 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
4955 + subject to reordering (many GOTOs in the original code)
4956 + so far opps is called for every (i,j) point, and then operates in
4957 the vertical; one may want to reorder the scheme in order operate in
4958 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
4959 fields)
4960 o overhaul of IO so that we now have flags for MDSIO and/or MNC
4961 - all verification tests compile and run with linux_ia32_g77
4962 - defaults are compatible with current input files--nothing
4963 should change if you were not previously using MNC
4964 - MNC output has been added in numerous places (eg. timeave)
4965 but there are still a few writes not yet do-able with MNC
4966 (this is in progress)
4967 - flags now allow for either/or/both use of MDSIO and MNC and
4968 documentation will soon follow
4969 - numerous small formatting cleanups for ProTeX
4970 o add version info (via BUILD_INFO.h) to MNC and stdout
4971
4972 checkpoint54e_post (2004/09/02)
4973 o add two new packages
4974 - pp81 (Packanowski and Philander, 1981), Richardson number and
4975 stratification dependent mixing
4976 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
4977 - these scheme operate in a similar manner as KPP (without ghat, of
4978 course), however there is only one diffusivity that is used for both
4979 temperature and salinity (and passive tracers)
4980 o add offline package
4981 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
4982 provided by Stephanie Dutkiewicz
4983 o genmake2: add ability to search for C compilers and cleanup test output
4984 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
4985
4986 checkpoint54d_post (2004/07/27)
4987 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
4988 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
4989 leading to additional shift by 5 days each year of integration
4990 (i.e. leading to considerable offset over the years)
4991 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
4992 o start with no AB and no initial filtering (staggerTimeStep):
4993 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
4994 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
4995 (external loading & cpl import/export stay in forward_step.F)
4996 o update coupling interface to work with new staggerTimeStep
4997 o change MDSIO ptracers_pickup.
4998 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
4999 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
5000 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
5001
5002 checkpoint54c_post (2004/07/18)
5003 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
5004 this affects (truncation error) output.txt of test-exp:
5005 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
5006 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
5007 o change Qnet to always be the net heat flux, (+upward).
5008 affects (truncation error) output of natl_box exp.: updated
5009 o define the max number of passive tracers in PTRACERS_SIZE.h
5010 o start to test mnc routinely in exp0
5011 o add sea-ice loading (sIceLoad) as a new forcing field.
5012
5013 checkpoint54b_post (2004/07/08)
5014 o add testreport "-j JOBS" option for parallel builds (tested and pretty
5015 impressive on Altix and Opteron systems)
5016 o diagnostics can now write NetCDF files through the mnc package
5017 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
5018 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
5019 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
5020 affects (truncation error) output of lab_sea & natl_box exp.: updated
5021 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
5022
5023 checkpoint54a_post (2004/07/06)
5024 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
5025 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
5026 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
5027 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
5028 + internal_wave (shift in writing cg2d_ini_res)
5029 checkpoint54a_pre (2004/07/05)
5030
5031 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
5032 - modified verification/lab_sea and natl_box_adjoint accordingly
5033
5034 checkpoint54 (2004/07/02)
5035 checkpoint53g_post (2004/07/02)
5036 o prepare splitting of thermodynamics: store convect.counter in common block
5037 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
5038 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
5039 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
5040 o new parameter "nShapS": allow to treat differently S from T (nShapT)
5041 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
5042 o restore adjointability
5043
5044 checkpoint53f_post (2004/06/25)
5045 o modifications that affect AIM experiment results (update output.txt):
5046 - no advection of S at top interface Nr (pkg/generic_advdiff)
5047 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
5048 o AIM pkg:
5049 - include stability function into surf.Flux derivative relative to Tsurf
5050 - calculate clear-sky radiation & surface temp. change (for diagnostics)
5051
5052 checkpoint53e_post
5053 o merged cylindrical coord configuration
5054 o added rotating_tank experiment
5055 checkpoint53e_pre
5056
5057 checkpoint53d_post (2004/06/14)
5058 o faulks upgraded: re-generate output.txt that have changed:
5059 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
5060 o Added Bryan and Lewis, 1979, vertical diffusivity profile
5061 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
5062 o added Sadourny discretization of Coriolis
5063 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
5064 - re-enabled use of omega3 (useAbsVorticity)
5065 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
5066 vector-invariant equations
5067 - note: does *NOT* yet use same variable visc. for no-slip BC's.
5068 o recoded the lateral boundary conditions for non-hydrostatic w, this time
5069 hopefully without new bugs
5070 - still to do: biharmonic friction for non-hydrostatic w
5071 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
5072 o regenerated output for global_ocean_ebm (using -ieee)
5073 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
5074 of mom_common/
5075 - simple re-arrangement of instructions within computing loop
5076 checkpoint53d_pre (2004/05/21)
5077
5078 checkpoint53c_post (2004/05/21)
5079 o new version of coupler for AIM+thSIce and Ocean models
5080 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
5081 - land: change Evaporation of snow
5082 - aim with thSIce: fix bug in snow-precip.
5083 o changes to calc_gw.F
5084 - bug fix for w^2 term near the bottom boundary
5085 - (hopefully) improve the lateral slip boundary condtions for use with
5086 partial/looped cells
5087 - because the bug fix changes two verification experiments anyway (exp5
5088 and plume on slope), change the lateral boundary condition from half slip
5089 to the value of no_slip_sides
5090 o ebm package wasnt quite up to the parallel task. Fixed that.
5091 o Adjoint of EBM package + verification
5092 * TLM OK
5093 * ADM not sufficient accuracy yet (needs further testing)
5094
5095 checkpoint53b_post (2004/05/14)
5096 o Commiting new energy balance model to repository
5097 * package is pkg/ebm
5098 * verif. is verification/global_ocean_ebm
5099 * references are in ebm_driver.F
5100 C * X. Wang, P. Stone and J. Marotzke, 1999:
5101 C Global thermohaline circulation. Part I:
5102 C Sensitivity to atmospheric moisture transport.
5103 C J. Climate 12(1), 71-82
5104 C * X. Wang, P. Stone and J. Marotzke, 1999:
5105 C Global thermohaline circulation. Part II:
5106 C Sensitivity with interactive transport.
5107 C J. Climate 12(1), 83-91
5108 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
5109 C Destabilization of the thermohaline circulation
5110 C by atmospheric eddy transports.
5111 C J. Climate 7(12), 1870-1882
5112 o Will need long integration testing.
5113 checkpoint53b_pre (2004/05/14)
5114
5115 o created pkg/mom_common in preparation for variable viscosity code
5116 o renamed and split ini_mnc_io
5117 o pkg/land: only liquid water can diffuse or run-off
5118 o AIM using land: soil wetness availability account for snow
5119 o added printMapIncludesZeros to EEPARMS namelist
5120
5121 checkpoint53a_post (2004/05/11)
5122 o restore TAMC compatiility for exf_constants.h
5123 (no usage of _d in .h)
5124 o Additional storing in KPP in an attempt to fix
5125 TAMC problem with adjoint of KPP code.
5126 (no success...)
5127 Identical code works fine with TAF.
5128 o Fixed verification/natl_box_adjoint experiments.
5129 Initial conditions for Experiments 4 and 5 are now
5130 set to "SEAICE_initialHEFF=0", which is more reasonable,
5131 and hence gives results closer to that of Experiment 2.
5132 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
5133
5134 checkpoint53 (2004/05/06)
5135 o stable checkpoint with up to date adjoint
5136 TLM tests only run for 1st grdchk at the moment. Its unclear if
5137 this is a code problem or a problem with resetting code for g_
5138 variables that is being autogenerated wrong.
5139 Otherwise:
5140 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
5141 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
5142 are both still in chaos following their security messes.
5143
5144 checkpoint52n_post (2004/05/06)
5145 o various build (mostly genmake2) changes including:
5146 - ability to build/run more easily within Cygwin and MacOS X
5147 - more complicated Makefiles with a stronger dependence on Gnu Make
5148 o pkg/seaice modifications
5149 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
5150 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
5151 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
5152 - changed proxy for geostrophic velocity and updated
5153 verification/lab_sea/results/* accordingly
5154 - removed ADI dynamic solver from pkg/seaice
5155 - replaced all occurrences of 1/CSTICE or 1/CSUICE
5156 they caused a segmentation fault under certain circumstances
5157 - removed unused field WATR
5158 o bug fix in exf-package:
5159 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
5160 now reflect that.
5161 o small fixes in the cal-package:
5162 - set reference date to first of January for the 'model'-calendar
5163 - failing of cal_CheckDate in cal_FullDate now actually results in a
5164 warning
5165 o small modifications in exf-package to increase flexibility:
5166 - change climtempfreeze from a constant to a runtime parameter that
5167 is specified in data.exf_clim (default = -1.9)
5168 - introduce runtime parameter windstressmax (default = 2.0) that is
5169 specified in data.exf
5170 o fix in pkg/thsice:
5171 - update Evap (Tsf changes) to be consistent with Latent heat flux
5172 - maintain snow precipitation unchanged (even if Tsf >=0).
5173 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
5174
5175 checkpoint52m_post (2004/04/18)
5176 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
5177 this does not change any of the results, because myIter=0 in swfrac always
5178 lead to jwtype=2 (the default anyway), but the call makes little sense
5179 as a default
5180 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
5181 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
5182 atmospheric model (AIM) to use it ; add a "slab ocean" component.
5183 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
5184 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
5185 o extending useSingleCpuIO option to work with new exch2 I/O format
5186 - old-style, missing-tile I/O is still accessible by defining CPP
5187 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
5188 o monitor package can write to NetCDF files and/or STDOUT
5189 o fix re-definition bug in MNC_GRID_INIT_ALL()
5190 o doc/api_reference added
5191 - a framework for building an API Reference Manual using all
5192 the "protex" comments embedded in the code
5193 - see pkg/generic_advdiff, pkg/mnc for examples
5194 o MNC:
5195 - make myThid the last argument for all subroutines
5196 - new default for the grid files: NO halos
5197 - add useMNC and other run-time flags
5198 - separate per-file-group handling of the unlimited dimension
5199 - early initialization of MNC w/ flags read at the eeboot stage
5200 and lookup tables set in initialize_fixed
5201 - write all MNC output to a freshly-created directory
5202 o thermodynamics sea-ice (thsice) is now tested with testreport.
5203 o test exp. advect_cs: use the standard cs32 grid ; update output.
5204 o Added functionality to grdchk:
5205 pick global i,j,k position (or nearest wet) where to perform check.
5206
5207 checkpoint52l_post (2004/03/11)
5208 o new land formulation:
5209 a) use ground enthalpy as prognostic variable to ensure exact
5210 energy conservation.
5211 b) account for water temperature and for latent heat of freezing
5212 in all processes (rain, run-off, ground storage)
5213 c) compute surface and ground temperature implicitly.
5214 o aim_v23 modification for new land model:
5215 a) Treat separately land / ocean / sea-ice surface fluxes
5216 to allow implicit computation of land & sea-ice surface temp.
5217 b) add snow precipitation.
5218 checkpoint52l_pre (2004/03/11)
5219
5220 o fix problem (when 1 tile is empty) in min/max monitor.
5221 o fix bug in timeAve (u,vZetatave in common block)
5222 o no restoring terms under ice for pkg/seaice
5223 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
5224 o bug fix for pkg/seaice pickups
5225 o change MNC call locations and add coordinate attributes
5226 o mask vorticity at the corner ; affects global_ocean.cs output
5227 o fix ini_curvilinear_grid ; test CS experiments with mpi
5228 o aim.5l_cs: modify sea-ice fraction input file ; update output
5229 o exf: Adding simple range check routine for exf fields after read
5230
5231 checkpoint52k_post (2004/02/23)
5232 o removed top-level directory "diags"
5233 - we migrated these functions to pkg/timeave a long time ago
5234 o fixed bug introduced in pkg/monitor
5235 o accuracy ctrlprec = 32 insuffient for gradient checks using
5236 averaged fields (I/O via cost_averages)
5237 -> use ctrl.h in active_file*.F to control I/O precision.
5238 o paramter list of CALL ADTHE_MAIN_LOOP
5239 o added initial do_the_model_io to ecco
5240 o set all ...Freq to zero after cost_final
5241 taveFreq, dumpFreq, pChkptFreq
5242 o MAIN and ECCO differentiability restored
5243
5244 checkpoint52j_post (2004/02/18)
5245 o fix nchklev in tamc.h for global_ocean...
5246 o Bringing flow and store directives up-to-date
5247 o Really weird thing!
5248 call do_the_model_io from the_main_loop with parameters
5249 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
5250 TAF places a faulty re-call of initialise_varia
5251 after cost_final call which should not be there!
5252 checkpoint52j_pre (2004/02/03)
5253
5254 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
5255 error messages
5256 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
5257 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
5258 debug output
5259 o modfied mdsio_writefield.F to handle non-global files under exch2
5260 o update AIM Cubed-Sphere exp (aim.5l_cs):
5261 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
5262 o update AIM Equatorial Channel exp:
5263 use standard aim_v23 pkg and change the SST fields to be more realistic.
5264 o globalFile now works with exch2
5265 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
5266 mon_vort3.F to make exch2 friendly with >1 tile per cube face
5267 o limit timeave output for hi-res integrations
5268
5269 checkpoint52i_post (2004/01/21)
5270 o removed CPP_EEOPTIONS.h from verification/*/code
5271 o updated the tiling for global_ocean_pressure
5272 checkpoint52i_pre (2004/01/20)
5273
5274 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
5275 the old pkg/aim).
5276
5277 checkpoint52h_pre (2004/01/20)
5278 o shortened offending lines in exch2_send_rx?.template
5279 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
5280 o genmake2: add build & execute test for NetCDF code
5281 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
5282 old grid files, moved CPP_EEMACROS.h to pkg/exch2
5283 o added useSingleCPUIO flag to monitor.F and mon_out.F
5284 o added temporary hack for sea-ice dynamics on the cube:
5285 metric terms are ignored and it is assumed that
5286 there is no sea-ice on cube faces 1, 2, 4, and 5.
5287
5288 checkpoint52f_post (2004/01/09)
5289 o added exch2 cube routines to pkg/exch2
5290 o modified hs94.cs-32x32x5 to use it
5291 o added new grid files to hs94.cs-32x32x5
5292 checkpoint52f_pre (2004/01/07)
5293
5294 checkpoint52e_post (2004/01/07)
5295 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
5296 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
5297 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
5298 to work with implicit vertical advection and AB ;
5299 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
5300 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
5301 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
5302 checkpoint52e_pre (2004/01/02)
5303
5304 o fix bug in impldiff when Nr=1 or Nr=2.
5305 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
5306 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
5307 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
5308 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
5309 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
5310 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
5311 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
5312
5313 checkpoint52d_post (2003/12/16)
5314 o re-tiled many expts to allow comparison in multi-processor mode
5315 - updated output accordingly
5316 - changed hs94.128x64x5 to use intial T from file rather than use the
5317 random number generator
5318 o add infrastructure in model routines for fizhi and gridalt packages
5319 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
5320 o changes to permit hi-res, cubed-sphere, configuration
5321 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
5322 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
5323 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
5324 of surface winds for the cube
5325 (A verification experiment, based on global_ocean.cs32x15, but with
5326 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
5327 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
5328 complete with example surface forcing files and matlab scripts to look
5329 at the output and compare it with that of global_ocean.cs32x15.)
5330 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
5331 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
5332 to conform to the common rule.
5333 o check-in the first version of the coupler + interfaces for multi-components
5334 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
5335 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
5336 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
5337 - ocean and atmos. share the same horizontal grid (no interpolation).
5338 - exchanges between component and coupler is done in forward_step
5339 o new verification experiment, cpl_aim+ocn:
5340 coupled ocean - AIM atmosphere on cs32 grid.
5341
5342 checkpoint52d_pre (2003/12/06)
5343 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
5344 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
5345
5346 checkpoint52c_post (2003/11/25)
5347 o Fixing OPTIONS files for use of exf:
5348 - ALLOW_ECCO not needed
5349 - ECCO_CPPOPTIONS.h should not be included from
5350 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
5351 as has been the case in the past
5352 - All cal/exf related options are currently set in
5353 single header file. Should remain so until we
5354 agree on a consistent new policy.
5355 o Removed all CPP options for cal package.
5356 cal has no more CPP options.
5357 o modified STOREs in GAD_ADVECTION
5358 o corrected key comp. for passkey
5359
5360 checkpoint52b_post (2003/11/23)
5361 o new version: "thsice" of thermodynamic sea-ice pkg:
5362 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
5363 - modify fluxes but do not change theta directly;
5364 - light cleaning of bulk_force pkg (still needed with thsice).
5365 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
5366 + output_thsice.txt to test thsice & bulk_force pkgs.
5367 o put back grid & coriolis monitor output.
5368 checkpoint52b_pre (2003/11/23)
5369
5370 o call "do_the_model_io" at the beginning (=> dump initial state)
5371 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
5372 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
5373 (need info on NUMBER_OF_PTRACERS)
5374 o missing PTRACERS headers in some routines
5375 o default tamc.h in pkg/autodiff supposed to crash
5376 to ensure proper customization
5377
5378 checkpoint52a_post (2003/11/17)
5379 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
5380 - moved surfaceTendencyTice from pkg/seaice to main code
5381 - subroutine FREEZE_SURFACE now limits only surface temperature
5382 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
5383 => new output.txt for global_ocean.cs32x15 & global_with_exf
5384 - keep the old version of FREEZE for backward compatibility;
5385 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
5386 - corresponding modifs for TAF directives
5387 o added surface flux output variables to TIMEAVE_STATVARS
5388 o time-averaged output for pkg/ptracers
5389 o fix problem with ECCO-related divided adjoint
5390 snapshot file was missing some ad-variables,
5391 but no warning issued by TAF
5392
5393 checkpoint52a_pre (2003/11/12)
5394 o some bug fixes for #undef REAL4_IS_SLOW
5395
5396 checkpoint52 = ecco_c52_e35
5397 o after testing adjoints of checkpoint51u_post
5398
5399 checkpoint51u_post (2003/11/06)
5400 o this is the post-merge tag of the ecco-branch
5401 (needs another clean checkout and re-testing)
5402 o various natl_box_adjoint configs and results
5403 but no input fields
5404 o obcs adjoint not yet merged!
5405 o adding ECCO global 1x1 and 2x2 degree configs
5406 o updated/extended some store directives for seaice
5407 o pkg/ecco now containes ecco-specific part of cost function
5408 o top level routines the_main_loop, forward_step
5409 supersede those in model/src/
5410 previous input data.cost now in data.ecco
5411 (new namelist ecco_cost_nml)
5412 o in ctrl/ cleaned some cross-dependencies and updated CPP options
5413
5414 checkpoint51t_post (2003/11/04)
5415 o this is the pre-merge tag of the ecco-branch
5416
5417 checkpoint51s_post (2003/11/04)
5418 o cleanup: removed various obsolete #define-s
5419 o pkg/grdchk
5420 - renamed 'ph-grd 3' to 'grad-res'
5421 - merged from ecco-branch
5422 (remaining bug fixes for obcs gradient checks)
5423 - additional high-precision output for testreport
5424 (grep for 'precision_grdchk_result')
5425
5426 checkpoint51r_post (2003/11/03)
5427 o cleaned up or removed CPP_OPTIONS.h files
5428 o updated results for some of the tests to reflect the new
5429 optfiles (-ieee: -O0 instead of -O3)
5430
5431 checkpoint51q_post (2003/10/30)
5432 o cd_code:
5433 - moved cd_scheme.F -> cd_code_scheme.F
5434 - separate read_checkpoint from cd_code_ini_vars.F
5435 - separated cd_code part from write_checkpoint
5436 - updated AD_SOURCE, generated .flow
5437 - added CD_CODE_VARS.h to the_main_loop
5438 - Moving cd_code specific store dir.s to pkg/cd_code
5439 o ctrl package totally restructured
5440 - pack/unpack now optional and decoupled from
5441 xx_/adxx_ I/O
5442 - ctrl_pack/unpack cleaned
5443 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
5444 - confined inclusion of AD_CONFIG.h to where necessary.
5445 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
5446
5447 checkpoint51p_post (2003/10/30)
5448 o create initial cd_code package
5449 - WARNING: the initialization of fields within packages
5450 is broken because INI_FIELDS (where READ_CHECKPOINT is
5451 called) is called *before* PACKAGES_INIT_VARIABLES.
5452 This seems to be backwards since
5453 1) its important to initially zero the entire field including
5454 the "halo" region
5455 2) zeroing needs to be done *before* reading pickup info
5456 and the pickup call might or might not happen in any
5457 particular run
5458 - this needs an overhaul for R2
5459 o cleanup verification/*/code/GMREDI_OPTIONS.h
5460 o cleanup testreport
5461
5462 checkpoint51o_post (2003/10/27)
5463 o bringing AD-related verif's up to date with genmake2
5464 - carbon/
5465 - global_ocean.90x40x15/
5466 - hs.94.1x64x5/
5467 - (front_relax/ )
5468 o (more) consistent directory structure for AD-related verif.'s
5469 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
5470 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
5471 o bug fix in find_alpha.F for MDJWF:
5472 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
5473 change rho -> rho-rhoConst
5474 - replace call find_rho to find_rhonum
5475 o initialisation of rFlx extended to full array (required by TAF)
5476 and shifted to thermodynamics
5477 o removed PTRACERS.h in ptracers routine
5478 o added surfacetendencyPtr to S/R parameter list pracers_forcing
5479 o Correcting initialisations for fVerU, fVerV.
5480 o helping TAF to recognize dependency on kUp for
5481 fVerU, fVerV
5482 o Replacing delZ by delR in pkg/ctrl/
5483 checkpoint51o_pre (2003/10/24)
5484
5485 o undid all of cp51 pending some cleanups and discussion
5486 o added the [#include "AD_CONFIG.h"] statement to all files that need
5487 it for adjoint/tl #defines
5488 o re-worked the build logic in genmake2 to support AD_CONFIG.h
5489 o removed tools/genmake since it no longer works
5490
5491 checkpoint51n_post (2003/10/23)
5492 o modifications to make FREEZE flux visible to pkg/kpp
5493 - moved surfaceTendencyTice from pkg/seaice to main code
5494 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
5495 - subroutine FREEZE now limits only surface temperature
5496 (this means new output.txt for global_ocean.90x40x15,
5497 global_ocean.cs32x15, and global_with_exf)
5498 o added surface flux output variables to TIMEAVE_STATVARS
5499
5500 checkpoint51n_pre (2003/10/23)
5501 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
5502 o added [#include "AD_CONFIG.h"] to all files that use the following
5503 defines:
5504 - ALLOW_ADJOINT_RUN
5505 - ALLOW_TANGENTLINEAR_RUN
5506 - ALLOW_ECCO_OPTIMIZATION
5507
5508 checkpoint51m_post (2003/10/21)
5509 o incorporating changes to get TAMC/TAF working in genmake2
5510 - added new TAMC/TAF targets to the Makefile
5511 - various cleanups related to package handling
5512 - these changes should have no impact on the forward model
5513
5514 checkpoint51l_post (2003/10/20)
5515 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
5516 - faster algorithm for cal_addtime.F
5517 - higher precision arithmetic, where needed
5518 - pkg/exf *startdate variables changed from calendar date to
5519 model integration time
5520
5521 checkpoint51l_pre (2003/10/17)
5522 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
5523 o enable to apply restoring on S & T only in a latitude band.
5524 o update output (external_forcing_surf modif. change truncation errors)
5525 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
5526
5527 checkpoint51k_post (2003/10/16)
5528 o change default to: useNHMTerms=.FALSE.
5529 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
5530 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
5531 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
5532 exp1, ideal_2D_oce
5533 - change data file of oceanic exp (leave the results unchanged for now)
5534 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
5535 o set gravitySign automatically according to the vertical coordinate used
5536 (and change sign: back to "logical" value: +1 when R increases downward)
5537 o added an include barrier to the default CPP_OPTIONS.h and
5538 removed the #include "PACKAGES_CONFIG.h" from it
5539 o fix a bug in mom_fluxform (from chk51j_post)
5540
5541 checkpoint51j_post (2003/10/10)
5542 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
5543 o adjusted some flow directives (dynamics, thermodynamics)
5544 o added cubed-sphere case to test cost function
5545 o heckpoint_lev?_directives.h now include
5546 pkg-specific directives, whenever those are enabled.
5547 o Moving pkg-specific flow directives to corresponding pkg
5548 Moving pkg-specific differentiation list to corresponding pkg
5549 Moving pkg-specific checkpoint-lev storing to corresponding pkg
5550 ---> conventions are
5551 - pkg_ad.flow
5552 - pkg_ad_diff.list
5553 - pkg_ad_check_lev?_dir.h
5554
5555 checkpoint51i_post (2003/10/09)
5556 o merge of the branch-genmake2
5557 - knowingly breaks the older genmake
5558 - automatic generation of all ALLOW_${PKG_NAME} defines
5559 - new testreport supersedes older testscript
5560 o large number of package inclusion and header cleanups
5561 checkpoint51i_pre (2003/10/08)
5562
5563 o new output for adjoin of global ocean vector invariant
5564 o fix for checkpoint of thermodynamic seaice and bulk_force
5565 o Steph gchem various cleanups
5566
5567 checkpoint 51h_pre
5568 o fixed some single quotes
5569 o modify gchem pkg to be more versatile
5570 o modifications to clean up dic pkg
5571 o add pkg/cfc
5572
5573 checkpoint51g_post (2003/10/02)
5574 o provide links for ARPACK and ADM*TLM
5575 o start removing verification/vero/
5576 o update AD-related stuff
5577 (in particular some IF-statements in model/src/ routines)
5578 o adding to verification/global_ocean.90x40x15/ adjoint of
5579 vector invariant setup
5580
5581 checkpoint51f_post (2003/10/02)
5582 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
5583 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
5584 of tracer Green's fucntions for ocean inversion project.
5585
5586 checkpoint51f_pre (2003/08/07)
5587 o Added on-the-fly spatial interpolation capability
5588 "USE_EXF_INTERPOLATION" to pkg/exf.
5589 - This is a temporary Cartesian-grid hack until
5590 the super-duper ESMF coupler becomes available.
5591 - See verification/global_with_exf/README for usage example.
5592 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
5593 flags and modified pkg/seaice accordingly.
5594 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
5595 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
5596 non-local transport term.
5597
5598 checkpoint51e_post (2003/08/03)
5599 o pkg/mom_vecinv:
5600 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
5601 - add time-ave diagnostic of vorticity advection.
5602 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
5603 o atmospheric geopotential: - include water vapor effect;
5604 - use p^kappa in p* scaling.
5605 o land pkg: read initial state from files.
5606 o AIM : add stratospheric drag in the upper level
5607
5608 checkpoint51d_post (2003/07/18)
5609 o change function ILNBLNK (=> last non-blank char.) to return zero
5610 (instead of the string length) when the string. char is empty
5611 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
5612 o modif's to restore TAMC compatibility
5613 - avoid "_d" constructs in PARAMETER declarations
5614 - avoid interrupting lines by comment lines
5615 o Use cluster local disks for purely local I/O
5616 vs. globally visible disks needed for ctrl stuff
5617 (merged from ecco-branch)
5618 - new active_file_loc... and mdsio_..._loc routines
5619 - affected packages: autodiff, ctrl, grdchk, mdsio
5620
5621 checkpoint51c_post (2003/07/08)
5622 o introducing integer flag debugLevel
5623 - debLevZero: suppress all output
5624 - debLevA: standard
5625 - debLevB: equivalent to current debugMode=.TRUE.
5626 o introducing pathname variable mdsioLocalDir for mdsio
5627 that can be specified at runtime
5628 (relevant for cluster I/O to local disk)
5629 `
5630 >>>checkpoint51b_post
5631 adjoint of ptracers
5632 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
5633 o extended state in checkpoint_lev?, etc.
5634 o alternative ctrl/cost with tr1 or ptracer
5635 o new comlev1_bibj_ptracers
5636 o new ptracers.flow
5637 o made ptracers_forcing same as external_forcing_s
5638 o added verification for adjoint with ptracers
5639 - adm. grdchk fail so far
5640 - tlm. grdchk OK
5641 - checked tapelev/comlev recomputations: OK
5642 <<<checkpoint51b_pre
5643
5644 checkpoint51a_post (2003/06/25)
5645 o added code for biogeochemistry package
5646 - new pkgs: dic, gchem
5647 - new subroutine in ptracers
5648 o modify code for biogeo packages
5649 - in model/src and pkg/ptracers
5650
5651 checkpoint51 (2003/06/24)
5652 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
5653 - autodiff, ctrl, exf, grdchk, seaice
5654 kept separate packages
5655 - cost, ecco, obcs
5656 o updating verification/internal_wave, verification/lab_sea
5657 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
5658
5659 checkpoint50i_post (2003/06/23)
5660 o Preparing next differentiable checkpoint and sync
5661 of MAIN vs. ecco-branch
5662 - 1st step: this one is differentiable
5663 - 2nd step: next(! not this) checkpoint will have updated packages
5664 from ecco-branch)
5665
5666 checkpoint50h_post (2003/06/20)
5667 o new package "land": provide surface BC for AIM.
5668 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
5669 o AIM: use true log-P extrapolation for near surface temp (= as in
5670 F.Molteni paper) ; update aim.5l_cs output.
5671 o New variable in PARM03 for more flexible pickups
5672 o somewhat cleaned package initialisation sequence for
5673 ctrl/ cost/ ecco/ in packages_... routines
5674
5675 checkpoint50g_post (2003/05/23)
5676 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
5677 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
5678 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
5679 made the default because of faster convergence than ADI
5680
5681 checkpoint50f_post (2003/05/23)
5682 o exf totally restructured
5683 - replaced all exf_set_ routines by one generic exf_set_gen.F
5684 and made sure it's still differentiable
5685 - split exf_getffields.F into new exf_bulkformulae.F
5686 - exf_inscal_/exf_outscal_ suffixes consistent with field names
5687 - updated adjoint/makefile and relevant verif. accordingly
5688
5689 checkpoint50f_pre (2003/05/23)
5690 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
5691 + change Evap over land. (update aim.5l_cs output)
5692 o added missing .cvsignores and made uniform across expts
5693 o changed configuration of tidal_basin_2d expt
5694 o added pkg/debug functions for tracing code in fatal crashes
5695 o tidied pkg/monitor to use MONITOR_OPTIONS.h
5696 o new fn in pkg/monitor to stop model if solution grows too big
5697 o removed lots of single quotes from comments
5698
5699 checkpoint50e_post (2003/05/14)
5700 o make KPP work with PTRACERS
5701 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
5702 nearly a copy of kpp_transport_s
5703 - there is no analogue to SurfaceTendencyS, so I have to use
5704 gPtr(of the surface layer) instead
5705 o add a new platform SunFire+mpi (SunFire 15000) to genmake
5706 checkpoint50e_pre (2003/05/13)
5707
5708 checkpoint50d_post (2003/05/13)
5709 o change kpp output from multiple-record state files to single-record state
5710 files analogous to write_state.F
5711 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
5712 analogous to the cg2d-related output.
5713 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
5714 so that writing to internal file fn (with length 512) fails.
5715 checkpoint50d_pre (2003/05/12)
5716
5717 checkpoint50c_post (2003/05/12)
5718 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
5719 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
5720 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
5721 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
5722 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
5723
5724 checkpoint50c_pre (2003/04/30)
5725 Merging from release1_p13:
5726 o bug fix for pkg/seaice dynamic solver
5727 o Added SEAICE_initialHEFF to pkg/seaice
5728
5729 checkpoint50b_post (2003/04/17)
5730 o store u*,v* in gU,V instead of in guNm1,gvNm1
5731 o in order to put the momForcing out of the Adams-Bashforth:
5732 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
5733 to timestep.F
5734 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
5735 o re-generate output for highly sensitive test-exp:
5736 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
5737
5738 checkpoint50b_pre (2003/04/17)
5739 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
5740 o corrected CPP option mismatch in exf_Bulk... functions for case
5741 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
5742
5743 checkpoint50a_post (2003/03/21)
5744 o Bug fix for merging between c50 and KPP.
5745 ikey was passed from thermodynamics to kpp_calc via
5746 common block rather than being recomputed in kpp_calc,
5747 in contradiction with new key itdkey.
5748 New key ikppkey created, and tamc.h headers updated.
5749
5750 checkpoint50 (2003/03/08)
5751 - 2nd step of merge with ecco-branch:
5752 merge changes in ecco-branch back into main trunk
5753 - bug fix in find_alpha
5754 - more storing in gmredi_calc_tensor.F, kpp_routines.F
5755 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
5756 - merged some sliced AD support routines
5757
5758 checkpoint49 (2003/03/06)
5759 merged from ecco-branch:
5760 o exf:
5761 - Enable initialisation of forcing fields to constant
5762 (runtime) values.
5763 - in exf_getffields.F
5764 Reduce i-/j-loop to interior domain, discarding overlaps.
5765 That also fixes wrong TAF-key computations for key_1, key_2
5766 with bulf formulae.
5767 - exf_init.F modify #ifdef for exf_init_evap
5768 - exf_getffieldrec.F, ctrl_getrec.F
5769 The following INT-usages are not safe:
5770 fldsecs = int(fldsecs/fldperiod)*fldperiod
5771 fldcount = int(fldsecs/fldperiod) + 1
5772 and were modified.
5773 o autodiff: checkpoint_lev...
5774 - updated storing for bulk formulae (some arrays were missing)
5775 - added state for seaice package
5776 - synchronized with main branch
5777 o DIVA:
5778 Modif.s in
5779 - the_main_loop.F
5780 - the_model_main.F
5781 and added cost_final_restore.F cost_final_store.F
5782 o With these changes, it is possible to fully separate
5783 the first forward run to compute the cost function (mdthe_main_loop)
5784 and adjoint runs over individual DIVA intervals (adthe_main_loop)
5785 into separate model executions.
5786 This enables better tuning of DIVA to given queue sizes.
5787 o Loss of cost function value in consecutive DIVA runs is
5788 fixed by storing to 'costfinal' file.
5789 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
5790 beginning/end of adjoint integration is accounted for.
5791 The current changes apply to TAF-1.4.26.
5792 TAF has one remaining bug, requiring one manual change
5793 (see MITgcm manual).
5794 o cal: synchronized between MAIN and ecco-branch
5795
5796 checkpoint48i_post (2003/03/05)
5797 o Changes to restore differentiability of code w.r.t. previous tag
5798 (mostly adding new routines to make list and replacing
5799 pressure by totPhiHyd).
5800 o Updated and merged grdchk package
5801 - has both ADM and TLM checks
5802 - works for single- and multi-proc.
5803 - output cleaned
5804 - worked successfully for parallel DIVA
5805 o genmake:
5806 - Adding -platform=SP4
5807 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
5808 o Modif. for DIVA:
5809 ctrl_unpack should not be called in intermediate DIVA interval.
5810 (similar thing would apply for active files such as
5811 tbar, sbar, psbar, which should not be reinitialised;
5812 only relevant for ecco-branch)
5813
5814 checkpoint48h_post (2003/02/28)
5815 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
5816 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
5817 o Added SEAICE_initialHEFF to pkg/seaice
5818 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
5819
5820 checkpoint48g_post (2003/02/18)
5821 --- EOS:
5822 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
5823 store total Potential in totPhyHyd for diagnostics & EOS.
5824 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
5825 --- Pressure/geopotential gradient:
5826 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
5827 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
5828 ( changes results of global_ocean_pressure )
5829 o NLFS + z-coord.: add eta*Rho' contribution.
5830 o accurate phiHyd when using interface-W at the middle between 2 centers
5831 ( changes results of ideal_2D_oce )
5832 o includes r* 2nd term in potential gradient.
5833
5834 checkpoint48f_post (2003/02/18)
5835 Merging from release1_p12:
5836 o Modifications for using pkg/exf with pkg/seaice
5837 - improved description of the various forcing configurations
5838 - added basic radiation bulk formulae to pkg/exf
5839 - units/sign fix for evap computation in exf_getffields.F
5840 - updated verification/global_with_exf/results/output.txt
5841 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
5842 (SBO) core products, including oceanic mass, center-of-mass,
5843 angular, and bottom pressure (see pkg/sbo/README.sbo).
5844 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
5845 to avoid negative values in shallow regions.
5846 - updated verification/natl_box/results/output.txt
5847 - updated verification/lab_sea/results/output.txt
5848 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
5849 o Added useSingleCpuIO option (see PARAMS.h).
5850 o Updated useSingleCpuIO option in mdsio_writefield.F to
5851 work with multi-field files, e.g., for single-file pickup.
5852 o pkg/seaice:
5853 - bug fix in growth.F: QNET for no shortwave case
5854 - added HeffFile for specifying initial sea-ice thickness
5855 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
5856 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
5857 kpp_transport_t.F, forward_step.F, and the_main_loop.F
5858 o pkg/seaice:
5859 - adjoint-friendly modifications
5860 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
5861
5862 checkpoint48e_post (2003/02/12)
5863 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
5864 o dynamics: change definition of computational domain & adapt mom_fluxform
5865 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
5866 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
5867 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
5868 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
5869 global_ocean.90x40x15 global_with_exf global_ocean_pressure
5870 inverted_barometer solid-body.cs-32x32x1
5871 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
5872
5873 checkpoint48d_post (2003/02/09)
5874 o in preparation for r*:
5875 a) use pre-computed gradient of hydrostatic potential:
5876 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
5877 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
5878 => affects results of glob_oce_pressure (different truncation error)
5879 update output.txt of ideal_2D_oce & global_ocean_pressure
5880
5881 checkpoint48d_pre (2003/02/08)
5882 o in preparation for r*:
5883 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
5884 pass the 2 comp. of the grad. as arguments to momentum S/R.
5885 but for the moment, only used if it does not change the results.
5886 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
5887
5888 checkpoint48c_post (2003/02/06)
5889 Modifications in treatment of initial flux forcing controls
5890 to avoid extra storing of flux fields.
5891
5892 checkpoint48c_pre (2003/01/21)
5893 o Added tidal_basin_2d experiment (currently 1D!)
5894 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
5895
5896 checkpoint48b_post (2003/01/27)
5897 o r* coordinate added in #ifdef NONLIN_FRSURF block.
5898 (modification to pressure gradient not yet implemented)
5899 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
5900 (for U & V) that are used for vertical advection of momentum.
5901
5902 checkpoint48a_post (2003/01/24)
5903 o In preparation for r*, use temp. array to compute vertical transport
5904 in flux-form momentum pkg. => change results of few test-exp.
5905 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
5906 lab_sea, natl_box & plume_on_slope
5907
5908 checkpoint48 (2003/01/23)
5909 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
5910
5911 checkpoint47j_post (2003/01/21)
5912 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
5913 o moved adexch from forward_step to addummy_in_stepping
5914 o added exch in ctrl_map_...
5915 o aveFreq.=0. at end of cost_final to avoid overwrite in
5916 reverse checkpointing loop
5917 o Yet more changes in gmredi:
5918 * adgmredi_calc_tensor
5919 avoiding all recomputation of gmredi_slope_limit
5920 * adgmredi_x/y/rtransport
5921 added flag for excessive storing to avoid recomp. of
5922 u/v/rtans, dTdx/y/z
5923 -> this is not really necessary and very memory-consuming
5924 * adgmredi_slope_psi:
5925 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
5926 * gmredi_slope_limit
5927 re-activated full calculation of taperfct for case 'ac02'
5928 o updating verification/ adjoints of carbon, global_ocean.90x40x15
5929
5930 checkpoint47i_post (2003/01/13)
5931 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
5932 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
5933 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
5934 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
5935 o gmredi: fix few bugs.
5936
5937 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
5938 This will be a good checkpoint to plug into the ecco-branch.
5939 o few modif.'s to get latest version adjointed
5940 (mainly kick out code in ini_linear_phisurf)
5941 o modif's to run adjoint with exactConserv
5942 o case GM_BOLUS_ADVEC should be cleaned
5943 S/R gmredi_slope_psi should be cleaned
5944 o verification/carbon now has exactConserv=.TRUE.
5945
5946 checkpoint47g_post (2003/01/10)
5947 o time-average AIM output: becomes independent from statvars time-average
5948 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
5949 o After TAF bug fix:
5950 Tested adjoint of gmredi package.
5951 Tests were done with checkpoint47 rather than with latest
5952 checkpoint47f_post since the latter is broken for the adjoint
5953 verification/carbon/ contains both ADM and TLM gradient checks.
5954 Here they are, before they get changed/lost/stolen.
5955 Mostly modif.'s to fix numerical sensitivities.
5956 Gradient checks OK for
5957 - GM_taper_scheme:
5958 * clipping
5959 * ac02
5960 * linear
5961 * glw91
5962 * dm95
5963 * ldd97
5964 - GMREDI_OPTIONS:
5965 * GM_VISBECK_VARIABLE_K
5966 * GM_NON_UNITY_DIAGONAL
5967 * GM_EXTRA_DIAGONAL
5968 * GM_BOLUS_ADVEC
5969 in conjunction with data.gmredi parameters to be checked in
5970 in a few minutes under verification/carbon/code/
5971
5972 checkpoint47f_post (2002/12/28)
5973 Merging from release1_p10:
5974 o modifications for using pkg/exf with pkg/seaice
5975 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
5976 and SEAICE_EXTERNAL_FLUXES
5977 - pkg/exf CPP options EXF_READ_EVAP and
5978 EXF_NO_BULK_COMPUTATIONS
5979 - usage examples are Experiments 8 and 9 in
5980 verification/lab_sea/README
5981 - verification/lab_sea default experiment now uses
5982 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
5983
5984 checkpoint47e_post (2002/12/27)
5985 o created a tag prior to creating a branch
5986
5987 checkpoint47d_post (2002/12/16)
5988 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
5989 at the bottom boundary had an erroneous half slip boundary condition
5990 o added bottom drag and no slip boundary condition capabilities to
5991 oceanic pressure coordinates code
5992 o added new verification experiment global_ocean_pressure, this experiment is
5993 also described in the tutorial section of the manual
5994 checkpoint47d_pre (2002/12/16)
5995
5996 checkpoint47c_post (2002/12/16)
5997 o Added a verification experiment for a global cubed-sphere ocean run
5998 - verification/global_ocean.cubed32x32x30
5999 - uses pkg/therm_seaice and pkg/bulk_forcing
6000
6001 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
6002 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
6003 when using P-coordinate; only implemented for atmospheric config.
6004 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
6005 NOTES: requires option NONLIN_FRSURF to be "#define".
6006 o update advect_xz/results/output.txt (left from checkpoint44g_post)
6007
6008 checkpoint47b_post (2002/12/05)
6009 Merging from release1_p9:
6010 o pkg/seaice
6011 - removed GOTO's and added taf directives
6012 - double precision constants to reduce the g77 (Linux)
6013 to F77 (SGI) differences reported in release1_p8
6014 o tools/genmake
6015 - added SGI options
6016 o verification/testscript
6017 - updated to that of checkpoint47a_post
6018 o verification/global_ocean.90x40x15/input/eedata
6019 - modified for SGI f77 compatibility
6020 o verification/lab_sea
6021 - added description of sea-ice model
6022 - added missing matlab routines
6023 - added test of thermodynamics parallelization
6024
6025 checkpoint47a_post (2002/11/23)
6026 o new pkg: aim_v23
6027 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
6028 for now, keep the same surface forcing as before.
6029 - Part-Cell implemented into AIM; check that Heat & Water are conserved
6030 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
6031 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
6032 o add diagnostic of surface correction term in monitor output
6033
6034 o bulk_force and therm_seaice
6035 - Two packages: bulk_force (Bulk forcing)
6036 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
6037 - Earlier integration from Stephaine Dutkiewicz
6038 and Patrick Heimbach.
6039 - Two ifdef statements for compile time,
6040 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
6041
6042 checkpoint47 (2002/11/15)
6043 differentiable version of checkpoint46n_post
6044 o bug fix in quasihydrostaticterms
6045 o * "clean" adjoint code (in terms of extensive recomputations)
6046 can now be obtained for all GMREDI options (i.e. for
6047 - GM_VISBECK_VARIABLE_K
6048 - GM_NON_UNITY_DIAGONAL
6049 - GM_EXTRA_DIAGONAL
6050 - GM_BOLUS_ADVEC )
6051 * However, wrong gradient check problem remains unsolved.
6052 * New CPP options have been introduced for different
6053 tapering schemes
6054 o external_fields_load now part of differentiation list
6055 o pressure needs multiple storing;
6056 would be nice to have store_pressure at beginning or
6057 end of forward_step, e.g. by having phiHyd global (5-dim.)
6058 (NB: pressure is needed for certain cases in find_rho,
6059 which is also invoked through convective_adjustment).
6060 o recomputations in find_rho for cases
6061 'JMD95'/'UNESCO' or 'MDJWF' are OK.
6062 o #define ATMOSPHERIC_LOADING should be differentiable
6063 o ini_forcing shifted to begining of initialise_varia
6064 o Incorporating QNVS line search routines into MITgcm
6065 (this is separate code, and therefore not under pkg)
6066 lsopt/, optim/
6067 o Updated verification/carbon/
6068 - #define GM_VISBECK_VARIABLE_K
6069 - GM_taper_scheme = 'ldd97'
6070
6071 checkpoint46n_post (2002/11/12)
6072 Merging from release1_p8:
6073 o verification/natl_box:
6074 updating new external_fields_load routine
6075 o New package: pkg/seaice
6076 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
6077 The sea-ice code is based on Hibler (1979-1980).
6078 Two sea-ice dynamic solvers, ADI and LSR, are included.
6079 In addition to computing prognostic sea-ice variables and diagnosing
6080 the forcing/external data fields that drive the ocean model,
6081 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
6082 The implied surface heat flux is then stored in variable
6083 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
6084 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
6085 non-local transport term. Because this call precedes model
6086 thermodynamics, temperature under sea-ice may not be "exactly" at
6087 the freezing point by the time theta is dumped or time-averaged.
6088 N.B.: fairly large differences in accuracy occur across
6089 different platforms/compilers; comparison between
6090 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
6091 generated output gives:
6092 T S U V
6093 C D M c m s m s m s m s
6094 n p a R g m m e . m m e . m m e . m m e .
6095 f n k u 2 i a a d i a a d i a a d i a a d
6096 g d e n d n x n . n x n . n x n . n x n .
6097
6098 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
6099 o GAD:
6100 - generated new common blocks to account for call of
6101 same gad routines with differing traceridentities
6102 (needed to modify tracerIdentity indices in GAD.h)
6103 - generated separate common blocks for case useCubedSphereExchange
6104 (Department of Futurology)
6105 - parameter lists to gmredi_?transport: added tracerIdentity
6106 - added new key indices to tamc.h
6107 o external_fields_load:
6108 - added this routine to TAF list
6109 - needed to make some common blocks global and additional storing
6110 along the same lines as exf package (checkpoint_lev?_directives.h)
6111 o exf:
6112 updated external forcing package
6113 - bug fixes carried over from ecco-branch
6114 (missing OBCS_OPTIONS.h in two routines)
6115 - enable easy to use "no forcing".
6116 - added exf I/O for atmospheric loading
6117 - added exf I/O for runoff data
6118 - transfered scaling between exf <-> MITgcm to exf namelist
6119 o Adding new verification experiment global_with_exf.
6120 This verification experiment is almost identical to the
6121 global_ocean.90x40x15 experiment, except that it uses
6122 the exf (and cal) package instead of the
6123 external_fields_load routine (cf README file).
6124
6125 checkpoint46m_post (2002/11/07)
6126 o modified testscript to return -- when there are no lines of "%MON" output
6127 o added new flag "quasiHydrostatic" for QH mode
6128 and new routine quasihydrostaticterms()
6129 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
6130 New routine: mom_u_coriolis_nh()
6131 o fixed sign of non-hydrostatic metric terms in u and v equations.
6132 Depend on correct sign of gravitySign.
6133 o added work.pc* to .cvsignore in aim directories using ifc
6134 o introduced flag for controllin non-hydrostatic metric terms
6135 o removed gravitySign from PARM04
6136 o switched to g77/ifc from pgf77 in aim experiments
6137
6138 checkpoint46l_post (2002/11/01)
6139 o made convective adjustment work with pressure coordinates:
6140 - changed the direction of k-loop in convective_adjustment.F for the
6141 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
6142 - adjusted the reference pressure k-index in convective_adjustment.F
6143 - adjusted the convection condition in convect.F (in analogy to
6144 calc_ivdc.F)
6145 - convective_adjustment no longer computes anything on the halos
6146 - removed the warnings about negative salinity from find_rho.F and
6147 find_alpha.F; instead the new routine look_for_neg_salinity, called
6148 at the beginning of find_rho, find_alpha, and find_beta, does a
6149 check of the entire slice, if CPP-option
6150 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
6151 checkpoint46l_pre (2002/10/23)
6152
6153 checkpoint46k_post (2002/10/23)
6154 o fixed the verification/global_ocean.90x40x15 experiment:
6155 - new bathymetry (the world according to A., JMC, and M.)
6156 - new initial fields and forcing fields (*.bin files)
6157 - new POLY3.COEFFS (for the next release one should switch to a full
6158 equation of state: JMD95P or MDJWF)
6159 - fixed several errors and redundancies in the data file
6160 - experiment uses looped cells
6161 - added matlab directory with diagnostic scripts for plotting of output
6162
6163 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
6164 - read AIM physics parameters from a file (data.aimphys)
6165 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
6166
6167 checkpoint46j_post (2002/10/07)
6168 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
6169 o move wVel computation at the end of the time step, in S/R integr_continuity
6170 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
6171 o update timeave pkg for wVel diagnostic.
6172 checkpoint46j_pre (2002/09/27)
6173
6174 checkpoint46i_post (2002/09/25)
6175 o Clean up AIM package (and keep the results unchanged):
6176 include CPP_OPTION and use IMPLICT NONE in all routines ;
6177 declare all the variables _RL ; use _d 0 for all numerical constants.
6178 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
6179
6180 checkpoint46h_post (2002/09/25)
6181 o cleaned up the use of rhoNil and rhoConst.
6182 - rhoNil should only appear in the LINEAR equation of state, everywhere
6183 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
6184 and the dynamical equations are all divided by rhoConst
6185 o introduced new parameter rhoConstFresh, a reference density of fresh
6186 water, to remove the fresh water flux's dependence on rhoNil. The default
6187 value is 999.8 kg/m^3
6188 o cleanup up external_forcing.F and external_forcing_surf.F
6189 - can now be used by both OCEANIC and OCEANICP
6190 checkpoint46h_pre (2002/09/18)
6191
6192 Added code to convert surface volume flux (fresh water) into
6193 a mass flux when using P coordinates in the ocean (OCEANICP).
6194 Note: It assumes you have set rho0=rhoConst=density of fresh water.
6195
6196 checkpoint46g_post (2002/09/18)
6197 o Include a new diagnostic variable phiHydLow for the ocean model
6198 - in z-coordinates, it is the bottom pressure anomaly
6199 - in p-coordinates, it is the sea surface elevation
6200 - in both cases, these variable have global drift, reflecting the mass
6201 drift in z-coordinates and the volume drift in p-coordinates
6202 - included time averaging for phiHydLow, be aware of the drift!
6203 o depth-dependent computation of Bo_surf for pressure coordinates
6204 in the ocean (buoyancyRelation='OCEANICP')
6205 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
6206 Theta, Salinity, and Pressure in the parameter list. This routine is
6207 presently contained in find_rho.F. This routine does not give the
6208 correct density for 'POLY3', which would be a z-dependent reference
6209 density.
6210 o cleaned up find_rho
6211 - removed obsolete 'eqn' from the parameter list.
6212 o added two new verification experiments: gop and goz
6213 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
6214 checkpoint46g_pre (2002/09/16)
6215
6216 checkpoint46f_post (2002/09/16)
6217 o Enable tangent linear (forward mode) gradient checks:
6218 - extended active file handling to g_... files
6219 - added TANGENT_SIMULATION to theSimulationMode
6220 - extended grdchk package accordingly
6221 o added tangent linear setup in verification/carbon/code_ftl
6222 o added adjoint setup in verification/front_relax/code_ad
6223
6224 checkpoint46e_post (2002/09/05)
6225 o Added new equation of state -> MDJWF
6226 - EOS of McDougall et al., 2002, JAOT, submitted
6227 - caveat: the equation of state is only valid for a smaller (more
6228 realistic?) range of values than JMD95P/Z and UNESCO
6229 - added masks to the calculation of pressure in store_pressure
6230 - added more check values for density in check_eos (ini_eos.F), some of
6231 the old check values are out of the range of the MDJWF-eos, so don't
6232 expect perfect matches for those
6233 checkpoint46e_pre (2002/08/19)
6234
6235 checkpoint46d_post (2002/08/19)
6236 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
6237 'OCEANICP', also initialised field pressure correctly in ini_eos in the
6238 case of pressure coordinates. eosType='JMD95Z' in
6239 combination with buoyancyRelation='OCEANICP' now causes an error.
6240 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
6241 in find_alpha/beta.
6242 checkpoint46d_pre (2002/08/15)
6243
6244 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
6245 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
6246
6247 checkpoint46c_post (2002/08/15)
6248 o Changes necessary for ocean in p-coordinates
6249 - Added new buoyancy relation = 'OCEANICP'
6250 - Added new parameters = gravitySign (this used to be contained inside
6251 the factor dRdZ which I added when we first switched to R coordinates).
6252 X GM/Redi is not compatible (yet)
6253 X bottom drag and no-slip need to be debugged.
6254 checkpoint46c_pre (2002/08/07)
6255
6256 checkpoint46b_post (2002/08/07)
6257 o Added new equation of state -> JMD95Z and JMD95P
6258 - EOS of Jackett and McDougall, 1995, JAOT
6259 - moved all EOS parameters into EOS.h
6260 - new routines ini_eos.F, store_pressure.F
6261 o Added UNESCO EOS, but not recommended because it requires
6262 in-situ temperature (see JMD95)
6263 o Modified formatting for knudsen2.f in utils/knudsen2 and added
6264 unesco.f to be used with POLY3
6265 checkpoint46b_pre (2002/07/31)
6266
6267 checkpoint46a_post (2002/07/31)
6268 o Added (atmospheric) pressure loading
6269 - new field in FFIELDS.h, etc...
6270 - new cpp flag ATMOSPHERIC_LOADING
6271 o Changed hFacC to _hFacC in calc_phi_hyd.F
6272 o Added SHORTWAVE_HEATING to some files for consistency
6273 checkpoint46a_pre (2002/07/13)
6274
6275 checkpoint46 (2002/07/13)
6276 further merges from release1_p5
6277 o new ctrl package
6278 - adopted from ECCO environment to enable optimization
6279 - added Eliassen Palm fluxes to controls
6280 o added Eliassen Palm flux controls to gradient check package
6281 o cost package
6282 - Compatible with new ctrl package
6283 - added Eliassen Palm cost hooks
6284 - modif's of existing cost functions
6285 o Adjoint-related bug fixes in kpp:
6286 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
6287 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
6288 o autodiff package
6289 - flow directives:
6290 + new for S/R do_the_model_io
6291 + enhanced for S/R checkpoint
6292 + new gmredi.flow
6293 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
6294 disable adcommon.h/g_common.h by default.
6295 - fixed problem for adjoint of global_max
6296 o modified verification/carbon/
6297 o New setup for adjoint of global_ocean
6298 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
6299 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
6300 o incorporated hooks for sponge layer code (external_forcing.F)
6301
6302 checkpoint45d_post (2002/07/12)
6303 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
6304 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
6305 (affects plume_on_slope "cg2d" output)
6306 o add new parameter deltaTfreesurf for free-surface time stepping
6307 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
6308 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
6309 o change phiMin in exp1 (to agree with documentation)
6310 o add new flags:
6311 - T,S forcing inside/outside Adams-Bashforth
6312 - turn off temp,salt advection and/or forcing
6313 - for each tracer, define internal flag for multiDimAdvection & A-B
6314 o monitor: change definition of KE to check conservation of Energy
6315
6316 checkpoint45c_post (2002/05/30)
6317 o Removed f90 comments ("!")
6318 o Modified initialisations to enable exf package for MITgcm
6319 (without invoking ECCO_PACKAGE).
6320 o modifications to gradient check package (Martin Losch)
6321 - enable centered differences
6322 - modified format of standard output
6323
6324 checkpoint45b_post (2002/05/30)
6325 o cleaned exchange calls in cg2d
6326 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
6327 o included CPP option SINGLE_LAYER_MODE in thermodynamics
6328 to configure barotropic setup (Martin Losch)
6329 o moved some initialisations within bi,bj loop in dynamics
6330 (TAF flow dependency)
6331 o in initialise_varia, moved call packages_init_variables
6332 before convective_adjustment_init
6333 (corresponding adjustment of TAF tape initialisation).
6334 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
6335
6336 checkpoint45a_post (2002/05/01)
6337 o compute Rho over the whole domain (extend iMin,jMin indices)
6338 o specific exchange for X-slice domain (case Ny=1)
6339 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
6340 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
6341
6342 checkpoint44h_post = checkpoint45
6343 o Fix to restore differentiability:
6344 place at which packages_init_variables is called in
6345 initialise_varia is crucial for reverse control flow.
6346 o modifications in GMRedi to enable stable adjoint
6347 (corresponding modif's in thermodynamics, dynamics)
6348 o added missing hook for sponge layer code in external_forcing
6349 o modified test cost functions
6350 o storing in gad_advection (plus removal of write(0,*)!
6351 o missing headers TR1.h added in convective_adjustment routines
6352 o errorMessageUnit set non-equal zero in eeboot
6353 (conflict on some platforms, e.g. IBM SP3)
6354 o modified carbon verif.
6355
6356 checkpoint44h_pre (2002/03/14)
6357 o vertical grid option: allow to put the Interface at the middle between
6358 2 cell-centers ; replace delZ in pkg/kpp by drF.
6359 o GM Advective form: Tracers are advected using the residual transport (=
6360 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
6361
6362 checkpoint44g_post (2002/03/05)
6363 o fix surface correction term in multiDimAdvection (affects plume_on_slope
6364 results) ; ifdef missing in thermodynamics.F
6365
6366 checkpoint44f_pre,checkpoint44f_post
6367 o added PTRACERS package
6368 This allows an arbitrary number of passive tracers to be integrated
6369 forward simultaneously with the dynamicaly model.
6370 + Implemented so far:
6371 - basic forward algorithm (time-stepping, advection, diffusion, convection)
6372 - I/O and checkpointing
6373 - GM/Redi *but* using the GM/Redi coefficient of Salt
6374 + Not implemented so far:
6375 - KPP
6376 - OBCS
6377 + No specific example supplied (yet) but global_ocean.90x40x15 has the
6378 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
6379 line in data.pkg.
6380 + This package is disabled by default since it increases storage.
6381
6382
6383 o testscript: added -cleanup option
6384 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
6385 b) enable to filter 2D fields.
6386
6387 checkpoint44e_pre,post
6388 o re-wrote convective adjustment to use pre-calculated weights
6389 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
6390 Adds: model/src/convective_weights.F, convectively_mixtracer.F
6391 Original calls to convect() still in place.
6392
6393 chkpt44d_pre,post
6394 o added missing EXCLUDE_MONITOR flags
6395 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
6396 (incompatible typ in MIN/MAX expressions caused problems
6397 on IBM SP3)
6398 o in genmake added variable MAKEDEPEND
6399 plus resetting for case SunOS
6400 o added timer_stats.c routine for IBM SP3
6401 o removed variables in dynamics
6402 !!! I forgot to create tag chkpt44d_pre !!!
6403 !!! But chkpt44d_pre = chkpt44c_post !!!
6404
6405 o real fresh water flux implemented with non-linear free-surface.
6406
6407 chkpt44c_pre,post
6408 o few fix (mask in shap_s2, EmPmR in external_field_load,
6409 USE_NATURAL_BCS in solve_for_P);
6410 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
6411
6412 checkpoint44b_pre/_post
6413 o merge of relevant stuff from the ecco-branch:
6414 - genmake: removed $S64 overwrite for case SunOS
6415 - pkg/exf: update and corrections for field swapping and obcs
6416 - pkg/ecco: parameter lists for the_model_main, the_main_loop
6417 harmonized between ECCO and MITgcm
6418 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
6419 updated checkpointing_lev... lists for obcs
6420 - model/src: minor changes in forward_step, plot_field
6421 added directive for divided adjoint in the_main_loop
6422 - pkg/mdsio: added mdsio_gl_slice
6423
6424 o check parameters & config (chkpt44a_pre,post)
6425 o OBC and NonLin_FrSurf.
6426
6427 checkpoint44 (2002/01/18)
6428 o fix bug in mom_vi_del2uv
6429 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
6430 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
6431 o update AIM experiments (NCEP input files)
6432 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
6433 o added some stuff for AD
6434
6435 checkpoint43 (2001/09/28)
6436 o added two new advection tests
6437 o added global 4x4 degree ocean test
6438 o added test of H&S94 with free surface on cube
6439 o some final mods for gradient check, adjoint,...
6440
6441 checkpoint42 (2001/09/27)
6442 Fixed AD-related problems:
6443 o Store directives up-to-date with re-arranged Adams-Bashforth
6444 (mainly thermodynamics.F)
6445 o New store directives for multi-dim. advection schemes
6446 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
6447 * new common block and key passkey
6448 (mainly gad_advection.F)
6449 o Modified store directives for split of dynamics/thermodynamics
6450 for the case ALLOW_KPP
6451 o Cleaned argument list for timestep_tracer.F
6452
6453 checkpoint41 (2001/09/27)
6454 o re-formatted/added comments in prologues of key subroutines
6455 to work with protex
6456
6457 checkpoint40 (2001/09/27)
6458 o moved calc_gs, calc_gt and calc_tr1 back to model/src
6459 o added FLT (floats) package from Arne along with demo. experiment
6460 o re-arranged Adams-Bashforth scheme for tracers to allow easier
6461 implementation of forward-in-time forcing terms
6462 o more mods for non-linear free-surface including new variable
6463 o modified multi-dim method to work on cube
6464 o bug fix in KPP (from DM)
6465
6466 checkpoint40pre9 (2001/09/27)
6467 o added DST advection schemes
6468 o fix MPI bug on SGI's
6469 o modifications for non-linear free-surface
6470 o fixed conditionals for fixed flow/passive tracer only mode
6471 o added tension/strain form of stress tensor
6472 o changes to commenting of arguments for TAF/TAMC
6473 o added/updated many matlab scripts
6474 o added multi-dimensional advection method for tracers
6475
6476 checkpoint40pre8 (2001/09/05)
6477 o new package rw/
6478 Added method for dumping intermediate local arrays:
6479 mdsio_writetile - same as mdsio_writefield except works from inside
6480 bi,bj loop
6481 mdsio_writelocal - same as mdsio_writetile except works for local
6482 arrays
6483 write_local_r? - higher-level wrapper for mdsio_writelocal
6484 Controlled by diagFreq. Defaults to zero (ie. no dumps)
6485 Example given at end of mom_vecinv.F that dumps some local arrays.
6486 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
6487 control flux-form versus vector invariant code.
6488 Switch is runtime flag vectorInvariantMomentum (defaults to false)
6489 or genmake -DISABLE ...
6490 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
6491 (additional storing is now needed for case vecinv;
6492 currently nothing implemented to switch this storing off
6493 in case fluxform is used since no CPP flag available).
6494
6495 checkpoint40pre7 (2001/08/14)
6496 o bug fix in dynamics.F
6497 calc_viscosity called before k=1,Nr loop.
6498 o added some #ifdef's ALLOW_PASSIVE_TRACER
6499 o cleaned initialisations in ctrl_map_ini
6500 related to TAF
6501
6502 checkpoint40pre6 (2001/08/13)
6503 o split dynamics into thermodynamics & dynamics
6504 o corresponding split of calc_diffusivity into
6505 calc_diffusivity, calc_viscosity
6506 (kpp_calc_diff, kpp_calc_visc).
6507 o Added diffkr, kapgm to control variables
6508 o bug fix in gmredi_slope_limit for ldd97
6509
6510 checkpoint40pre5 (2001/07/31)
6511 o proper initialization of Adams-Bashforth time stepping
6512 + uses forward step for very first step of model (iter=0)
6513 o re-generated *all* output since almost all output is modified by this
6514 change (sorry but we've been putting this one off for about 2 years)
6515 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
6516 *not* regenerated since they are already out of date and I don't
6517 want to create the impression that they are suddenly working.
6518 o removed KAP stuff for DEC's
6519 o modified/added many .cvsignore files in */code and */input
6520 o added new expt "solid-body.cs-32x32x1"
6521 + this uses an alternative form of ini_curvilinear_grid.F which
6522 is not necessarily any better than the current one...
6523
6524 checkpoint40pre4 (2001/07/30)
6525 o added re-initialisations of utrans,vtrans,rtrans in
6526 calc_common_factors which are crucial for TAF.
6527 o extended iMin,jMin range for calc_common_factors,
6528 calc_diffusivity
6529 o added option ALLOW_PASSIVE_TRACER
6530 o a few minor updates and fixes
6531
6532 checkpoint40pre3 (2001/07/13)
6533 o created calc_gtr1.F for gad package
6534 o split the_main_loop and re-introduced forward_step
6535 o some recomputations of nIter0 for TAMC
6536
6537 checkpoint40pre2 (2001/07/13)
6538 o Updated to latest branch of AJA, JMC
6539 o Added gradient check package
6540 o Added routines for passive tracer handling
6541 o Added carbon sequestration sensitivity experiment
6542
6543 checkpoint39 (2001/05/14)
6544 o Modifications and fixes to support TAMC
6545 (mainly missing or wrong directives)
6546 o Corrected common blocks when fooling TAMC to produce adjoint I/O
6547 in addummy_in_stepping
6548 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
6549 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
6550 o Included following packages:
6551 cal: calendar
6552 exf: external forcing
6553 ecco: essential routines to control use of cal, exf
6554 (NB: this is not the full ECCO environment)
6555 o disabled some packages by default in genmake
6556
6557 checkpoint38 (2001/04/10)
6558 o see notes_c37_adj.txt
6559 o corrected wrong layer index in external_forcing_t
6560 o replaced the_main_loop/forward_step by the_main_loop
6561 o removed forceoutput from write_state
6562 (replaced criteria for initial/final state)
6563 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
6564
6565 checkpoint37 (2001/03/13)
6566 o mdsio.F routine split and packaged in pkg/mdsio
6567 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
6568 used unless genmake -disable=mdsio)
6569 o allow a more precise surface-geopotential gradient for the atmosphere
6570 taking into account the change in space of Alpha (=1/rho) at the surface.
6571 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
6572 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
6573 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
6574 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
6575 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
6576 o Time-Average diagnostics defined as a pseudo package "timeave".
6577 o pickup files : old pickup (before c35) did not work with new code (c35
6578 and after) unless activating 2 commented lines in initialise-varia.
6579 o Non-Hydrostatic pickup file Pb fixed.
6580 o bug with Rigid-lid version (since c35) fixed.
6581
6582 checkpoint36 (2001/02/20)
6583 o implement Crank-Nickelson barotropic time-stepping
6584 o recover Time-Average diagnostics
6585 o fix Pb in checkpoint (PR#19)
6586 o AIM become a standard package ; clean unused CPP_kees
6587
6588 checkpoint35 (2001/02/08)
6589 o subtantial rewrite of dynamics.f
6590 o allows staggered time-stepping
6591 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
6592 o added bottom drag (linear + quadratic)
6593
6594 checkpoint34 (2001/01/30)
6595 o Modified exchange routines for correct reverse simulation.
6596 o Added verification output to comply with bug fix in impldiff.F
6597 as of c33 (exp2, natl_box).
6598 o Corrected store directives in dynamics.F
6599 o Corrected array boundaries in impldiff.F
6600 o Corrected array dimensions in gmredi.
6601 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
6602 o Added routine GLOBAL_SUM_INT to global_sum.F
6603 o Added mdsio_gl.F for ECCO purposes.
6604
6605 checkpoint33 (2000/11/30)
6606 o Fixed bug in lower BC in impldiff.F
6607 o Fixed confusion about units of forcing arrays in FFIELDS.h
6608 namely Fu,Fv,Qnet,Qsw,EmPmR:
6609 - Removed verification/natl_box/code/external_fields_scale.F
6610 (did not differ from that in model/src)
6611 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
6612 (see FFIELDS.h for description)
6613 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
6614 kpp_calc.F and kpp_transport_t.F
6615 - Removed model/src/external_fields_scale.F and calls to it
6616 - verification/natl_box uses flux data with "atmospheric" sign so
6617 a special version of external_fields_load.F is used to
6618 change the data as it's read in. This way, the arrays
6619 have the right units and signs at all times tha a user could
6620 possibly use them.
6621 o Corrected genmake to delete a temporary file during configuration
6622
6623 checkpoint32 (2000/11/13)
6624 o Scaling of forcing fields moved from external_forcing.F to
6625 external_fields_scale.F, called directly after loading fields.
6626 o Surface relaxation terms added to surface tendency fields in
6627 extra subroutine.
6628 o impldiff.F changed to avoid storing by TAMC of huge intermediate
6629 fields.
6630 o Changes in GMRedi to comply with packaging structure.
6631 o Modifications and bug fixes in KPP package.
6632 o Verification experiment for KPP added (verification/nat_box/)
6633
6634 checkpoint31 (2000/09/11)
6635 o Packages interface brought in line with defined standard
6636 -> new routines packages_...F
6637 -> changes in initialise_fixed.F, initialise_varia.F
6638 -> enables initialisation interface for ECCO package
6639 o Rescaling of external forcing fields immediately after read
6640 (removed from external_forcing.F)
6641 -> new: surface_fields_scale.F
6642 -> affects ini_foorcing.F, external_fields_load.F
6643 o Computation of surface tendencies before tendency updates.
6644 -> new: external_forcing_surf.F
6645 o Change of variable names useGMRedi, useKPP, useECCO
6646 o Further changes in dynamics.F, impldiff.F for TAMC
6647 o Tested for experiments 0, 2, 4.
6648 - not yet tested for GMRedi.
6649 - not yet tested for KPP.
6650
6651 checkpoint30 (2000/07/13)
6652 o Updates for OBCs
6653 o New experiment for test OBCs (internal_wave)
6654 o New output.txt in verification/exp4/results/
6655 o Updates for KPP: calculation of viscosity corrected, new variables
6656 kpp_dumpFreq and kpp_taveFreq
6657 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
6658 and entry for T90 in genmake
6659
6660 checkpoint29 (2000/06/21)
6661 o packaged KPP and GM/Redi
6662
6663 checkpoint28 (2000/06/09)
6664 o Corrected initialization of hFacMin for difference vertical coordinates
6665 o Modified calculation of partial cell thickness to more robust algorithm
6666 o config_summary.F: replaced write_1D_... by write_0D_...
6667 read_write.F: added subroutines write_0D_...
6668 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
6669 included some initialisations required for TAMC.
6670 o routine calc_isoslopes: modified sqrt computation to make it
6671 differentiable for zero argument.
6672 o routines dynamics, impldiff:
6673 included store directives and tape key computations required for TAMC.
6674 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
6675
6676 checkpoint27 (2000/04/10)
6677 o fixed calc_isoslopes() to so that cancellation of terms in tensor
6678 formulation works properly with variable resolution.
6679 o restructured the calling tree between the_model_main() and dynamics()
6680 o split initialise() into initialise_fixed() and initialise_varia()
6681 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
6682 in new routine ini_psurf()
6683
6684 checkpoint26 (2000/04/05)
6685 o moved some #ifdef in optional routines to encompass everything
6686 except the argument declarations. This was using up some memory.
6687 o fixed macros like _ADT to work with both versions of Linux cpp
6688 o cleaned up some unused and uninitialized variables
6689 (helps when debugging with strict compile options)
6690 o split up CPP_EEOPTIONS.h into options and macros
6691 (macros are now in eesupp/inc/CPP_EEMACROS.h)
6692 o patch for 2 processor JAM mode
6693
6694 checkpoint25 (2000/03/15)
6695 o updates for OBCs and NH
6696 o dramatically reduced memory usage
6697 o added "JAM" routines for use on Artic network
6698 o parameterization of convection by implicit vertical diffusion
6699 o added a diagnostic of convective index
6700 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
6701 (this is was partly for OBCs and NH but also in anticipation of
6702 an explicit free-surface option)
6703 o initial state input files for U and V
6704
6705 checkpoint24 (1999/08/02)
6706 o Removed some spurious "REAL"s
6707 o Updated KPP to latest version from JPL
6708 o Added a COS(latitude) in horizontal viscosity
6709
6710 checkpoint23 (1999/05/26)
6711 o Added del^4 diffusion for salt and temperature
6712 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
6713
6714 checkpoint22 (1999/05/18)
6715 o Made many small changes: implicit none, format(i5), etc...
6716 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
6717
6718 checkpoint21 (1999/05/18)
6719 o Introduced new I/O package that supports direct-access records (mdsio.F)
6720 o Split-up mid-level I/O routines
6721 o Updated input data for experiments 0,1,2,4 and 5
6722 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
6723
6724 checkpoint20 (1999/03/22)
6725 o Tidied up open-boundaries some more
6726 o Added non-hydrostatic code
6727 o Fixed some input data
6728 o Modified MPI start-up to work in "coupled" context.
6729
6730 checkpoint19 (1998/12/15)
6731 o Tidied up directory structure for verification experiments.
6732 o Added new code for open boundaries.
6733 o Corrected advective terms near boundaries.
6734 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
6735 o Implemented free-slip/no-slip BCs and del^4 dissipation.
6736 o Split default parameters out of ini_parms.F into set_defaults.F.
6737
6738 checkpoint18 (1998/11/30)
6739 o Further changes for optional code generation with
6740 CPP - ugh!
6741
6742 checkpoint17 (1998/11/03)
6743 o Beginning to incorporating modularity
6744 for supporting atmos. and ocean configs.
6745 o Small changes for TAMC complinace
6746 o New ultra simple test case. Barotropic box
6747 configuration "exp0".
6748
6749 checkpoint16 (1998/10/28)
6750 o Minor changes to exchange routines to support
6751 accumulation in reverse mode. Adjoint of an
6752 assignment is an addition.
6753 o Changes to support compilation by TAMC (LR(1)
6754 syntax) and by g77 under Linux ( 72 character
6755 limit ).
6756
6757 checkpoint15 (1998/09/29)
6758 Rewrote exchange routines to allow
6759 o General tile <-> tile connectivity.
6760 o TAMC reverse mode flag ( is this really needed? )
6761 o Variable width overlap and exchange region widths.
6762 o Hooks for sharing data via DMA, Arctic, Memory Channel,
6763 shmput/shmget, VIA, SYSV shmem and every other cool
6764 communication method.
6765
6766 checkpoint14 (1998/09/09)
6767 Consistent isomorphism chages made. These allow dynamical core
6768 to support both pressure and meters as a vertical coordinate.
6769
6770 checkpoint13 (1998/07/17)
6771 Release which corrects global_max problem and a couple
6772 of KGM time-averaging diagnostic errors. Also contains
6773 a double-gyre experiment setup as well as the baseline
6774 4 degree global template. The double gyre template is
6775 organised to allow it to be applied automatically to
6776 the baseline configuration.
6777
6778 branch-point-rdot
6779 A few tidy-ups have been made bt the real point of this
6780 check-point (excuse the pun) is to allow a branch to be
6781 made for the purposes of adding the rDot alterations.
6782 I don't want to commit the rDot to the main-trunk until
6783 we've actually tested it...
6784
6785 checkpoint12 (1998/07/08)
6786 Tidy up and added generic genmake script (formerly
6787 configure script).
6788 Released to testers.
6789
6790 checkpoint11 (1998/07/02)
6791 Re-arranged initialise() and introduced ini_vertical_grid()
6792 and ini_masks_etc().
6793
6794 checkpoint10 (1998/07/01)
6795 Introduced the configure script.
6796 Separated out the diags package.
6797 Added template for writing time-averages of tile/intermediate quantities.
6798 Updated SIZE.h in exp2 and made the data big-endian.
6799
6800 checkpoint9 (1998/06/22)
6801 MPI fix. Filename changes (meta/data). salbin*y stuff.
6802 General tidy-up.
6803 SST.bin SSS.bin added to verification/exp2
6804
6805 checkpoint8 (1998/06/22)
6806 Inludes time-dependant forcing and time-averaging.
6807 Works at 4x4 and 2.8125x2.8125 global
6808
6809 checkpoint7-4degree-ref
6810 Branch from checkpoint7. Released for application to
6811 global modeling and general modeling - process studies, regional
6812 model etc..
6813 Configured for verification/exp2 - 4 degree global, two process.
6814
6815 checkpoint7 (1998/06/15)
6816 Created by cnh
6817 Simple 4 degree global simulation
6818 configuration.
6819 Includes climatological wind,
6820 hydrography, bathymetry etc
6821 Does not include Heat Flux and E-P
6822
6823 checkpoint6 (1998/06/08)
6824 Created by cnh
6825 merged checkpoint5 with CD and
6826 spherical polar code.
6827 Still some problems with GM Redi
6828 abd full topography.
6829
6830 checkpoint5 (1998/06/08)
6831 Created by AJA
6832 contains updates to GM Redi
6833 and reordered timestepping loop
6834 for Implicit Diffusion.
6835
6836 checkpoint4 (1998/05/30)
6837 Created by cnh
6838 Contains memory saving macros ( _rdxc etc..) for when
6839 grid variations are limited.
6840 Contains polynomial coeffs for EOS and knudsen program
6841 for generation.
6842
6843 checkpoint3 (1998/05/26)
6844 Created by cnh
6845 Added extra flags for runtime options
6846 Added this file
6847 Added implicit free-surface
6848 Added pre-conditioner
6849 Put compare01 into repository ( compare01/... )
6850 Put data and eedata into repository ( verification/exp1 )
6851
6852 checkpoint2
6853 Created by AJA
6854 Added GM/Redi
6855
6856 checkpoint1
6857 Created by AJA
6858 Restructured kloop in dynamics.F
6859 Added non-linear EOS
6860
6861 baseline
6862 Original checked in code

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