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Revision 1.1587 - (show annotations) (download)
Thu Feb 2 02:06:32 2012 UTC (12 years, 4 months ago) by jmc
Branch: MAIN
Changes since 1.1586: +8 -1 lines
document changes in pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef)

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1586 2012/01/31 17:12:24 jmc Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
8 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
9 conductive heat flux F_c , and add it explicitly when updating tsurf as
10 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
11 so that now F_ia has a consistent meaning through the entire routine.
12 This causes differences at truncation level: update output of fwd exp.
13 global_ocean.cs32x15.seaice.
14 o pkg/seaice:
15 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
16 of arrays, sign/direction of fluxes; no effect on results.
17 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
18 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
19 note: this should have been done before changing celsius2K default.
20 - to keep results unchanged, add back old value of celsius2K in verification
21 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
22 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
23 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
24 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
25 freezing temp is consistent with value in seaice_growth.F ; this causes
26 differences at machine truncation level: update lab_sea AD output (3/4).
27 o pkg/seaice:
28 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
29 and climsst/sss even when using seaice (to prevent calculation that might
30 use SST on land); does not affect any verification exp.
31 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
32 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
33 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
34 over land (non-legacy code)
35 o vectorize salt_plume package:
36 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
37 - this code computes plumebk everywhere (also over land), thus requires
38 code to avoid divisions by zero and catch the case of kLev=Nr.
39 - efficiency of salt_plume_frac is still sub-optimal
40 o tools (genmake2):
41 - fix makefile NAME specification (option: -makefile NAME) by adding
42 "-f $MAKEFILE" in few places where it was missing including makedepend
43 command (contribution from Paul).
44
45 checkpoint63i (2012/01/24)
46 o model/src:
47 - add factorized versions of some EOS code to find_rho.F,
48 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
49 o model/src:
50 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
51 - change default celsius2K from 273.16 to 273.15
52 - to keep results unchanged, add back old value of celsius2K in verification
53 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
54 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
55 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
56 to make TAF generate vectorizable code
57 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
58 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
59 have flags that do this more efficiently.
60 o pkg/diagnostics/diagstats_calc.F
61 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
62 o pkg/obcs (with exch2):
63 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
64 and remove code (in obcs_readparms.F) which was based on EXCH of indices
65 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
66 o pkg/exf and seaice exp:
67 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
68 so that switching off area & heff advection flags does not affect results.
69 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
70 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
71 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
72 results of verification experiments: 1D_ocean_ice_column(fwd),
73 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
74 and offline_exf_seaice (all 4).
75 o pkg/seaice:
76 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
77 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
78 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
79 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
80 not multi-dim advection;
81 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
82 SHORTWAVE_HEATING #undef.
83 o optim: make Makefile more robust (?)
84 o pkg/obcs:
85 * fix treatment of obcs_read_pickup for TAF
86 o pkg/shelfice:
87 * add missing initialisation of num_shifwflx
88 * new adjoint verification exp. for isomip
89 * change Prandtl and Schmidt numbers from generic formulations
90 (in terms of model diffus. and visc.) to separate runtime
91 parameters, with Holland and Jenkins (1999) default values.
92 o pkg/exf (interpolation):
93 - extended input field (2 rows) near the N & S poles:
94 * fill in with the symetric value (when even Nb of data in longitude)
95 * add average value at the poles only for scalar quantities ; for vector
96 component interpolation, skip the averaging and keep duplicated values,
97 unless the 2 components have same location (uvInterp=T) in which case
98 interpolate the 2 components together using S/R EXF_INTERP_UV.
99 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
100 together: this allows to account properly for local orientation when
101 averaging at N & S pole.
102 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
103 exf-interpolation near N & S poles. Undef by default.
104 - add debug check/print on 1rst iter if debugLevel >=2.
105 o pkg/exf:
106 - change masking flags definition (no longer "parameter"), put them in
107 common block and set them in S/R EXF_INIT_FIXED.
108 - change recognized masking flag from s,u,v to c,w,s since the mask
109 to use (maskC,W,S) depends on position on model grid and has little to
110 do with scalar/vector difference; fix masking if using P-coordinates.
111 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
112 and update results of exp. global_with_exf (x2).
113 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
114 o pkg/obcs
115 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
116 o pkg/exf (interpolation):
117 - assume periodicity in X only if input field cover full longitude range.
118 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
119 and should vectorise).
120 - fix input lat of the 2 added row (in case we provide N.pole data).
121
122 checkpoint63h (2011/12/30)
123 o pkg/seaice:
124 - change declaration of UVM from _RL to _RS in order to get B-grid
125 uIce,vIce monitor when _RS = real*4
126 o pkg/offline:
127 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
128 - compute vertical velocity if not read from file (switch on exactConserv
129 & staggerTimeStep);
130 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
131 o verification:
132 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
133 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
134 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
135 - update output of exp. global_ocean.cs32x15.viscA4 after changing
136 grid-file angles (used here for coriolis-3d);
137 - remove (or gzip) few files not needed to run fizhi-cs experiments.
138 o pkg/exf (vector interpolation):
139 - rotate vector component toward local grid-axis orientation using grid-angles
140 (stored in GRID.h) instead of locally computed rotation angle; keep old code
141 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
142 o pkg/seaice:
143 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
144 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
145 o pkg/PKG_OPTIONS.h files:
146 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
147 outside of the #ifdef ALLOW_THISPKG / #endif block.
148 - update verification/*/code/PKG_OPTIONS.h files.
149 o add a verification experiment (offline_exf_seaice/input.seaice) that test
150 the B-grid LSOR solver
151 o pkg/seaice: sort out emissivity and long wave radiation step 2:
152 - add emissivity for snow and ice as new run-time parameters
153 (unfortunately) that default to the corresponding exf values; this
154 changes results in most verification experiments so that for backward
155 compatibility these parameter have to be set explicitly to inconsistent
156 values (ugly);
157 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
158 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
159 until we agree how to handle this bug properly
160 o pkg/exf (interpolation):
161 - add a set of run-time param ({inputfield}_interpMethod), one for
162 each interpolated input field, to select the interpolation method
163 with a value of zero switching off the interpolation;
164 - print interpolation parameters to standard output;
165 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
166 (to use instead runoff_interpMethod=0 in data.exf).
167 - simplify default setting of interpolation parameters (for all fields,
168 set position to match model grid cell-center position, leading to trivial
169 interpolation in case of regular Lat-Lon grid) and fix for the case of
170 non-uniform delY.
171 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
172 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
173 this factor is absolutely required, because the lw exitance (= out-going
174 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
175 where the reflectivity rho = 1-emissivity for conservation reasons. Once
176 this is established, we can remove the CPP-Flag (if we want to).
177 o pkg/seaice:
178 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
179 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
180 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
181 what the name implies (and not emissivity*BoltzmannConstant), this means
182 the old default value of 5.5e-8 now means
183 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
184 S/R exf_readparms
185 - FV-discretization of the B-grid LSOR solver, turn on with
186 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
187 of the calling routine dynsolver, so that B and C-grid code look a
188 little more alike.
189 - fix index bugs in ostres.F (B-grid code)
190 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
191 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
192 default for SEAICE_emissivity, if useEXF; requires setting a wrong
193 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
194 backward compatiblity
195 o model/src: use sigmaR in calc_ivdc
196
197 checkpoint63g (2011/12/16)
198 o pkg/seaice/seaice_growth.F:
199 fix heat conservation of the coupled ocean-seaice system.
200 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
201 solid vs liquid water treatment is resolved via QNET.
202 o pkg/seaice/seaice_growth.F:
203 add missing term for sublimation in saltFlux, which was breaking conservation.
204 o pkg/seaice/seaice_model.F:
205 Remove this patholigical case treatment in evolution branch,
206 where it is un-necessary and breaks conservation.
207 Update global_ocean.cs32x15/results accordingly for
208 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
209 o model/src:
210 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
211 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
212 o pkg/obcs:
213 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
214 tendency for temperature and salinity that is then applied to update
215 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
216 horizontal advection and diffusion contributions on the boundary (in
217 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
218 removing the mask in S/R timestep_tracer. The advantage of this approach is
219 that the updated tracer values include contributions from the surface
220 forcing and vertical diffusion.
221 This modification changes exp4.stevens because of vertical diffusion.
222 o model/src:
223 change non-curvilinear grid setting to also work with exch2 + blank tiles:
224 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
225 face dimensions.
226 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
227 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
228 and INI_SPHERICAL_POLAR_GRID.
229 change test-experiment global_ocean.90x40x15:
230 - split the domain in many more tiles (9x4 tiles of 10x10 each);
231 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
232 - update results of both test (std & dwnslp).
233 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
234 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
235 o model/src:
236 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
237 and fix initialisation when using sigma-coords.
238 o model/src:
239 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
240 to their current value at the beginning of forward_step.F": add a new run-time
241 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
242 - set doResetHFactors=T in the following test exp:
243 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
244 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
245 and tutorial_global_oce_in_p (nonLinFS in p)
246 o pkg/ecco
247 - added IES cost term
248 o verification/advect_xz
249 - scale down the depth by 1/100 (from 200 km to just 2.km)
250 - add secondary test using divergent flow, r-star and implicit vertical advection.
251 - add note (check_conserve_TS.txt) and matlab script to check global
252 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
253 o pkg/rbcs:
254 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
255 o pkg/obcs (Stevens BCs):
256 - fix various problems in the phase speed computations of the Stevens
257 boundary conditions:
258 - sign error for western and southern boundaries,
259 - time tendencies were underestimated by factor of dTracerLev and some just
260 zero (for multidim advection schemes) -> now estimate time tendencies
261 from difference between previous (n) time level and the one before (n-1);
262 this requires storing a field per tracer per boundary, also in the pickup
263 files.
264 - replace deltaTmom in cflMer/Zon computation with dTracerLev
265 - set default phase velocity to cflMer/Zon
266 - update verification experiment exp4.stevens
267 o pkg/generic_advdiff (implicit_r):
268 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
269 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
270 - fix implicit vertical diffusion or advection with NonLin FreeSurf
271 (was using current recip_hFacC instead of future recip_hFacC): set future
272 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
273 solver S/R ;
274 - fill diagnostics of vertical advective fluxes (computed from tendency)
275 when using implicit vert. advection;
276 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
277 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
278 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
279 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
280 o pkg/diagnostics:
281 - add diags for T & S tendency which goes through Adams-Bashforth.
282
283 checkpoint63f (2011/11/30)
284 o pkg/obcs/obcs_calc_stevens.F:
285 - join some loops to reduce number of if-statements
286 - fix a bug in code for northern and southern boundaries.
287 o pkg/seaice/seaice_init_varia.F
288 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
289 caused zero ice-velocities for the B-grid code
290 o pkg/seaice/seaice_init_fixed.F
291 - fix a bug in the initialisation of the second metric terms
292 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
293 - this affects all seaice configurations with useCurviLinearGrid = .true.
294 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
295 = .true. (default)
296 - the only verification experiment affected is global_ocean.cs32x15:
297 icedyn, seaice, and seaice_dynmix (AD)
298 o pkg/thsice/thsice_diagnostics_state.F
299 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
300 not contain garbage that can lead to surprises in diagstats_calc.F
301 o model/src:
302 - move bi,bj loops inside INTEGR_CONTINUITY ;
303 - call INTEGR_CONTINUITY directly from forward_step.F
304 (previously called from momentum_correction_step.F)
305 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
306 forward_step.F and pkg/ecco/the_main_loop.F
307 o model/src/do_oceanic_phys.F:
308 - reset addMass to zero only if useICEFRONT ;
309 - separated k-loop for rhoInSitu calculation ;
310 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
311 and at constant T,S (= WdRHOdP);
312 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
313 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
314 transport of locally-referenced potential density);
315 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
316 o gluemnc:
317 - replace ncrcat with ncks when adding variables to *.glob.nc
318 - change the way variables without record dimensions are handled so that
319 files that have variables with and without record variables can be glued:
320 add a record dimension with a new unique name to be able to differentiate
321 between variable with and without a-prior record dimensions. Remove
322 this record dimension before adding the variable to the *.glob.nc file.
323 This procedure automatically works also for grid.*.nc files that do not
324 have any record dimension.
325 o verification/cpl_aim+ocn:
326 - generate new reference output on baudelaire (gfortran, mpich2) (previously
327 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
328 o pkg/obcs/obcs_calc_stevens.F:
329 - add code for northern and southern boundaries.
330 - reorder some loops to save some operations and so that drFBar can be scalar
331 o model/src:
332 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
333 truncation) and add diagnostics for Adams-Bashforth tendency increment.
334 - update test-exp. AD output:
335 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
336 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
337 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
338 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
339 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
340 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
341 tutorial_plume_on_slope.
342 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
343 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
344 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
345 does not even come with an F77 compiler anymore, this should not be
346 a limitation
347
348 checkpoint63e (2011/11/06)
349 o pkg/seaice adjoint of LSR:
350 - substantially rework STORE dirs.
351 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
352 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
353 and only perform SOLV_MAX_FIXED adjoint iters.
354 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
355 always goes to same record, meaning that the last forward field will be
356 the one used in the adjoint - an approximation.
357 - now produces non-zero LSR-related gradients, and acceptable gradients for
358 An's zonal (x-z) test case (to be checked in)
359 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
360 (but these are screwed up by the thermodynamics in the first place);
361 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
362 output_adm.txt also reflects changes to seaice_lsr
363 - global_ocean.cs32x15:
364 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
365 (output_adm.seaice.txt was updated)
366 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
367 (output_adm.seaice_dynmix.txt)
368 o test-exp. exp4+stevens:
369 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
370 o pkg/seaice (lsr solver):
371 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
372 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
373 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
374 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
375 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
376 - compute (with new S/R) and print initial (+ free-driff sol. if available)
377 and final residual of linearised system.
378 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
379 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
380 o pkg/obcs: Stevens BCs (still only for east and west)
381 - fix Stevens BCs by using intermediate velocities of previous
382 time step as "baroclinic" contribution rather velocity of one grid cell
383 inside the boundaries; more consistent but makes the entire treatment
384 more complicated, requires new pickup files and two new S/Rs:
385 obcs_copy_uv_n and obcs_save_uv_n
386 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
387 (undefined by default)
388 - silently move computation of some grid factors into separate loops to
389 save some recomputations
390 - add a hack for non-linear free surface
391 - add a verification experiment to exp4 that tests this code
392 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
393
394 checkpoint63d (2011/10/25)
395 o pkg/obcs + seaice-dynamics:
396 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
397 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
398 values (consistent with an implicit method).
399 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
400 return to older implementation (same results as before); note that none of
401 the "experimental" OBCS_SEAICE options are implemented in the new version.
402 - switch test exp. seaice_obcs to use new version (update output).
403 o pkg/seaice:
404 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
405 - add parenthesis in Water-Ice drag calculations (evp & lsr);
406 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
407 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
408 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
409 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
410 o pkg/layers:
411 - Include potential density as new coordinate (Thanks to David Munday)
412 o pkg/dic:
413 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
414 carbonate computation/output to CALC_PCO2_APPROX
415 o pkg/generic_advdiff
416 - make TAF generate code that vectorizes:
417 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
418 o model/src:
419 - improve vectorization also for adjoint code of
420 solve_tridiagonal and solve_pentadiagonal. As this requires up to
421 5 new 3D-fields, this code is only turned on for the combination of
422 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
423 for singular matrix check (only for TARGET_NEC_SX).
424 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
425 ALLOW_AUTODIFF. This flag now needs to be set outside of
426 solve_tri/pentadiagonal.F
427 o pkg/exf:
428 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
429 optional namelist EXF_NML_OBCS).
430 - add many debug-print (to trace down where pkg/cal error msg comes from)
431 o pkg/mom_vecinv/mom_vi_hdissip.F
432 - rearrange loops so that vectorization is improved and in particular
433 the adjoint routine vectorizes. The code is a little longer now, but I
434 think easier to read.
435 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
436 o pkg/seaice:
437 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
438 o pkg/exch2:
439 - alternative code (without tile x tile matrix) for cumulated (global) sum;
440 used as default; keep using matrix version in adjustment.cs-32x32x1.
441 o tools/build_options:
442 - after merging some MPI and/or multi-threads specific optfiles so that
443 the modified default optfile support both built (using genmake2 -mpi
444 for the MPI built, using genmake2 -omp for OpenMP built),
445 move now obsolete optfiles to tools/build_options/unsupported/
446 (add copy of email sent to support list in doc/optfiles_changes.txt)
447
448 checkpoint63c (2011/09/28)
449 o pkg/ebm:
450 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
451 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
452 o pkg/seaice (SItracer pickup)
453 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
454 To be done:
455 - thorough testing of missing fields in S/R seaice_read_pickup
456 - thorough matching between generic tracers and specific fields used
457 (e.g. volume-weighted age, area-weighted age, salinity, ...)
458 o pkg/grdchk:
459 - all procs calculate and print finite-difference gradient (for testreport)
460 - change description output used by testreport;
461 - AD testing: also compare and report Finite-difference gradient;
462 => update all output_adm*.txt
463 o test exp. global_ocean_ebm:
464 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
465 and turn on exactConserve; update (fwd) output.
466 o pkg/seaice (LSR):
467 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
468 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
469 * identical results with non-CS topology (but save up to half of EXCH calls)
470 * no much changes in cs-32 verification tests since no ice at face edges
471 (differences due to convergence criteria, since nb of iterations changed)
472 * expect some differences on lat-lon-cap grid.
473 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
474 o pkg/exch2:
475 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
476 many tiles); until alternative coding is added, just add a stop.
477 o pkg/kpp:
478 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
479 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
480 o optfiles:
481 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
482 into corresponding standard one, which now support different build:
483 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
484 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
485 o pkg/obcs (seaice):
486 - add missing EXCH for uIce,vIce after applying OBCS;
487 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
488 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
489 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
490 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
491 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
492 and eedata.mth for MPI and mutlti-threaded testing.
493 o pkg/flt:
494 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
495 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
496 - fix pickup and trajectories + profiles output with multi-threads;
497 - add parameter to select group of fields to write along trajectory and
498 profile (default unchanged);
499 - only call PORT_RAND* function when flt_noise <> 0;
500 - add multi-threaded test for verification exp. flt_example.
501 o eesupp/src:
502 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
503 - USE_OMP_THREADING: check that number of threads (from eedata) matches
504 actual number (from env.var. setting).
505 o pkg/ebm:
506 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
507 - add multi-threaded test for verification exp. global_ocean_ebm
508
509 checkpoint63b (2011/08/29)
510 o pkg/ebm:
511 - fix sign of runoff;
512 - update directly forcing fields (Qnet,EmPmR) to use standard
513 external_forcing_surf.F (remove ebm_forcing_surf.F);
514 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
515 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
516 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
517 - update global_ocean_ebm parameters file data and update output (fwd+ad).
518 o verification/matrix_example:
519 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
520 MPI and mutlti-threaded testing.
521 o pkg/matrix:
522 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
523 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
524 - fix for multi-threaded (remove DATA statement);
525 - use standard DIFFERENT_MULTIPLE function;
526 - add MATRIX_OPTIONS.h
527 o verification/matrix_example:
528 To allow to split the domain in several tiles, change the domain size
529 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
530 Western side) of land points.
531 o (*_)write_pickup:
532 - fix few bugs in mypackage_read/write_pickup.F
533 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
534 array of length 1 (was caught by compiler syntax-check).
535 o pkg/diagnostics (velocity potential solver):
536 - fix initialisation of main diagonal matrix (for overlap values)
537 o tools/build_options:
538 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
539 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
540 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
541 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
542 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
543 and use "-devel" testreport option for standard testing on baudelaire.
544 o pkg/grdchk:
545 - Assume that all gradient-check position are within the same tile
546 corresponding to global indices (iGloTile,jGloTile) and that
547 positions (i,j indices or nbeg) are local to this tile;
548 - set tile local-indices and proc. number according to tile global-indices;
549 - remove grdchkwhichproc from namelist (retired param);
550 - send adjoint gradient to all procs so that all procs print it to STDOUT;
551 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
552 o adding package bbl (Bottom Boundary Layer)
553 description in MITgcm/pkg/bbl/bbl_description.tex
554 example/test experiment in MITgcm_contrib/bbl
555 o adjoint verifications
556 - changed 5 experiments to multi-tiles
557 * global_ocean.90x40x15
558 * obcs_ctrl
559 * offline_exf_seaice
560 * tutorial_dic_adjoffline
561 * tutorial_tracer_adjsens
562 changed reference output for those that crossed tile boundaries
563 (changed choices of gradient check positions)
564 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
565 - temporary bug fix in grdchk_loc.F for obcs
566 o genmake2 & testreport
567 - add target "obj" (just for OBJFILES files) to Makefile;
568 - add option to specify FEXTRAFLAGS on command line.
569 o pkg/mypackage:
570 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
571
572 checkpoint63a (2011/08/02)
573 o pkg/diagnostics (velocity potential):
574 - fix velocity-potential calculation when using OBCS: balance net inflow
575 at each level (new S/R OBCS_DIAG_BALANCE).
576 - fix some of the problems with OBCS in stream-function calculation.
577 o pkg/exf/exf_readparms.F
578 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
579 EXF_NML_OBCS) more consistent, so that you need not have these lists
580 in data.exf when they are not used.
581 o optim/optim_readdata.F:
582 - add some output about obcs variables that might help debugging
583 - add a check about nvarlength
584 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
585 o pkg/diagnostics (velocity potential):
586 - fix mask for OBCS (still problems in stream-function with OBCS);
587 - add specific parameter (default = main code CG2D params) for solver;
588 - in case of poor convergence, use solution corresponding to lowest residual.
589 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
590 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
591 and should be avoided where possible.
592 o model/src (rStar):
593 - include r* effect on reference-state (PhiRef) in totPhiHyd
594 (so that it's really the potential anomaly at the cell center);
595 affect solution only if z* with full pressure in EOS.
596 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
597 update output (because of z* in totPhiHyd and viscA4 changes);
598 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
599 @ constant r) until interpolation at constant r is implemented.
600 o pkg/diagnostics
601 - fix RCENTER diagnostics in case cell center is not at interface middle
602 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
603 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
604 that THETA and SALT are "conservative temperature" and "absolute
605 salinity"
606 o pkg/ctrl
607 - fix computation of endrec in s/r ctrl_init_rec
608 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
609 o pkg/seaice/seaice_growth.F
610 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
611 remove then obsolete STORE directives
612 - fix STORE directives for tice and tices, so that only the
613 appropriate part of the fields are stored (and not the entire
614 field); update global_ocean.cs32x15.seaice AD output.
615 - cosmetic changes: adjust CPP flags and indentation for better
616 legibilty
617 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
618 Chris Wilson)
619 o pkg/gmredi:
620 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
621 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
622
623 checkpoint63 (2011/07/11)
624 o pkg/exch2:
625 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
626 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
627 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
628 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
629 o pkg/diagnostics:
630 - deal with pairs of post-processed diags which are computed together; in
631 particular, re-order list of diags within 1 file to save 2nd computation.
632 - add S/R to compute velocity stream-function (called after velocity-potential
633 calculation) from divergence free transport -> new diagnostics "PsiVEL".
634 - add parameter to select grid-point location where PsiVEL == 0.
635 o eesupp/src:
636 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
637 (specific S/R needed with exch2 topology - for now, just print an error msg)
638 o pkg/shelfice
639 - Implement friction velocity-dependent transfer coefficients following
640 Holland and Jenkins, JPO, 1999
641 Original code by M. Losch with small modifs.
642 Enable with CPP option SHI_ALLOW_GAMMAFRICT
643 and runtime flag SHELFICEuseGammaFrict
644 o verification lab_sea & global_ocean.cs32x15:
645 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
646 does not miss some dependencies (but is slower) and also works with many files
647 (default makedepend limitation for AD built).
648 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
649 o pkg/diagnostics:
650 - add run-time parameter "useMissingValue" (def=False) to fill land-point
651 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
652 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
653 - Extend the use of "missing_value" setting from data.diagnostics for the case
654 of counter-diagnostics (where fraction-weight is zero). This applies both to
655 MNC and MDS output files.
656 o pkg/seaice/seaice_growth.F:
657 - add 'a priori' cap of latent heat flux based on actual mass considerations
658 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
659 non-legacy seaice_solve4temp.
660 - add diagnostic of the residual sublimation freshwater flux (the freshwater
661 flux taken from the ocean if the total actual latent heat fluxes exceed
662 the maximum)
663 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
664 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
665 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
666 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
667 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
668 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
669 o verification 1D_ocean_ice_column:
670 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
671 update results
672 o pkg/diagnostics:
673 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
674 which are not filled-up but computed from other diags ; In this case, the mate
675 diag points to the primary (filled-up) diag to used for post processing.
676 - Update Velocity-potential computation using post-processed diag framework.
677 ==> Change the ordering of fields and time-periods in MDS output file
678 when using periodic averaging: now writes one time record with the full set
679 of fields for this time period, then the next time reccord (it used to be
680 one field with the full set of time records then the next field).
681 Note: this is now similar to NetCDF (MNC) output file. <==
682
683 checkpoint62z (2011/06/21)
684 o adjoint monitor:
685 - Add adjoint monitor output for packages exf, seaice
686 and update relevant testreport output
687 o pkg/seaice:
688 - re-order diags inits so that they appear in order in available_diagnostics.log
689 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
690 area/heff/hsnow preceeding thermodynamic growth/melt.
691 - modified diag: SIdA; output actual effect, as the description states.
692 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
693 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
694 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
695 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
696 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
697 - added diagnostics for seaice generic tracers (SItr*).
698 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
699 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
700 I. Fenty: 18-Jun-2011:
701 Minor changes to seaice package:
702 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
703 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
704 - Differentiated "regularization variables" from "floor variables"
705 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
706 * hiceMin became SEAICE_hice_reg (old hiceMin)
707 (with _reg meaning regularization variable)
708 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
709 so as to ensure energy conservation when going between phases
710 - A22 was not used anywhere
711 2) Changed regularization procedure for heffActual and hsnowActual to ensure
712 well-boundedness and smooth adjoint in seaice_growth.F
713 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
714 because the old regularization always set heffActual >= 0.05 cm
715 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
716 on AREA when HEFF > 0.
717 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
718 requiring that DISABLE_AREA_FLOOR *not* be defined
719 Affected verifications:
720 - 1D_ocean_ice_column (output.txt output_adm.txt)
721 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
722 o pkg/diagnostics:
723 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
724 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
725 (was _RL, now integer) with option = 0 to retrieve all levels.
726 - add pieces of code to compute velocity potential at each level (new diagnostics
727 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
728 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
729 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
730 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
731 and in diagnostics_fract_fill.F (do not need a valid pointer for the
732 diagnostics counter-mate); check that definition of counter-diagnostic
733 includes a valid counter-mate (in diagnostics_set_levels.F).
734 o model/src (rStar):
735 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
736 affect solution only if z* with full pressure in EOS;
737 update output of test-exp global_ocean.90x40x15.
738 o pkg/seaice:
739 - introduce siEps=1e-5 parameter
740 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
741 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
742 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
743 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
744 as well as ice cover age and ridging index (attached to AREA).
745 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
746 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
747 Up to SItrMaxNum=3 tracers can be used simultaneously.
748 o pkg/salt_plume:
749 -introduce SPsalFRAC run time parameter that sets the fraction of the
750 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
751 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
752 o model debug options:
753 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
754 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
755 - Refine debug-msg printing selection (3 new levels):
756 debugMode : controls printing of debug messages (sequence of S/R calls).
757 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
758 debLevZero = 0 ; /* level of disabled aux. msg printing */
759 debLevA = 1 ; /* level of minimum aux. msg printing */
760 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
761 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
762 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
763 debLevE = 5 ; /* level of extensive debug printing */
764 New debugLevel default: with default debugMode value (=F),
765 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
766 and if debugMode=T, default debugLevel = 4 (debLevD).
767 Relation with previous settings:
768 debLevB (=2) corresponds to former debLevA (=1)
769 debLevD (=4) corresponds to former debLevB (=2)
770 Note:
771 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
772 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
773 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
774 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
775 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
776 o pkg/obcs:
777 - change OBCSfixTopo default from True to False (should not change the results);
778 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
779 o pkg/thsice:
780 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
781 2nd layer seaice sublimation (unlikely to happen)
782 - use Interior mask for OBCS in thsice_advection.F (similar to what is
783 done in gad_advection & seaice_advection).
784 o adjoint:
785 bug fix spotted by Gael Forget:
786 seaice_advection and thsice_advection still had
787 legacy CPP options to avoid CS corner updates for adjoint
788 o pkg/seaice:
789 => Change some of the defaults (2011/05/29):
790 - change SEAICEuseFluxForm default (from False to True)
791 - change DIFF1 default (from 0.004 m/s to 0. m/s)
792 And print warnings if DIFF1 is not set in data.seaice and centered
793 avection scheme is used without any diffusion.
794 also:
795 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
796 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
797 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
798 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
799 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
800 update results of test exp.:
801 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
802 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
803 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
804 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
805 seaice_obcs: output (SEAICEuseFluxForm=T)
806 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
807 for standard fwd & AD lab_sea tests (to keep the same output).
808 o pkg/seaice/seaice_growth.F:
809 - use Ian Fenty's capping formulas for actual ice
810 thickness thoughout EVOLUTION branch.
811 - put treatment pathological case #2) in CPP brackets
812 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
813 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
814 o pkg/seaice:
815 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
816 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
817 also pass fac as a param, which can be 1. (to update the tendency
818 field) or the time step (to update the field itself).
819 - seaice_advdiff.F: for multidim, call seaice_diffusion with
820 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
821 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
822 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
823 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
824 o pkg/seaice:
825 diffusion with centered advection scheme (diffus.F & advect.F):
826 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
827 to just compute the laplacian of input-field.
828 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
829 - fix flux-form version in diffus.F to conserve tracer.
830 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
831 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
832
833 checkpoint62y (2011/05/26)
834 o pkg/seaice:
835 - seaice_growth.F : in EVOLUTION branch, always include
836 a_QSWbyATM_cover in qnet (as it should be).
837 - verification/global_ocean.cs32x15 : update results accordingly
838 (output.seaice.txt output_adm.seaice.txt).
839 o pkg/seaice + obcs:
840 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
841 equivalent of assuming no tracer gradient outside the OB region.
842 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
843 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
844 after changes above);
845 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
846 only at OB location (instead of over a band of OLx width).
847 o pkg/seaice:
848 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
849 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
850 o pkg/obcs:
851 - split header file "OBCS.h" into 4 separated files:
852 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
853 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
854 (contain no conditional statement which depends on OBCS options).
855 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
856 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
857 o ctrl, cost, grdchk & autodiff pkgs:
858 - make options file more standard (like other {PKG}_OPTIONS.h file but
859 with AD_CONFIG.h); clean-up some of the included header files.
860 o pkg/obcs:
861 - do not mask tracer when applying OB (tracer == 0 could generate problems)
862 - apply tracer OB values to tracer field only at OB location (instead of
863 over a band of OLx width)
864 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
865 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
866 obcs_apply_tloc.F & obcs_apply_sloc.F
867 o obcs in model/src:
868 - call OBCS_APPLY_W only if NonHydrostatic.
869 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
870 - reset dEtaHdt and wVel to zero outside OB interior region ;
871 - leave tracer unchanged outside OB interior region: This has no effect
872 on the solution but just to prevent unrealistic tracer value outside OB.
873 - zero out velocity outside OB interior region: This has no effect on
874 the solution but just to prevent unrealistic velocity outside OB.
875 o obcs and non-lin free-surf:
876 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
877 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
878 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
879 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
880 update results of test-exp. exp4(nlfs).
881 o exp4 (nlfs) test-exp:
882 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
883 with NonLin-FreeSurf); update output.nlfs.txt
884 o obcs and 2d/3d solver norm:
885 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
886 and outside OB interior region (will allow to place OB further inside the
887 domain). Depending on the domain, can affects cg2d-Norm (previous
888 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
889 and cg3d-Norm (previous Norm was computed before canceling OB terms),
890 e.g. in tutorial_plume_on_slope.
891 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
892 o pkg rbcs:
893 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
894 - add capability to apply relaxation to horizontal velocity uVel & vVel.
895 o pkg/grdchk: add gradient check for control variable xx_shifwflx
896 o pkg/shelfice/shelfice_init_fixed.F
897 fix CPP-flag combinations
898 o pkg/seaice: Merge iceage code of Pierre Rampal
899 * update/change/correct ice age calculations
900 * add age updates for pathological cases
901 Probably needs more testing...
902
903 checkpoint62x (2011/05/13)
904 o pkg/mom_vecinv:
905 high-order vorticity scheme: use interior masks (maskInW & S)
906 to zero-out (outside OB) gradient of vorticity.
907 o verification exp.:
908 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
909 hs94.128x64x5 and seaice_obcs ; update results.
910 o pkg/obcs:
911 fix bug in OBeta for YZ sections in obcs_exf_load.F
912 o pkg/ctrl, pkg/shelfice, and optim:
913 - add new control variable xx_shifwflx (fresh water flux underneath ice
914 shelves). This is almost as tedious as obcs-ctrl, because the
915 variables needs its own mask.
916 - add a cost function term that penalizes the deviation of xx_shifwflx
917 from the first guess (zero) in analogy to other control variables
918 o pkg/shelfice:
919 - start basic adjoint
920 o pkg/ctrl:
921 - remove extra 2D field "for good measure" when initializing in
922 ctrl_set_globfld_[xy/xz/yz].F
923 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
924 - improve error messages in ctrl_set_unpack_*
925 o OBC implementation in momentum:
926 use interior masks (maskInC,W & S) in momentum S/R:
927 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
928 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
929 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
930 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
931 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
932 (and also with Leith/Smagorinsky harmonic-viscosity).
933 Update output of experiment dome and exp4 (+nlfs).
934 o exp4 test-exp:
935 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
936 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
937 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
938 time-varying OB at Western-side for wVel (NonHyd); update output.
939 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
940 and biharmonic-viscosity ; also use prescribed time varying OB.
941 o pkg/obcs:
942 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
943 o model/src:
944 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
945 - initialise startTime & nIter0 with unlikely values: allows to set one
946 from the other without ambiguity.
947 o seaice_obcs test-exp.:
948 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
949 o pkg/obcs:
950 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
951 no longer needed with maskInC,W,S in pkg/generic_advdiff.
952 o pkg/seaice:
953 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
954 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
955 - fixed bug in the initialization of sea ice salinity variable HSALT
956 in seaice_init_varia.F (removed dependence on ICE2WATR)
957 o fizhi-cs test exp.:
958 switch reference output convention for these 2 non-standard test-exp,
959 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
960 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
961 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
962 o model/inc:
963 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
964 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
965 o pkg/seaice:
966 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
967 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
968 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
969 and initial HSALT
970
971 checkpoint62w (2011/04/26)
972 o pkg/mom_fluxform:
973 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
974 - use parameter "sideDragFactor" in no-slip BC side-drag part.
975 - update output of exp. global_ocean.90x40x15
976 o pkg/mom_vecinv:
977 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
978 o update seaice exp.:
979 use more consistent parameter values (remove "backward compatability only":
980 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
981 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
982 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
983 o update test-exp global_ocean.90x40x15:
984 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
985 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
986 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
987 o turn on zStar & viscA4 in standard set-up (dir input/)
988 and update output files: output.txt & output.dwnslp.txt
989 o new AD-test experiment: obcs_ctrl
990 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
991 o pkg/dic:
992 fix two bugs in handling water vapour pressure in carbonate chemistry
993 and air-sea fluxes. Found by Val Bennington and Galen McKinley
994 (add DIC Option = WATERVAP_BUG to recover old results)
995 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
996 o adding allowInteriorFreezing option to check for water below freezing point
997 at depth and bring the negative heat anomaly to the surface level
998 o pkgs _fields_load:
999 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1000 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1001 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1002 rbcs to get interpolation weights and time reccord number.
1003 - fix multi-threading in aim_fields_load.F
1004 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1005 o external_fields_load:
1006 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1007 interpolation weights) to use in a periodic time-series ; do not divide by
1008 time-step to convert to integer:
1009 - this fixes case where externForcingPeriod is not multiple of time-step
1010 (Thanks to Christopher L. Wolfe)
1011 - this fixes case where externForcingPeriod is an odd multiple of time-step
1012 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1013 store index of time-record which is currently loaded:
1014 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1015 - needed for the adjoint but not yet used because of extensive recomputations;
1016 (to be fixed soon)
1017
1018 checkpoint62v (2011/04/02)
1019 o verification/1D_ocean_ice_column added to test Ian Fenty's
1020 pkg/seaice_growth.F modifications for improving sea ice code differentiability
1021 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1022 (new velocity statistics after changing maskInW & maskInS definition)
1023 o pkg/generic_advdiff with OBCS:
1024 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1025 equivalent to assumption of no tracer gradient outside the OB region.
1026 This will affect the results if using obcs+biharmonic diffusion.
1027 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1028 o pkg/obcs:
1029 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1030 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1031 in Interior region. No impact on solution but affects Velocity monitor stats.
1032 o pkg/ptracers (adjoint)
1033 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1034 tape file for each tracer
1035 o model/inc/src and pkg/autodiff: add parameters that allow to turn
1036 of parts of the adjoint code at run time. For now, there are only
1037 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1038 parameters are set in data.pkg.
1039 This is the lazy coward's version of doing this, but still useful for
1040 debugging. In order to do it right, everything needs to be moved to
1041 pkg/autodiff.
1042 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1043 the end; this fixes the adjoint balancing code for open boundaries.
1044 o pkg/ctrl:
1045 - change behavior of xx_${varname}period to be analogous to exf-conventions:
1046 xx_${varname}period = 0., means time-independent control part
1047 xx_${varname}period = -12., means one-year-periodic monthly control part
1048 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1049 clean up ctrl_init a little, remove unused variables
1050 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1051 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1052
1053 checkpoint62u (2011/03/15)
1054 o model/src:
1055 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1056 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1057 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1058 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1059 o pkg/ctrl/obcs/ecco:
1060 - remove obsolete, unused, and partially broken code:
1061 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1062 ALLOW_CTRL_OBCS_BALANCE
1063 - put a stop statement into ecco/cost_obcsvol.F, but also add
1064 cost_obcsvol to ecco_ad_diff.list
1065 o pkg/ecco: fix counting cost function contributions for obcs (code
1066 by Matt M.) and diffkr for diagnostics
1067 o pkg/ecco, pkg/ctrl, pkg/grdchk:
1068 add cost penalty terms for initial uvel, vvel, eta controls
1069 and I/O for prior error files
1070 o pkg/mdsio:
1071 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1072 (new argument) to check for tiled file in mdsioLocalDir : this fix the
1073 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1074 o pkg/ctrl:
1075 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1076 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1077 unused and superfluous variables
1078 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1079 o pkg/ecco
1080 - enable adjoint of Stevens OB
1081 o pkg/ctrl/ecco/grdchk:
1082 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1083 Fortunately, we do not have any tests for the numerous cpp-flagged
1084 option of "obcs as control parameters" so we will never know
1085 if this is an improvement (but at least now things compile).
1086 - remove an obsolete initialization from ecco_cost_init_barfiles.F
1087 - fix some problems within never used ifdefs to make the code compile
1088 o pkg/obcs:
1089 - Refine Interior mask definition to work with more complex OB (e.g.
1090 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
1091 read in Interior mask from file. Check if Interior mask is consistent
1092 with OB list of indices.
1093 o pkg/seaice
1094 - beginning code for a seaice tracer package,
1095 but currently only used for seaice age: SEAICE_AGE
1096 SEAICE_num = 4
1097 iTracer = 1: area-weighted ice age
1098 = 2: volume-weighted ice age
1099 = 3, 4: template for one-year vs. multi-year ice
1100 data.seaice has new namelist SEAICE_PARM03 for arrays related to
1101 SEAICE_num
1102
1103 checkpoint62t (2011/03/05)
1104 o pkg/obcs:
1105 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
1106 then normal component. This ensures that the normal component is set
1107 correctly even when it conficts with tangential setting from an other OB.
1108 Affects results of test-experiment seaice_obcs: update the output.txt
1109 o pkg/obcs:
1110 - add code to monitor statistics of dynamical fields at OB.
1111 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
1112 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
1113 - change default: balance the Net inflow through all OB (instead of balancing
1114 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
1115 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
1116 to match Nortern OB inflow (OBCS_balanceFacN=0).
1117 o pkg/seaice:
1118 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
1119 o pkg/seaice (seaice_growth v 1.113):
1120 - reverting seaice_growth to v 1.111 in order to have code with exact bit
1121 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
1122 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
1123 runtime flag SEAICEareaFormula is kept but is inactive
1124 o model/src:
1125 - add new param to scale curvilinear grid distance and area when using
1126 a different sphere radius from the grid-files.
1127 - test/check multi-threads EXCH applied to local variable (cg2d_x)
1128 o adjoint:
1129 - enable adjoint of Stevens OB
1130 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
1131 (a bit delicate because of potentially modified adj. common block structure;
1132 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
1133
1134 checkpoint62s (2011/02/15)
1135 o pkg/seaice (seaice_growth v 1.112):
1136 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
1137 computing the ice cover tendency from effective thickness tendencies. Include
1138 Ian Fenty's formula.
1139 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
1140 SEAICEareaFormula.
1141 - simplify notations for the various d_HEFF/d_AREA terms.
1142 o pkg/gmredi:
1143 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
1144 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
1145 add a verification test-run (front_relax.bvp) to test GM_useBVP.
1146 o pkg/seaice (seaice_growth v 1.111):
1147 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
1148 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
1149 also melt ice.
1150 o pkg/seaice:
1151 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
1152 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
1153 o pkg/cheapaml:
1154 - from Nico Wienders: New version of this package.
1155 o pkg/flt:
1156 - add CPP options to prevent floats to re-enter the opposite side of
1157 a periodic domain (default: keep periodicity)
1158 o pkg/gmredi:
1159 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
1160 (needed for multi-dim advection).
1161 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
1162 o model/src:
1163 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
1164 o tutorial_tracer_adjsens
1165 - extend to NLFS and replace maskC by hFacC
1166 (change reference output accordingly)
1167
1168 checkpoint62r (2011/01/24)
1169 o testreport:
1170 - add option -deloutp (-do) to remove output file after successful run
1171 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
1172 extract exact list of procs from this file ; adjust COMMAND by
1173 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
1174 o pkg/ecco: replace old ineffective way of penalizing deviations from
1175 first guess (of obcs) with code by Matt Mazloff
1176 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
1177 exf/cal
1178 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
1179 and handle case of obcs?period == 0
1180 Not affected by these changes: There is still an inconsistency in
1181 the computation of start/endrec for the obcs variables for ALLOW_CAL
1182 defined (see comment by Menemenlis, 7-Mar-2003)
1183 - make S/R ctrl_get_gen_rec return something meaningful even if
1184 ALLOW_CAL is not defined
1185 - ctrl_getobcs?: simplify code so that it does not need to use
1186 S/R exf_swapfields
1187 o testreport:
1188 allow to test MPI with different number of processors for each experiment:
1189 create file "SIZE.h.mpi" in each build dir.
1190 Note: update of "-command" argument not yet implemented.
1191 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
1192 alleviate the need for additional 3D tapes when using
1193 the non-inear free surface in the adjoint. This is done
1194 by adding an 'update' of hfacc etc. to their current
1195 value at the beginning of forward_step.F.
1196 o pkg/seaice
1197 seaice_lsr: move stress-divergence computations out of outer pseudo-
1198 timestepping loop
1199 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
1200 up, so that the calls of the ctrl_* subroutines are really at the end
1201 of the routine.
1202 o pkg/gmredi:
1203 allow to specify a 2-D horizontal map and a 1-D vertical profil
1204 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
1205 o pkg/seaice:
1206 move lsr iterations from seaice_dynsolver to seaice_lsr.
1207 o pkg/seaice:
1208 reduce memory footprint of seaice mutldim advection tapes,
1209 by using a 2D tape independent of the generic_advdiff ones,
1210 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
1211
1212 checkpoint62q (2010/12/29)
1213 o model/src:
1214 - check horizontal grid-spacing for unset or zero/negative values.
1215 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
1216 o pkg/flt:
1217 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
1218 - precision of input and output files set according to readBinaryPrec
1219 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
1220 - initial float position from tiled file was not converted to index space
1221 (looks like a bug): fixed to make it similar to initial pos. global file.
1222 o global_ocean.cs32x15:
1223 change SIZE.h of AD set-up to get same tiling as with MPI.
1224 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
1225 o model/src:
1226 add flag to control printing of domain fields (bathymetry, hFac ...) in
1227 ini_mask_etc (call to plot_fieds_xy*).
1228 o pkg/thsice:
1229 if useEXF, some forcing fields are not valid in overlap: fixed by computing
1230 over the interior only + apply EXCH at the end (like with SEAICE advection).
1231 o pkg/mdsio:
1232 - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
1233 to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
1234 - change barrier call for safe multi-threads access to 3-D shared buffer.
1235 - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
1236 - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
1237 remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
1238 o pkg/flt:
1239 - add fourth-order Runge-Kutta integration
1240 - add basic exch2 support (only 1 facet supported so far!)
1241 o pkg/mdsio+rw:
1242 new S/R to read local (or tile independent) vector (read counterpart of
1243 mds_writevec_loc, and front-end write_glvec_rl/rs).
1244 o global_ocean.cs32x15: additional input_ad.seaice experiment
1245 that uses pkg/seaice rather than pkg/thsice.
1246 (using multidim advection for seaice)
1247 o towards more F95 syntax for array specification in namelist:
1248 - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
1249 of all verification experiments.
1250 e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
1251 was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
1252 - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
1253 o global_ocean.cs32x15: additional input.seaice experiment
1254 that uses pkg/seaice rather than pkg/thsice.
1255
1256 checkpoint62p (2010/12/17)
1257 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
1258 to THSICE_SIZE.h to avoid conflict with pkg/seaice.
1259 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
1260 allow for use of multim. advection in seaice adjoint.
1261 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
1262 - first attempt to close budgets by taking into account the freshwater
1263 flux implied by the sublimation of snow and ice. So far only the
1264 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
1265 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
1266 o eesupp/src:
1267 new S/R with new option (NML_EXTENDED_F77) to change array specification
1268 from F95 standard to commonly accepted extended F77 form.
1269 This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
1270 and to revert back to the original syntax (with -DNML_EXTENDED_F77)
1271 for less tolerant f77 compiler (e.g., pgf77, g77).
1272 o globalFiles:
1273 commented out in parameter file "data" since it's not safe with MPI
1274 (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
1275 in this case); no longer commented out in restart test (tst_2+2).
1276 o add adTapeDir to specify a special directory where adjoint tapes are
1277 written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
1278 and cannot be used together with mdsioLocalDir.
1279 o nesting pkgs:
1280 - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
1281 - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1282 - add parameter files + utils dir + output from short run on beagle.
1283 o pkg/seaice:
1284 fix seaice_growth.F store directives; update results of exp. lab_sea.ad
1285 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
1286 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
1287
1288 checkpoint62o (2010/11/25)
1289 o pkg/exf:
1290 - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
1291 o pkg/seaice:
1292 - seaice_ocean_stress: split a loop for better vectorization of the
1293 adjoint code
1294 - seaice_growth.F: fix bug in conservation of freshwater connected to
1295 capping of heff, put contribution into d_HEFFbyNEG
1296 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
1297 by something more sensible (parameters that are what their name implies)
1298 - change some defaults, so that by default exf-parameters are used for
1299 things like rhoAir, cpAir,latent/sensible heat parameters, in order
1300 to reproduce the old results, many data.seaice now contain funny values
1301 for cpAir and latent heat of sublimation
1302 o packages_readparms.F: move exf_readparms up in line so that
1303 exf-parameters are visible for other packages (e.g. seaice)
1304 o debugMode & debugLevel=2:
1305 - differentiate between debugMode & debugLevel=2:
1306 debugMode: controls printing of debug messages (sequence of S/R calls).
1307 debugLevel: controls printing of algorithm intermediate results and stats.
1308 - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
1309 => allows to print debug-stats without all sequence of call messages.
1310 - switch control of debug print from debugLevel to debugMode in many S/R.
1311 o pkg/obcs (obcs-sponge):
1312 fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
1313 call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
1314 o pkg/generic_advdiff:
1315 - record overlap minimum size for each advection scheme;
1316 - refine criteria on overlap minimum size;
1317 - check and stop (in gad_check) if overlap size is too small.
1318 o pkg/obcs:
1319 - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
1320 once, in ptracers_implicit.F)
1321 - with seaice: remove test on empty file name in obcs_apply_seaice (always
1322 apply OB values when tile has OB)
1323 o model/src, coriolis setting:
1324 - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
1325 useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
1326 files (selectCoriMap=3) with any grid.
1327 - add parameter "fPrime" for constant second Coriolis coeff (default=0).
1328 o pkg/seaice/seaice_growth.F:
1329 a few cosmetic changes that reduce the number of lines of code
1330 o pkg/obcs: add boundary conditions following Stevens (1990)
1331 - the code follows old MOM/NAOSIM code
1332 - so far it is only implemented for the eastern and western boundaries
1333 and NOT for pTracers
1334 o pkg/rbcs:
1335 - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
1336 beginning of the first rbcs forcing period.
1337 - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
1338 offline package, i.e., one file per time, labeled by iteration number;
1339 deltaTrbcs sets the timestep with which the data was generated;
1340 rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
1341 - rbcsForcingCycle=0 makes forcing non-cyclic.
1342 - make arithmetic safe for negative times and odd forcing periods.
1343
1344 checkpoint62n (2010/11/09)
1345 o pkg/seaice:
1346 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
1347 o pkg/obcs:
1348 New S/R to copy tracer value from the OB location to narrow band region
1349 (width = same as overlap) beyond the OB: preserve OB value (needed for
1350 high-order scheme) which were overwritten by EXCH call if in overlap
1351 region. Applied to theta, salt, ptracer and advected seaice variables.
1352 With seaice: use maskInC in similar way as in gad_advection.F,
1353 in seaice_advection.F and advect.F.
1354 Update output of experiment seaice_obcs and change exp4 to test OBCS with
1355 4th order Adv.Scheme. for pasive salt and ptracer.
1356 o tools/genmake2:
1357 - when looking for an optfile (not specified), only search for Fortran compiler
1358 (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
1359 - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
1360 (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
1361 - set default for CPP to "cpp -traditional -P" (was the case without specifying
1362 an optfile, but otherwise default was just "cpp".
1363 - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
1364 - when "CC" is not set in the optfile, look for possible C compiler
1365 (instead of just setting CC=cc)
1366 - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
1367 => add a ".F" to ".o" rule for source files with no "#include" (such as
1368 port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
1369 - move gfortran before g77 in list of possible Fortran compiler (consistent
1370 with reference compiler switch from g77 to gfortran)
1371 o pkg/seaice:
1372 o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
1373 seaice_check that stops the model, when the CPP flag is used.
1374 o seaice_growth.F: make capping of ice volume conserving by returning the
1375 capped ice as freshwater to EmPmR. This does not change the verification
1376 experiments but will change runs where the capping is acutally active
1377 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
1378 (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
1379 global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
1380 lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
1381 o tools/genmake2:
1382 - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
1383 - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
1384 - clean previous genmake log files before anything else.
1385 - change Makefile to remove testreport log files (*.tr_log) and genmake log
1386 files only with "CLEAN" target (instead of "Clean");
1387 o pkg/generic_advdiff:
1388 Change OBCS in multiDim advection (gad_advection.F):
1389 Use maskInC to prevent intermediate update of tracer-field in OB regions,
1390 thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
1391 which were applying future time-step OB values.
1392 This way, all explicit calculations use current-time-step OB values
1393 (simpler and more consistent).
1394 Affects results when set-up uses time-varying OBC and multi-dim advection;
1395 update output of experiment seaice_obcs.
1396 o pkg/seaice:
1397 move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
1398 this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
1399 SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
1400 Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
1401 but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
1402 unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
1403 o pkg aim (2010/10/26):
1404 - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
1405 formulation with obliquity, eccentricity, ... as run-time parameters,
1406 - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
1407 upward shortwave radition at the surface (all-sky and clear-sky).
1408 o pkg/obcs:
1409 - writing sections with globalFiles=T does not work: switch to tiled-files
1410 when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
1411 - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
1412 - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
1413
1414 checkpoint62m (2010/10/21)
1415 o pkg/seaice: vectorize seaice_solve4temp.F
1416 - move iterations loops outside of i/j-loops
1417 - requires 2D arrays for TB and effConduct
1418 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
1419 modified in this routine
1420 - a little bit of clean up, adjusting indentation, etc.
1421 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
1422 performance and '**TWO' by '**2' (because TWO is a float),
1423 replaced ONE, ZERO
1424 o eesupp/src:
1425 fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
1426 o pkg/seaice/seaice_growth.F
1427 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
1428 merging process. The merged routine has two branches, and one activates the 'evolution'
1429 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
1430 In summary, here is what the '10/10 revision' did consist of
1431 part 1: seaice_growth.F revisions 1.71 to 1.75
1432 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
1433 The emphasis here was on improving readability (e.g. by trying to use meaningful
1434 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
1435 part 1.5:
1436 - revising the lab_sea experiment to make it a more useful (i.e. stable
1437 and representative of an actual model run). This was done by generating a
1438 (winter) pickup to start from, switching back the main experiment dynamic
1439 solver from evp to lsr, having one of the experiments use the free drift solution.
1440 part 2: seaice_growth.F revisions 1.76 to 1.85
1441 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
1442 - Sorting out the various fields units and sign (set early on and reset at the end)
1443 to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
1444 fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
1445 - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
1446 and simplifying logical expressions to further improve readibility.
1447 part 3: seaice_growth.F revisions 1.86 to 1.89
1448 - Re-organize the blocks of code more logically.
1449 - Merging the '_if.F' pieces that add something new.
1450 o pkg/thsice:
1451 - vectorize thsice_solve4temp and thsice_get_exf.
1452 Problem: thsice_solve4temp has an unvectorizable statement that
1453 might also be problematic for TAF
1454 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
1455 does not change the verifcation experiment, but will change all
1456 experiments that have this flag undefined (not tested in verification);
1457 a little reorganization to save a few 2D fields and recomputations
1458 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
1459 - 2nd step: fix some store dirs
1460 o seems to work somewhat, i.e. using ifort but not g77
1461 o likely cause are incomplete init. or recomputation
1462 o start verification/global_ocean.cs32x15/input_ad.thsice
1463 o pkg/obcs: add support for exch2
1464 - the position of the boundary and prescribed values are specified using
1465 a global domain with exch2 facets stacked
1466 - in x for N,S boundaries (like W2_mapIO=-1)
1467 - in y for E,W boundaries (so E,W boundaries do not overlap)
1468 o pkg/mdsio: add support for writing global sections with exch2
1469 file layout is as for obcs described above:
1470 - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
1471 - for y-z sections, facets are stacked in y
1472 o pkg/thsice:
1473 - change a few routines for better vectorization: thsice_albedo.F,
1474 thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
1475 not affected, but in particular the latter routine has changed
1476 dramatically (not necessarily easier to read now).
1477 - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
1478 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
1479 o verification/lab_sea:
1480 - overhaul of the forward model experiments. The main motivation
1481 for this revision is that lab_sea has proven quite fragile (when
1482 changing the sea-ice code, and switching platforms) to a point
1483 when failures were very hard to attribute to specific code problems.
1484 - the suspected reason for this fragility is noise amplification by evp so,
1485 to start with, we decided to replace evp with lsr in the main experiment.
1486 - the input.lsr experiment thus became obsolete and was removed.
1487 - it was replaced with the input.fd experiment that uses an
1488 analytical "free drift" solution as the ice velocity field.
1489 - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
1490 will hopefully allow us to discriminate problems due to dynamic solvers
1491 from problems due to the thermodynamic code. input.salt_plume (lsr) allows
1492 us to test additional options, along with the salt plume package.
1493 - Finally a pickup was generated (at the end of a one year run) to
1494 make the tests more representative of an actual model run. Previously
1495 the tests starting point was a 1m thickness of ice everywhere.
1496 o pkg/seaice:
1497 - introducing S\R seaice_freedrift.F that compute the
1498 analytical solution to an approximate ice momentum
1499 equation (i.e. the simple stress/coriolis balance).
1500 - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
1501 of the free drift velocity field, and enable its use.
1502 To actually use the free drift solution as the model ice
1503 velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
1504 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
1505
1506 checkpoint62l (2010/10/04)
1507 o pkg/seaice:
1508 -fix the USE_ORIGINAL_SBI version (for variable freezing point);
1509 -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
1510 version (with USE_ORIGINAL_SBI undef);
1511 o add hooks for new packages OASIS, the package will follow
1512 (hooks exclude the seaice pkg for now)
1513 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
1514 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
1515 rather than mdsio_readvector.F/mdsio_writevector.F, within
1516 adread_adwrite.F to read/write adjoint-related tapes to disk.
1517 o eesupp and pkg/mdsio: ALLOW_WHIO
1518 Option to write/read 2D fields to files including tiles halos.
1519 The main purpose is for adjoint related "tape I/O".
1520 The secondary purpose is for debugging phases.
1521 A word on those rather specifically intended purposes.
1522 The code was meant to be stripped down to the bare minimum.
1523 Typically, there is a unique and basic mapping to the global
1524 buffer (tile by tile, then proc by proc, then level by level), and
1525 byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
1526 meant to generate user friendly outputs of various shapes and forms.
1527 Rather it is intended, for the knowledgeabale developers,
1528 to be largely independent of the many mdsio options, to allow
1529 outputs of tiles+halos in debugging phases and in adjoint runs,
1530 and to allow some flexibility in tuning (adoint) I/O depending on each
1531 file system behavior. With regard to tuning, most of the potential knobs
1532 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
1533 to specify directories, to specify the typical size of I/O calls, etc.)
1534 are not yet included, and will be added if they prove useful.
1535 o pkg/seaice:
1536 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
1537 o pkg/seaice:
1538 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
1539 code (seaice_budget_ice_if.F) which enable to recover old standard
1540 code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
1541 temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
1542 o model/src (rStar):
1543 use simple average (not area weighted) of rStarFac at U,V point when using
1544 vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
1545 update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
1546
1547 checkpoint62k (2010/09/17)
1548 o adjoint
1549 * changed verification/global_ocean.cs32x15 ; adjoint now tests
1550 Adams-Bashforth 3 + NLFS + RSTAR
1551 * some more modifs required for ECCO-GODAE v4
1552 o pkg/seaice
1553 add SEAICE_AGE_VOL option to use volume instead of area for
1554 integrating SEAICE_AGE
1555 o model/src:
1556 first check-in of sigma & hybrid-sigma coordinate code ; also includes
1557 non-linear free-surface parts ; but pressure-gradient not yet coded.
1558 o pkg/ptracers:
1559 option for ptracer to convert Salt Relax into additional EmP.
1560 tested in exp. global_ocean.90x40x15.dwnslp (update output)
1561
1562 checkpoint62j (2010/08/25)
1563 o pkg/ggl90:
1564 other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
1565 o pkg/dic: car_flux.F, phos_flux.F
1566 - reduce number of exp-calls in order to improve performance
1567 - clean up a little (replace fields by their macros, etc., fix
1568 typo in CPP-flag)
1569 o pkg/ggl90: minor changes
1570 - GGL90diffKrS was removed --> always use GGL90diffKr
1571 - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
1572 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
1573 (commented out for now)
1574 - change in max/min operations to ensure that smoothing is ok
1575 - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
1576 - always use diffKrNrT as background profile (i.e. never use diffKr field)
1577 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
1578 o pkg/dic:
1579 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
1580 vectorization
1581 - small bug fix in insol for the unlikely case of a cartesian grid
1582 - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
1583 + now vectorize, which also removes adjoint recomputations;
1584 + replace integer maksp1 by _RL maskp1
1585 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
1586
1587 checkpoint62i (2010/07/21)
1588 o pkg/flt:
1589 - with OBCS: stop floats which enter the OB region
1590 o model/src:
1591 - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
1592 for implicit vertical advection.
1593 o pkg/seaice:
1594 - account for melting in seaice age evolution.
1595 - remove double counting of seaice ridging effect on seaice age.
1596
1597 checkpoint62h (2010/06/18)
1598 o pkg/exch2:
1599 - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
1600 o tools/genmake2
1601 - remove "-pdefault" option: redundant with the use of "packages.conf";
1602 - remove file pkg/pkg_default : set the default as a pkg group
1603 ("default_pkg_list") defined in pkg/pkg_groups;
1604 - fix for case pkg/pkg_depend is missing (was hanging before);
1605 - add option "-pgroups" to specify a different pkg_groups than the default.
1606 o verification/adjustment.cs-32x32x1:
1607 add a "minimal" set-up test (code_min & input_min) which only compiles
1608 eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
1609 o tools/genmake2
1610 - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
1611 - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
1612 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
1613 files are nearly the same anyway.
1614 Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
1615 - redefinition of tau(i,i) (by a factor of ustar)
1616 - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
1617 - replace rhonil by rhoConstFresh in computation of evap (bug fix)
1618 - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
1619 - replace
1620 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
1621 shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
1622 by
1623 shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
1624 (changes results)
1625 -> exf_bulkformulae v1.22,
1626 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
1627 (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
1628 output.txt 1.63
1629 offline_exf_seaice: output.seaicetd.txt 1.7
1630 seaice_obcs: output.txt 1.10)
1631 Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
1632 -> exf_bulkformulae v1.23,
1633 unfortunately requires updating lab_sea.salt_plume (6 matching digits),
1634 and global_ocean.cs32x15.icedyn (only 11 matching digits)
1635 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
1636 o adjoint of exch-1:
1637 - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
1638 (note: was already like this when using EXCH-2) and remove flow dir
1639 and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
1640 - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
1641 - update pkg/exch2 diff list.
1642
1643 checkpoint62g (2010/05/19)
1644 o eesupp/src (exch-1):
1645 - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
1646 and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
1647 (renamed to exch1_*rx_cube.F).
1648 - change accordingly exch_*_rx.template and AD version in pkg/autodiff
1649 to call new exch1 S/R ; update Makefile and .cvsignore.
1650 - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
1651 exch2_xy_rx later)
1652 Note: after updating your code, need to run "make clean" in eesupp/src
1653 o test experiment bottom_ctrl_5x5:
1654 new output_adm.txt with fewer grdchk & less monitor output.
1655 o model/src:
1656 remove the call to ini_cori in initialise_varia.F (just keep the usual one
1657 in initialise_fixed.F). More consistent with coriolis & horizontal grid
1658 beeing treated in the same way (ini_grid is not called a 2nd time).
1659 o pkg/exf:
1660 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
1661 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
1662 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
1663 - cosmetic changes to exf_bulkformulae.F to make it look more like
1664 exf_bulk_largeyeager04.F
1665 o eesupp/src (exch-1):
1666 - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
1667 - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
1668 array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
1669 (even without using MPI).
1670 - Message mode: move RecvAck setting (indicator of buffer being ready)
1671 from send_put to recv_get S/R (was useless before, but not sure if
1672 it's much more useful now);
1673 - Switch the order of sync: MPI-proc 1rst and then threads;
1674 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
1675 - fix AD code for communication mode ='get' (but not used).
1676 o model/src:
1677 initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
1678 not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
1679 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
1680 o pkg/ctrl: require a specific set of control variables and exf-flags for
1681 adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
1682 o model/src:
1683 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
1684 1rst forward sweep, to avoid over-writing output files during recomputations
1685 recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
1686 b) 2nd version:
1687 - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
1688 - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
1689 writePickupAtEnd) + seaice & ptracers output;
1690 - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
1691 o model/src:
1692 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
1693 o pkg/exch2:
1694 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
1695 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
1696 o pkg/autodiff & exch2:
1697 process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
1698 (for now, only if ALLOW_EXCH2 is defined).
1699 o pkg/autodiff:
1700 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
1701 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
1702 + clean-up comments (_RS is not always real*4)
1703 - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
1704 - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
1705 was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
1706 o testreport (AD-tests):
1707 no longer link files from dir "../input" (1rst link files from
1708 "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
1709
1710 checkpoint62f (2010/04/29)
1711 o model/src/the_main_loop.F:
1712 adjust store directives for seaice evp and multicategory according to
1713 pkg/ecco/the_main_loop.F
1714 o adjoint:
1715 global_sum_ad was incomplete (noted many times by many people ;)
1716 nice description by Jean U. as follows:
1717 * allreduce(var) in global_sum.F can be interpreted as
1718 reduce(sum) followed by broadcast of sum.
1719 * The adjoint of that is
1720 sum(adjoint) followed by broadcast(summed adjoint value)
1721 or in other words, allreduce(sum, adjoint vars)
1722 We were missing the sum(adjoint)!
1723 Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
1724 (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
1725 The fix should produce 16-digit accuracy between
1726 single-CPU multi-tile (e.g. nSx=2, nPx=1) and
1727 multi-CPU single-tile (e.g. nSx=1, nPx-2)
1728 We'll probably change this yet again shortly
1729 o eesupp/src:
1730 - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
1731 o pkg/icefront
1732 - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
1733 specification of addmass array based on a 2D field, which is added
1734 at bottommost wet level at each horizontal location.
1735 o model/src:
1736 horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
1737 layout; (not always compatible with delX,delY setting; commented out for now).
1738 o pkg/exch2:
1739 change tile to processor setting (case nSy*nPy > 1): allows default model mapping
1740 (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
1741
1742 checkpoint62e (2010/04/15)
1743 o pkg/obcs:
1744 - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
1745 o pkg/dic:
1746 -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
1747 (note: not presently tested in any forward verification exp.)
1748 update tutorial_global_oce_biogeo AD output file.
1749 o pkg/exf:
1750 - account for the variation of albedo as a function of zenith angle
1751 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
1752 o build_options:
1753 - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
1754 o pkg/dic:
1755 change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
1756 - use binary pickup file for restart;
1757 - initialise atmos-CO2 box from dic_pCO2 parameter;
1758 - fix multi-threaded.
1759 o pkg/rbcs:
1760 - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
1761 change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
1762 - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
1763 and update output.txt
1764 o pkg/kpp:
1765 - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
1766 - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
1767 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
1768 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
1769 - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
1770 KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
1771 o pkg/offline:
1772 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
1773 (bug was added in version 1.10 on 2007-08-23).
1774 o pkg/offline:
1775 - no need to specify periodicExternalForcing, etc ... to use offline pack
1776 - offline input files no longer just single prec --> parameter offlineLoadPrec
1777 o verification/lab_sea:
1778 change AD test to multi-tile setup and update all 4 AD output.
1779 NOTE: while cost function values remain very similar,
1780 gradients are very different, although gradient checks are self-consistent
1781 Should try to get to the bottom of this (cost function summation order?)
1782 o pkg/dic:
1783 in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
1784 a weakness of TAF that drops part of double precision in log10 derivative.
1785 <= changes removed since problem has been fixed in current TAF version 1.9.71
1786 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
1787 o pkg/ecco:
1788 add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
1789 update all 4 lab_sea AD output.
1790
1791 checkpoint62d (2010/03/22)
1792 o build_options:
1793 remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
1794 o remove unbalanced quote (single or double) in commented line of source code
1795 (may cause some warning with some preprocessor/makedepend versions).
1796 o pkg/seaice:
1797 fix seaice_model.F for adjoint (gael) and update AD results of experiments
1798 lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
1799 o testreport:
1800 add option '-runonly' (short: '-ro') to just do the run part (without make).
1801 o eesupp: remove JAM communication code (obsolete).
1802 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
1803 (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
1804 to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
1805 (update also the output).
1806
1807 checkpoint62c (2010/03/02)
1808 o tools/build_options :
1809 move (some) old optfiles from build_options/ to build_options/unsupported/
1810 o model/src and pkg/exf
1811 surface relaxation -- separating data and data.exf options
1812 The point is to ensure that we specify the surface relaxation
1813 either in data or in data.exf (but not half and half) and to
1814 avoid an accidental relaxation to 0 (which happened if a time
1815 scale was specified but the file name was left empty)
1816 o model/src model/inc and pkg/mom_common
1817 ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
1818 => addition to the viscosity field as computed by others schemes
1819 o tools/build_options:
1820 - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
1821 but keep the former optfile for few weeks for smooth transition
1822 o pkg/ecco
1823 - allow user defined cost function contributions
1824 CPP: ALLOW_USERCOST_CONTRIBUTION
1825 USAGE: compute contributions in cost_usercost_all.F
1826 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
1827 the two options are complementary.
1828 o pkg/smooth
1829 - migration from contrib to the main repository
1830
1831 checkpoint62b (2010/01/26)
1832 o pkg/monitor:
1833 - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
1834 (in case someone forgot to update customized pieces of code)
1835 o nonHydrostatic:
1836 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
1837 - add a simple 2-D experiment (short_surf_wave) to test it.
1838 o pkg/icefront:
1839 adding the shell of, and the hooks to, a new package that
1840 will model melting and freezing of vertical glacier ice fronts
1841 o momentum:
1842 add diagnostics of momentum tendency from Hydrostatic pressure gradient
1843 (without surf.pressure term: would need a 2nd filling since implicit term).
1844 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
1845 two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
1846 cannot deal with the former
1847 o cleaning:
1848 - remove all (except OpenAD) old TLM output from results_ad dirs.
1849 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
1850 - comment out maskH definition (replaced by maskInC)
1851 o pkg/monitor:
1852 - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
1853 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
1854
1855 checkpoint62a (2010/01/15)
1856 o model/src:
1857 - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
1858 o pkg/diagnostics:
1859 - add optional level number diagnostics (i.e., level number to be define
1860 explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
1861 - strictly check for valid parser-code(10) ;
1862 - check if adding diag to the list from the right place.
1863 o pkg/longstep:
1864 - change parameters and fix tracer conservation with rstar/nonlinear free surface
1865 o diagnostics:
1866 - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
1867 S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
1868 o pkg/diagnostics:
1869 - Add option for writing vertical integral (sum of selected levels) of an output
1870 field instead of writing output field levels. Activate this option on a per
1871 output-file basis, by setting the 2nd character of fileflag to 'I'.
1872 - Add field-specific information relative to level integral in 3rd postion
1873 of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
1874 vertically (x level-thickness x hFac), "r"=same but without hFac.
1875 o do_the_model_io:
1876 - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
1877 in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
1878 writing pickups and stopping.
1879 o pkg/diagnostics (for now, only with mdsio):
1880 - write time information to meta file (and modify accordingly rdmds.m) :
1881 time-averaged diagnostics output: write starting and ending time of the
1882 time-averaging interval ; snap-shot diagnostics output remains unchanged;
1883 o pkg/timeave:
1884 - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
1885 always Nr), now assumed to be equal to number of levels of averaged field;
1886 only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
1887 o pkg/sbo:
1888 - fix ocean bottom pressure global-average & 2-D time-ave output (was
1889 neither initialised nor filled).
1890 - add starting iteration in suffix of global-average output file
1891 (to avoid over-writing the file after a restart)
1892 - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
1893 o time-average:
1894 - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
1895 (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
1896 ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
1897 this fix DIC_COST cumulative-time array (previously: bi,bj,k)
1898 - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
1899 - fix missing accumulation for pkg/opps.
1900 - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
1901 (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
1902 - fix initialisation of time-ave vars and do only full time-step increment
1903 (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
1904 o pkg/layers:
1905 - use standard RW pkg S/R to write the output
1906 and remove local write_fld version (which had a problem).
1907 - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
1908 - fix LAYERS_CALC argument list.
1909 o pkg/timeave:
1910 - store cumulative-time in a simple tiled array (drop the level index)
1911 - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
1912 o pkg/ocn,aim_compon_interf
1913 - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
1914
1915 checkpoint62 (2009/12/23)
1916 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
1917 (was not previously tested in any other exp.)
1918 o pkg/monitor:
1919 - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
1920 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
1921 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
1922 - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
1923 - change del2 calculation.
1924 - use interior masks (instead of maskH, <- to be remove).
1925 - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
1926 o mask & obcs:
1927 - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
1928 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
1929 (called after packages_init_fixed)
1930 o pkg/obcs:
1931 - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
1932 Fixes bug in obcs+exf with nSx*nSy.GT.1
1933 - fix multi-tile handling in obcs balance code
1934 o nonHydrostatic:
1935 - Implement AB-3 for non-hydrostatic vertical momentum ;
1936 (change ordering of var. stored in pickup file when using NH)
1937 - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
1938 - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
1939 (in prep. for new NH free surface form).
1940 o pkg/obcs:
1941 add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
1942 o model/src:
1943 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
1944
1945 checkpoint61z (2009/12/01)
1946 o nonHydrostatic:
1947 Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
1948 a spurious source of energy in simple baroclinic adjusment test case.
1949 Update all non-hydrostatic exp output.
1950 o model/src (3-d solver):
1951 Change again 3-D solver free-surface RHS term when exactConserv=T:
1952 simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
1953 (which was not the case with previous formulation).
1954 To recover previous version, just reset "oldFreeSurfTerm" to previous value.
1955 Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
1956 o nonHydrostatic:
1957 - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
1958 for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
1959 - change 3-D solver to work with r* (for now, only with linear free-surf.)
1960 - add few debug diagnostics (cg3d_x, residual)
1961 o model/src:
1962 fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
1963 update output of exp. global_ocean.cs32x15.viscA4
1964 o update output of exp. global_ocean.cs32x15.icedyn after removing
1965 #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
1966 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
1967 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
1968 for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
1969 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
1970 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
1971 runtime flag useSRCGSolver. Modify verification experiment global_with_exf
1972 to test this code
1973 o pkg/cd_code:
1974 Change defaut D-grid time-stepping to get the same for D-grid momentum as for
1975 C-grid momentum. D-grid velocity used to be stepped forward in time with
1976 Adams-Bashforth only on surface pressure term. Tests show that using AB on
1977 D-grid coriolis term improves stability (as expected from CD-scheme paper).
1978 To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
1979 Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
1980 lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
1981 tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
1982 Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
1983 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
1984 o pkg/obcs:
1985 - fix bug in initialisation (broken since Oct 1rst modification)
1986 for useOBCSprescribe without useEXF.
1987
1988 checkpoint61y (2009/11/15)
1989 o pkg/seaice
1990 - change (once again) the discretization for the evp solver: rather than
1991 squaring the averages of strain rates, average the squares to give
1992 a better approximation to VP behavior (in simple test); this breaks
1993 verification experiments that use EVP (lab_sea and lab_sea.hb87)
1994 --> update outputs
1995 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
1996 to improve vectorization of adjoint code on TARGET_NEC_SX
1997 o verification/vermix:
1998 - change vermix to a more "classical" 1d column with high vertical
1999 resolution, seasonal heat flux forcing and constant wind forcing
2000 --> update outputs
2001 o pkg/seaice
2002 - fix diagnostics of principal stress components for EVP
2003 - add optional diagnostics of non-linear convergence for LSOR solver
2004 - make maximum zeta a runtime parameter
2005 o model/src (3-d solver):
2006 Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
2007 which consisted in removing the Surf. Non-Hydrostatic pressure from the
2008 whole column and adding it to Eta (inspired from Casualli, 1999):
2009 Only affects 3-D solver initial guess and only if using ExactConserv,
2010 but tests did show a degradation of solver convergence. For this reason,
2011 decide to disable this piece of code.
2012 to recover previous version, just set zeroPsNH = exactConserv (line 78).
2013 Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
2014 o pkg/ggl90:
2015 - fix previous modif (unfortunatly has not been documented here).
2016 o pkg/seaice/autodiff:
2017 - add CPP flag to include clipping of zeta in EVP code;
2018 although clipping of zeta is not necessary for EVP and not recommended
2019 it was done by default, now clipping is disabled by default
2020 - modify computation and store zetaC/Z in seaice_evp for TAF
2021 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
2022 - change seaice_calc_viscosities/strainrates for better
2023 vectorization after AD by TAF
2024 - rearrange common blocks in SEAICE.h once again for easier dumps of
2025 adjoint output, adjust adcommon.h and g_common.h
2026 - change flux form of default advection scheme for better vectorization
2027 of adjoint code
2028 - modify lab_sea/input.lsr to test the flux form of default advection
2029 scheme
2030 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
2031 transition in checkpoint61r)
2032
2033 checkpoint61x (2009/10/19)
2034 o adjoint: adding two new verification experiments
2035 * tutorial_global_biogeo: an online dic sensitivity experiment
2036 (work with G. Forget)
2037 * tutorial_dic_adjoffline: an offline dic sensitivity experiment
2038 (an update of the Dutkiewicz et al., 2006 paper)
2039 Both use the same CO2FLUX cost function, but different controls
2040 Gradient checks look good, but some recomp. could still be traightened out
2041 Should add xx_dic control variable to test at some point
2042 o model/src:
2043 add run-time parameters to check and/or mask initial Temp & Salt
2044 o pkg/ptracers:
2045 apply zonal filter (if used) to all passive tracers
2046
2047 checkpoint61w (2009/10/12)
2048 o adjoint:
2049 * update and finish work on adjoint of dic package (G. Forget)
2050 * start adjoint of offline package
2051 * bug fix for cube-sphere TLM code (active_file_g.F)
2052 o tutorial_global_oce_optim:
2053 now tested with 4 tiles (change data.grdchk and update output_adm.txt)
2054 and add SIZE.h_mpi for MPI testing
2055 o pkg autodiff
2056 - fix bug in autodiff_restore
2057 - make genmake2 remove comments and empty lines from ad_input_code.f in
2058 order to reduce file size (new script file remove_comments_sed)
2059 o allows to specify vertical profile of vertical viscosity (viscArNr)
2060 o pkg autodiff
2061 autodiff_ini_model_io: comment out writing of grid information to netcdf
2062 files, because at this time the grid fields are a bunch of zeros
2063 (this is analogous to ini_mnc_vars.F)
2064 o pkg seaice/autodiff:
2065 left-over from removing the 3-time-level fields:
2066 - small rearrangement of common blocks (SEAICE.h)
2067 - fix field declaration in order to get meaningful output in
2068 adseaice.*.nc (adcommon.h)
2069 o pkg obcs:
2070 - go through NH code only if nonHydrostatic=T
2071 - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
2072 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
2073 => Update output of experiment seaice_obcs
2074 - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
2075 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
2076 - fix restart for useOBCSprescribe + useEXF
2077 o pkg ctrl
2078 - make obcs as control parameter work also with useSingleCPUio
2079 - replace a few sny and snx by Ny and Nx to be consistent with
2080 ctrl_set_globfld_x/yz.F
2081 o pkg seaice
2082 - re-introduce global field frWtrAtm for the case of
2083 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
2084 - catch the case of an empty filename in seaice_cost_init_fixed.F
2085 o pkg ecco:
2086 - small bug fixes in the_main_loop
2087 . fix order of monitor arguments
2088 . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
2089 . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
2090 that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
2091 - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
2092 imbalance diagnostics for wmean_h/sflux = 0
2093 - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
2094 - catch the case of empty filenames in ecco_cost_init_fixed.F
2095 and ecco_readparms.F
2096 - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
2097 to make this statement meaningfull in ecco_cost_weights.F
2098 o pkg zonal_filt:
2099 - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
2100 - when using rStar, filter uVel*hFacW instead of uVel
2101 (tested without topography: fix a Pb of growing instability with NLFS)
2102 o pkg/aim/thsice:
2103 -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
2104 (works as SST restoring)
2105 o pkg/thsice:
2106 -add specific parameter for salt restoring in slab mixed-layer
2107 (by default equal to the temperature restoring)
2108
2109 checkpoint61v (2009/09/21)
2110 o pkg/kpp:
2111 -add double diffusive contributions as a hack, turned off by default
2112 for now, and the code can be excluded with a CPP-flag
2113 EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
2114 -add a verification experiments to "vermix" to test this code
2115 o pkg/mom_common:
2116 Move computation of length scales to mom_init_fixed.F (avoid recomputation
2117 at each time-steps*levels).
2118 o pkg/layers:
2119 Created a new package for computing volume fluxes in temperature or
2120 [not yet implemented] density layers, e.g. for calculating residual
2121 overturning circulations.
2122 o pkg/diagnostics:
2123 implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
2124 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
2125 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
2126 To avoid mixing type (RS/RL) of input/output array argument,
2127 replace single mixed-type array with a pair from each type (RS/RL).
2128 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
2129 is now implemented for all pkgs (previously only done for the main pickup)
2130
2131 checkpoint61u (2009/08/25)
2132 o pkg/obcs:
2133 - change OB?eta from _RS to _RL and put them into a separate commen block
2134 - add code to read OB?eta from a file via obcs_prescribe_read: the code
2135 compiles and does not destroy any other experiments, the data is read
2136 properly, but the code is not tested in actual applications
2137 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
2138 create a meaningful unit attribute for the time coordinate variable
2139 o pkg/ebm: add plenty of missing "_d 0" ;
2140 update results of experiment global_ocean_ebm (fwd + adjoint tests)
2141 Notes: several pieces of code only works for (very) specific set up
2142 (domain size, lat range, etc ...); should be documented & stop if one
2143 of those assumptions is not meet.
2144 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
2145 update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
2146 and offline_exf_seaice (seaicetd + adjoint).
2147 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
2148 update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
2149 seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
2150 o few changes to pass when compiling with strick checking of arguments
2151 across S/R (allow to find few bugs in S/R calls).
2152 o pkg/seaice:
2153 - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
2154 2d-fields, for slightly better performance
2155
2156 checkpoint61t (2009/07/22)
2157 o pkg/seaice:
2158 - remove unused variables in seaice_evp
2159 - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
2160 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
2161 named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
2162 each processor opens a different file (a fix from Matt).
2163 o cg2d:
2164 use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
2165 this reduces number of EXCH calls by 2 when using exch2.
2166 For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
2167 directives and missing simple EXCH (exch_s3d_rx) adjoint code.
2168 o pkg/thsice:
2169 add code for Near Infra-Red albedo (from Jeff)
2170 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
2171 o ini_model_io:
2172 move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
2173 MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
2174 to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
2175
2176 checkpoint61s (2009/06/30)
2177 o pkg/exch2 (exch2_rxN_cube*):
2178 remove last BARRIER (no need to synchronise after getting data from shared
2179 buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
2180 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
2181 and generate new output (for the 2 tests) using default rotationPeriod.
2182 o pkg/exch2:
2183 - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
2184 (was already the case with AUTODIFF_EXCH2 defined)
2185 - add bj in exch2 arrays and S/R.
2186 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
2187 MLAdjust to exch2 (identical results except with MPI -> truncation diff);
2188 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
2189 - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
2190 GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
2191 - verification experiment natl_box.longstep
2192 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
2193 allow different versions of ifort (8 or 9) and different versions
2194 of mpi (mpich or mpich2) to be used with the same optfile.
2195 requires to load a netcdf module and set MPI_INC_DIR (see comments inside
2196 optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
2197 o pkg/seaice:
2198 fix previous modif (3-level field removed) for old-pickup reading
2199
2200 checkpoint61r (2009/06/25)
2201 o pkg/seaice:
2202 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
2203 1. introduce fields for time step (N-1)
2204 2. do not use levels 2 and 3 anymore (but keep them)
2205 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
2206 includes changes to pkg/thsice/thsice_get_velocity.F,
2207 model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
2208 pkg/obcs/obcs_apply_uvice.F.
2209 - completely remove code for leap-frog time stepping for second order
2210 advection
2211 - adjusted adjoint accordingly;
2212 gradient checks have improved by an order of magnitude!
2213
2214 checkpoint61q (2009/06/22)
2215 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
2216 - the boundary conditions along open boundaries are unclear, because the
2217 associated masks are set to zero and are thus treated as closed when
2218 applying the slip-boundary conditions.
2219 - move initialisation of grid variables from seaice_init_varia to _fixed
2220 o adding doc/diags_changes.txt
2221 o model/src:
2222 do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
2223 to avoid "_diags" naming if no relation to pkg/diagnostics.
2224 ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
2225 file and only call PLOT_FIELD_XYZ if debugMode=T.
2226 remove few PLOT_FIELD_XY calls outside initialisation.
2227 remove few unnecessary BARRIER.
2228 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
2229 of salt_plume package in Southern Ocean
2230 o pkg/thsice:
2231 - fix hOceMxL in overlap (needed for sea-ice advection);
2232 update output of experiment global_ocean.cs32x15.icedyn.
2233 o pkg/seaice:
2234 - make the (placeholder-)tracer IceAge a little more meaningful
2235 by avoiding ridging of age due to convergent ice flow
2236 - add diagnostics for surface temperature, atmospheric and oceanic
2237 heat flux, and atmospheric and oceanic ice growth
2238
2239 checkpoint61p (2009/06/10)
2240 o eesupp (global_max & global_sum):
2241 - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
2242 - remove starting & endding barrier (no longer needed)
2243 o pkg/mdsio, writelocal:
2244 works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
2245 (remove the STOP): uses shared buffer IO to store data from all threads
2246 and then let master-thread write nThreads tiles.
2247 o pkg/mdsio (read/write field):
2248 - tiled IO done in 1 piece (all levels at a time);
2249 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
2250 - multi-threaded: allow to read/write local (non-shared) array
2251 (was already working with singleCpuIO ; now works also without);
2252 => no longer needs barrier call after reading a file (added inside
2253 mds_read/write field).
2254 - move barrier calls outside gather/scatter_2d to mds_read/write_field
2255 o pkg/obcs/exf
2256 - exf_getffieldrec.F: add a few ". _d 0" and
2257 add code to catch the case fldperiod = 0.
2258 - obcs_precribe_read.F: change if statements so that they match
2259 the variable type (_RL)
2260 - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
2261 exf_iprec) as part of namelist EXF_NML_01
2262 o pkg/mdsio:
2263 - read/write tiled (local) files: read/write 1-level tile chunk at a time
2264 (instead of segment of length sNx); expected to speed up tiled IO.
2265 o pkg/exch2:
2266 - take buffer copy from/to array out of S/R exch2_send/recv into new
2267 S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
2268 (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
2269 - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
2270 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
2271 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
2272 including Topology header file (and common blocks).
2273 - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
2274 remove 2nd exch call in exch2_s3d_rx (no longer needed).
2275 - document S/R arg. list (+ update some comments)
2276 o pkg/seaice:
2277 - added SEAICE_CLIM_AIR code, which permits modulation of surface air
2278 temperature and humidity over sea ice based on climatological values.
2279 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
2280 of LSR (this change is expected to change the results slightly because now
2281 it uses slightly difference moduli from the second last LSR solution, but
2282 that is more consistent with the stress computations; this part of the code
2283 is not tested in the verification experiments)
2284 - fix diagnostics for flux of ice in case of B-grid
2285 - turn strain rates eij and press into global fields within global
2286 common block in SEAICE.h for more straighforward diagnostics
2287 - fix diagnostics for principal stress components, press, zeta, eta
2288 to give something meaning full
2289 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
2290 new output (all 4 tests) using default rotationPeriod.
2291 o pkg KPP:
2292 - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
2293 - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
2294 and normal grid from 1 to Nr)
2295 o Fix computations of L4rdt in mom_calc_visc.F
2296 o eesupp:
2297 new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
2298 should be called before a "stop" if we know that all process are going
2299 to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
2300
2301 checkpoint61o (2009/05/26)
2302 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
2303 o model/src/ini_curvilinear_grid.F:
2304 compute angleSin/CosC when they are not read from a file
2305 o pkg/seaice:
2306 add pseudo time stepping for LSOR
2307 o pkg/exch2:
2308 temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
2309 o pkg/seaice:
2310 Adding separate sea ice albedo, drag coefficients, and HO in Southern
2311 Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
2312 o SingleCpuIO:
2313 fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
2314 o pkg/seaice:
2315 put exchanged variable in (local) common block for MPI+Multi-Threads
2316 to work (necessary with exch1, and for now with exch2 too).
2317 o verification: to get more experiments tested with mpi, mth and mpi+mth,
2318 change tiling of:
2319 aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
2320 hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
2321 update output of exp:
2322 exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
2323 tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
2324 + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
2325 (note: output.txt generated on faulks using only 1 tile)
2326 o eesupp & mdsio (SingleCpuIO):
2327 - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
2328 parameter "W2_useE2ioLayOut" (read from file "data.exch2").
2329 Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
2330 - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
2331 - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
2332 gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
2333 o pkg/exch2:
2334 - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
2335 read parameter file "data.exch2" if it exists; otherwise try default regular
2336 cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
2337 - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
2338 with new code (not to be used, just as a backup solution).
2339 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
2340 in utils/exch2/input.
2341
2342 checkpoint61n (2009/05/12)
2343 o eesupp & mdsio (SingleCpuIO):
2344 - move mapping to global io-buffer inside gather_2d/scater_2d: this save
2345 memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
2346 receive real*4 array (instead of real*8) to read/write 32.bit files.
2347 (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
2348 and remove new mapping S/R)
2349 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
2350 - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
2351 xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
2352 when using exch2. Add S/R to map global io-buffer to global model array.
2353 - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
2354
2355 checkpoint61m (2009/04/29)
2356 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
2357 and add 3 other S/R for other types (R4,R8,RS).
2358 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
2359 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
2360 - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
2361 - reduce number of macro definitions (keep only those which are used);
2362 can always call directly the corrresponding S/R if needed.
2363 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
2364 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
2365 Fixed wrong type of arg in:
2366 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
2367 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
2368 To fix: global_sum of var in common block is wrong (multi-threaded) in:
2369 dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
2370 To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
2371 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
2372 "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
2373 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
2374 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
2375 edges are closed (zero depth); might happen with "blank tiles";
2376 for now, disabled if using OBCS.
2377 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
2378 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
2379 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
2380 to reduce length of 1.D array print in STDOUT.
2381 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
2382 + use 48 tiles (16x8): this will allow to test "blank tiles".
2383 o start to test MPI + multi-threaded (change testreport to skip tests
2384 where number of tiles do not match).
2385 o genmake2: add option "-omp" to turn on Open-MP ;
2386 passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
2387 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
2388 and keep the original tile numbering. Note: compatible with old
2389 W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
2390
2391 checkpoint61l (2009/04/07)
2392 o Overlaps had been forgotten in calculating ijk keys : fixed
2393 o fix cyrus makedepend for gcc 4.4
2394 o experiment fizhi-cs-aqualev20:
2395 switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
2396 and generate new output. Note: new output is much closer to the old
2397 one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
2398 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
2399 o pkg/fizhi:
2400 - change to avoid indices going deliberately over array-bounds
2401 - remove unnecessary MPI stuff
2402 - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
2403 - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
2404 does not go over array-bounds and therefore returns reliable output.
2405 - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
2406 this S/R has 4 output arguments, which are used inside "get_alarm";
2407 when it is called with the same variable "ndum" in place of several
2408 output arguments, this produces weird side effect inside "get_alarm"
2409 (e.g., datein=dates(n) is overwritten by timein=times(n) since both
2410 datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
2411 address) and produces error.
2412 o tools/gemake2: (March 27-29 2009)
2413 with option "-mpi": link *_mpi files from "MODS" dir (this is what
2414 testreport does).
2415 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
2416 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
2417 update lab_sea.lsr & lab_sea.salt_plume results
2418 o pkg/seaice:
2419 Major overhaul of the LSOR solver: change discretization from original
2420 finite differences to finite volume. The old routine is still in the
2421 file seaice_lsr.F and can be turned on with the CPP-flag
2422 SEAICE_OLD_AND_BAD_DISCRETIZATION
2423 Along with this change, the discretization of the strain rates is changed.
2424 The same flag turns on the old discretization in seaice_calc_strainrates.F
2425 All verification experiments with seaice are affected (except for
2426 seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
2427 results by setting the above flag.
2428 Further changes involve changes in defaults:
2429 - ALLOW_FLOODING is defined and turned on by default
2430 - SEAICEadvSnow = .true. is now the default
2431 - SEAICEadvSalt = .true. is now the default
2432 - SEAICEadvAge = .true. is now the default
2433 - SEAICE_clipVelocities = .false. is now the default
2434 (as per J. Zhang's recommendation)
2435 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
2436 is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
2437 - seaice_growth: replace computation of UG by a simple copy from wspeed
2438
2439 checkpoint61k (2009/03/18)
2440 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
2441 seaice_lsr: fixed a few metric terms,
2442 affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
2443 add more debugging diagnostics
2444 seaice_evp: removed superfluous many metric terms of FV discretization
2445 of stress divergence
2446 affects lab_sea, lab_sea.hb87
2447 seaice_ocean_stress: removed superfluous many metric terms of FV discretization
2448 of stress divergence for non-evp solver
2449 (this part is not tested anywhere)
2450 seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
2451 they were effectively only half slip
2452 affects lab_sea.hb87
2453 updated all relevant verification experiments (except lab_sea//output_adm.txt
2454 which was left over, but fails at level 7 & 6)
2455
2456 checkpoint61j (2009/03/17)
2457 o pkg/seaice: turn a few hard wired parameters into run time parameters
2458 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
2459 time in seconds as promised by the usints in seaice_monitor and exf_monitor
2460 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
2461 that are not cubed-sphere grids
2462 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
2463 o pkg/ctrl:
2464 fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
2465 o non-hydrostatic (calc_gw.F):
2466 fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
2467 update output of exp. global_ocean.cs32x15.viscA4
2468 o remove backward compatibility for thetaMin,phiMin
2469 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
2470 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
2471 interpolated wind field not only for curvilineargrid=.true., but also
2472 for a rotated grid (rotateGrid=.true.)
2473 o pkg/exf: add capability to bypass interpolation for runoff
2474 by setting yet another CPP-flag
2475 o eesupp/src, B-grid exchange:
2476 add simple (6 tiles, non MPI) CS exch + standard interface S/R.
2477 o autodiff
2478 new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
2479 allows to switch to single-prec common blocks;
2480 corresponding switch occurs in tamc.h, integer isbyte
2481 TAF store directivs "byte" and "kind" seem equivalent;
2482 Most tamc.h have been updated correspondingly.
2483
2484 checkpoint61i (2009/02/13)
2485 o autodiff:
2486 fix autodiff_sore/_restore indices for obcs
2487 (spotted by I. Hoteit, M. Mazloff)
2488 o pkg/autodiff, pkg/ctrl:
2489 Add flag to reduce all tapelev I/O to single-prec.
2490 In data.ctrl set
2491 doSinglePrecTapelev = .TRUE.
2492 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
2493 check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
2494 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
2495 real fresh water flux (not yet)
2496 o pkg/mdsio & rw:
2497 - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
2498 - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
2499 o pkg/flt:
2500 - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
2501 init_fixed & ini_varia.
2502 - clean-up & simplify linear interpolation S/R:
2503 move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
2504 - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
2505 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
2506 - add vert. coordinate & horiz. indices to output files.
2507 - change vertical position in initial condition, from index to depth [m].
2508 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
2509 (easier to get to a curvilinear grid) ; delX,delY no longer used.
2510 o pkg/ggl90: a few modifications:
2511 - fix bottom boundary condition, and interpolation of KappaE
2512 near top and bottom
2513 - use same set of viscosity/diffusivity for TKE/momnetum/tracer
2514 - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
2515 - add a few options for mixing-length upper limit (--> mxlMaxFlag)
2516 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
2517 (maintain temporary backward compatibility, until next checkpoint)
2518
2519 checkpoint61h (2009/01/27)
2520 o pkg/diagnostics with "periodic averaging diagnostics":
2521 fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
2522 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
2523 o pkg/obcs: fix loop ranges for balancing code
2524 o pkg/flt:
2525 - improve criteria for finding which tile owns a float.
2526 - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
2527 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
2528 aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
2529 with ocean biogeo)
2530 o pkg/flt:
2531 - do some cleaning and fix the restart ;
2532 - add output.txt in flt_example/results to get this pkg tested.
2533 o genmake2: add an EXTENDED_SRC option and flag.
2534 for now, cannot be turned on on command line (only through genmake_local)
2535 o pkg/mdsio: read/write vector:
2536 - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
2537 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
2538 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
2539 - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
2540 (drop to 4 digits matching for grad). But this test does not look very
2541 reliable (was already failling on eddy, fc5, at 6.digits). Update output.
2542
2543 checkpoint61g (2008/12/29)
2544 o pkg/flt:
2545 - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
2546 + make OPTIONS file more standard.
2547 - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
2548 - fix _BYTESWAPIO CPP-Flag
2549 - standard reading of file-parameter "data.flt"
2550 - fix argument list of S/R FLT_RESTART
2551 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
2552 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
2553 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
2554 a still unfixed compiler/optimization bug
2555
2556 checkpoint61f (2008/11/21)
2557 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
2558 update results of global_ocean.cs32x15.icedyn test.
2559 o move getcon.F from model/src to pkg/fizhi.
2560 o pkg/exf: add parameter for extrapolation of temp up to the surface
2561 and option to prevent negative evap (in bulk_largeyeager04 only).
2562 o Prather Advection scheme: fix tracer conservation for divergent flow
2563 (e.g., when using NonLin Free-Surface).
2564 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
2565 o gmredi (Visbeck-variable-K):
2566 - add more parameters to Visbeck-variable-K.
2567 - use a 5 points average for dSigmaR in Visbeck-K calculation
2568 (more "homogenous": same stencil and same weights as in dSigmaH)
2569 - update output of ideal_2D_oce experiment.
2570 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
2571 (#undef REAL4_IS_SLOW)
2572 - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
2573 coordinate variable
2574 - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
2575 (surface forcing fields), removes some of the functionality
2576 - model/src/write_grid.F: write _RS variables as RS-netcdf variables
2577 - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
2578 probably not all: copy _RS surface flux fields to RL field before
2579 calling DIAGNOSTICS_FILL
2580 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
2581 real*4 (CALL EXCH_*_RS) versions.
2582 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
2583 (generate new output).
2584
2585 checkpoint61e (2008/10/23)
2586 o gmredi (Visbeck-variable-K):
2587 - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
2588 - change computation of Visbeck-K where Slope > Smax :
2589 now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
2590 previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
2591 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
2592 to be the same as with Z-coord. (i.e., m/s & no-units respectively).
2593 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
2594 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
2595 does not become too large (to avoid precision problems in implicit-diffusion
2596 solver); update ideal_2D_oce output.
2597 o pkg ggl90:
2598 - in ggl90_cal.F: compute only one set of visc/diff, used to
2599 step forward TKE/T/S/momentum
2600 - default value of GGL90viscMax/GGL90diffMax larger and equal (to
2601 have Prandlt =1)
2602 o gmredi (fm07):
2603 - add lower limit on Transition layer thickness + lower limit on 1/lambda
2604 - allow to set few more params from data.gmredi
2605 o pkg ggl90:
2606 - add missing sqrt(2) factor in computation of mixing length
2607 scale in ggl90_calc.F
2608 (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
2609
2610 checkpoint61d (2008/09/25)
2611 o adjoint modifs
2612 - adapt to new field rhoInSitu
2613 - allow to revert from StoreDynVars2D, StoreDynVars3D
2614 to individual fields
2615 (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
2616 o store 3-D (in-situ) density in commom block (DYNVARS.h)
2617 - save 1 rho computation.
2618 - no longer modify T & S inland when using down_slope pkg.
2619 o gad_som : allow to switch to SOM advection for T & S without corresponding
2620 pickup files (using new S/R: MDS_CHECK4FILE).
2621 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
2622 (for useSingleCpuIO to work in multi-threaded)
2623 o pkg/shelfice:
2624 - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
2625 with SHELFICEtopoFile in data.shelfice
2626 - move code for reading ice shelf topography and modifying hFacC into separate
2627 subroutines of the shelfice package
2628 - separate initialisation of "fixed" and "variable" variables
2629 - kTopC is not (yet) replaced by kSurfC, although this is possible
2630 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
2631 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
2632 and rename:
2633 ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
2634 ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
2635 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
2636
2637 checkpoint61c (2008/08/30)
2638 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
2639 to add mass source/sink of fluid in the interior (3-D generalisation
2640 of oceanic real-fresh water flux).
2641 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
2642 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
2643 o new pkg: down_slope
2644 density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
2645 - presently, modify T & S inland (dwnslp_calc_rho.F).
2646 can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
2647 - implementation for ocean in P-coords not tested.
2648 - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
2649 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
2650 (to facilitate conversion of oceanic pkg to p-coordinate).
2651 o change FIND_RHO to FIND_RHO_2D :
2652 pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
2653 o new pkg: cheapaml
2654
2655 checkpoint61b (2008/08/05)
2656 o exch2:
2657 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
2658 - no longer depend on the order sequence (N,S,E,W).
2659 - 3rd exchange no longer needed (tested with 24 tiles).
2660 - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
2661 - exch_UV_A-grid readily available (but not yet tested).
2662 comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
2663 (both are no longer needed) in exch_uv: no effect in forward run; but
2664 get truncation error differences with adjoint exch.
2665 o exch2:
2666 - change index-bounds storage (moved from target to local tile,
2667 more intuitive this way) ; rename/remove some variables.
2668 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
2669
2670 checkpoint61a (2008/07/29)
2671 o exch2/matlab-topology-generator:
2672 fix bug in index bounds for N-S internal exchange (hard to tell if this
2673 had any effect on the solution).
2674 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
2675 is exceeded
2676 o testreport: modify syntax of awk, so that it works also with
2677 awk, and not only with nawk and gawk
2678
2679 checkpoint61 (2008/06/24)
2680 o autodiff
2681 Change default for TAF usage by removing argument '-nonew_arg'
2682 This changes TAF subroutine argument list (ordering of active var.)
2683 Omission of this flag leads to incompatibility w.r.t. TAMC
2684 To restore TAMC-compatibility, need following modifs:
2685 * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
2686 * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
2687 Tested TAF version is 1.9.22
2688 N.B.: exch2 hand-written adjoint code currently not TAMC compatible
2689
2690 checkpoint60 (2008/06/19)
2691 --->>> This is the last checkpoint for which generating the adjoint
2692 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
2693 --->>> by default.
2694 --->>> Future checkpoints will ommit this flag by default.
2695 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
2696 o pkg/grdchk: Add gradient check to etan0 perturbations.
2697 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
2698 o pkg/autodiff: more flexibility in zeroadj.
2699 model/src: modifying do_oceanic_phys.F accordingly.
2700 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
2701 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
2702 special setup of gmredi for which the adjoint is stable
2703 enough for parameter optimization.
2704 o bridging the gap between eddy stress and GM.
2705 -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
2706 along with a change in CPP option (now ALLOW_EDDYPSI).
2707 -> when using GM w/ GM_AdvForm:
2708 The total eddy streamfunction (Psi = eddyPsi + K x Slope)
2709 is applied either in the tracer Eq. or in momentum Eq.
2710 depending on data.gmredi (intro. GM_InMomAsStress).
2711 -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
2712 The key modifications are in model/src/taueddy_external_forcing.F
2713 pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
2714
2715 checkpoint59r (2008/05/29)
2716 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
2717 from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
2718 fix option to read coriolis(@ cell-corner) from files with CS-grid.
2719 o pkg/mnc: add some attributes to standard 1D-coordinate variables
2720 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
2721 mass points, when using mnc for output
2722 - add runtime parameter (missing_value, missing_value_int) to override
2723 default (which is the value of getcon('UNDEF'))
2724 o pkg/mnc: prepare mnc for the actual use of missing values with the
2725 diagnostics package: small fix in mnc_cw_readwrite.template and more
2726 initialisation of never used fields
2727 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
2728 versions
2729 o pkg/thsice/thsice_ini_vars.F added default initial values so that
2730 thermodynamics sea ice solver does not blow up when some initial fields
2731 are missing.
2732 o move from external_forcing_surf.F to ini_forcing.F
2733 the p-coord. hack consisting in using pLoad to set phi0surf ;
2734 update output of tutorial_global_oce_in_p (affected @ truncation level).
2735 o Freshen up a bit hs94.1x64x5, notably:
2736 remove rotationPeriod and tRef=5*0. (adjoint only), and add
2737 exactConserv=.TRUE.
2738 o pkg/generic_advdiff:
2739 change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
2740 applies to files where Temperature & Salinity 2nd Order moments are used.
2741 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
2742 this uses a dynamically allocated internal state data structure
2743 (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
2744 and requires a fortran 90 compiler
2745
2746 checkpoint59q (2008/05/06)
2747 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
2748 (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
2749 o Refresh tutorial_global_oce_biogeo, notably:
2750 - change bathymetry (put back seamounts in ACC, use hFacs)
2751 - change EOS (POLY3 --> JMD95Z)
2752 - use Bryan-Lewis vertical diffusivity
2753 - use multidimensional advection
2754 - remove old virtual virtual in dic pkg, now done through ptracer pkg
2755 - change a couple of parameters in dic pkg
2756 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
2757 o pkg/obcs: change default to OBCSfixTopo = .true.,
2758 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
2759 - replace "debugMode" with "debugLevel .GE. debLevB"
2760 o implementation of TAF directives for gchem,cfc,dic
2761 o remove "exp5" (replaced by tutorial_deep_convection).
2762 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
2763 this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
2764 the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
2765 --> changes results in exp4, seaice_obcs
2766 o tutorial_deep_convection :
2767 update the set-up and increase resolution and domain size ; start
2768 from pseudo initial conditions = output at t=120mn in order to see
2769 something happening when running testreport.
2770 o pkg/seaice: add os7mp as an advection scheme
2771 add check for advection schemes
2772 add a flag for restoring T and S underneath sea ice
2773 o pkg/my82: add netcdf-support and diagnostics
2774 o thsice pkg:
2775 - Now hsMax limits snow height by turning it into ice following
2776 flooding scheme (and now conserving energy)
2777 - Slight rewriting of the formula in thsice_calc_thick.F
2778 - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
2779 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
2780
2781 checkpoint59p (2008/04/10)
2782 o gchem / dic / cfc :
2783 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
2784 - add new parameter files: "data.dic" & "data.cfc" ;
2785 - various re-arrangement in initialisation & header file ;
2786 - fix tutorial_global_oce_biogeo for multi-threaded test.
2787 o pkg/dic: test for "pickup_dic" file when restarting ;
2788 if no pickup-file, can restart with a re-initialised pH (same as it did
2789 before) providing pickupStrictlyMatch is set to False.
2790 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
2791 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
2792 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
2793 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
2794 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
2795 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
2796 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
2797 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
2798 scheme to use for vorticty-term ;
2799 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
2800 (with default selectVortScheme, return to original discretisation)
2801 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
2802 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
2803 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
2804 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
2805 also fix diagnostics VISCAHW & VISCA4W.
2806
2807 checkpoint59o (2008/03/07)
2808 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
2809 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
2810 move a few statemens out the main loop into separate loops
2811 o pkg/shelfice:
2812 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
2813 (kg/m^2/s), does not break tests, because in verification/isomip,
2814 rhoConstFresh=rhoConst (by accident)
2815 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
2816 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
2817 new file model/src/seawater.F, so that they are available for all pkgs.
2818 - convert potential temperature into in-situ temperature. This changes the
2819 isomip tests => update tests
2820 o add a flag writePickupAtEnd (default=true) to be able to suppress
2821 writing a pickup at the last timestep
2822 o tools/mpack-1.6 :
2823 - disable automake (not working) and autoconf (not needed).
2824 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
2825 also cleaner with much less compilation warnings.
2826 o pkg/profiles:
2827 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
2828 (for "less than 32 characters name" compiler requirement)
2829 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
2830 conditions that have a different sampling frequency than S/T/U/V obcs
2831 o pkg/diagnostics (stats-diags):
2832 - fix global Min/Max in case 1 processor get only empty tiles
2833 o genmake2: replace (4 times)
2834 make genmake_tc_1.o >> genmake_warnings 2>&1
2835 with
2836 COMM="$CC $CFLAGS -c genmake_tc_1.c"
2837 echo $COMM >> genmake_warnings
2838 $COMM >> genmake_warnings 2>&1
2839 to make genmake2 always see the value of CC as specified in the optfile.
2840 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
2841 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
2842 - modify verification advect_cs test to test SOM-advection on CS-grid.
2843 o pkg/ctrl:
2844 - Rewrite of ctrl_map_ini_ecco.F,
2845 introducing a generic routine (ctrl_map_ini_gen.F).
2846 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
2847
2848 checkpoint59n (2008/02/09)
2849 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
2850 number in dedicate array "hdiag":
2851 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
2852 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
2853 - many small changes (integer format) for large number of diagnostics
2854 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
2855 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
2856 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
2857 usingSphericalGrid, this allows to define the rotated grid coordinates
2858 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
2859 geographical coordinates according to the inverse of the rotation defined
2860 by the Euler angles, so that Coriolis parameter and online-interpolation by
2861 exf works with the geographical coordinates on XC/YC/XG/YG.
2862 Naturally, this feature does not work with all packages, so some
2863 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
2864 profiles), because there the coordinates are assumed to be regular
2865 spherical grid coordinates.
2866 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
2867 - introduce isopycnal diffusion coefficient control.
2868 o tools/adjoint_options:
2869 - additional control vector components.
2870 o pkg/mnc: have mnc create marginally meaning full coordinate variables
2871 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
2872 o pkg/mypackage:
2873 - add example of read/write pickup for state-var ;
2874 - add entry points to the main code for state-vars diags & write-pickup.
2875 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
2876 transitions for useExfYearlyFields
2877 - add new subroutine that determines the file to read from for
2878 use*YearlyFields = .TRUE. and .FALSE.
2879 - add a verification experiment to global_with_exf that tests
2880 useExfYearlyFields with USE_EXF_INTERPOLATION defined
2881 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
2882 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
2883 subroutines (which could be generated from a template, because they are
2884 almost identical), for now they are included in obcs_prescribe_read.F for
2885 simplicity
2886 o pkg/exf:
2887 - add a little more diagnostic to exf_interp_read (in analogy to
2888 mds_read_field, can be turned off with debugLevel < debugLevA=1)
2889 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
2890 ugly but fast by unrolling short inner loops, inserting a unroll=8
2891 directive in routine lagran, and splitting a loop and making do while the
2892 outermost loop (the latter requires the intoduction of index arrays)
2893 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
2894 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
2895 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
2896 o verification/seaice_obcs: updated for restart test and latest options
2897 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
2898 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
2899 for now this is only available for the C-grid code and also within
2900 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
2901
2902 checkpoint59m (2008/01/14)
2903 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
2904 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
2905 o gad_som : fix flux output (& diagnostics) to have same units as other
2906 advection scheme fluxes (was previously multiplied by deltaT).
2907 o added verification/seaice_obcs both to test seaice open boundaries
2908 and to provide an example matlab scrpt for generating them
2909 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
2910 o pkg/salt_plume: clean up salt_plume_frac.F to
2911 remove redundancy in PlumeMethod 1 and 4
2912 o pkg/kpp: added saltplume diagnostics
2913 o pkg/obcs and pkg/seaice:
2914 - do not set uice and vice to zero when OB*icefile are unspecified
2915 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
2916 - moved seaice tracer obcs after call to seaice_growth
2917 o pkg/salt_plume: added various options for salt plume depth
2918 criterion and for vertical distribution of the salt
2919
2920 checkpoint59l (2007/12/18)
2921 o pkg/ptracers: new version of ptracers pickup:
2922 read meta file and write only fields which are needed to restart.
2923 ( same logic as main pickup file ; also using pickupStrictlyMatch )
2924 o pkg/seaice:
2925 - add timescale for melting due to warm mixed layer as a means of
2926 setting SEAICE_availHeatFrac more conveniently
2927 - add a CPP-flag/runtime parameter check for flooding algorithm
2928 - reformulated availHeat in seaice_growth.F to be independent of AREA
2929 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
2930 unit changes
2931 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
2932 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
2933 SX vector computer.
2934 o pkg/seaice:
2935 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
2936 seaice forcing fields can now be read only through pkg/exf
2937 - removed some unused halos
2938 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
2939 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
2940 or U/VICE from U/VWIND before computing U/VSTRESS
2941
2942 checkpoint59k (2007/11/30)
2943 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
2944 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
2945 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
2946 all experiments pass when compile with un-initialised var. checking option.
2947 o added pkg/salt_plume
2948 o script to test restart (for now, in MITgcm_contrib/jmc_script)
2949 o pkg/seaice: new read/write pickup version.
2950 read meta file and write only fields which are needed to restart.
2951 ( same logic as main pickup file ; also using pickupStrictlyMatch )
2952 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
2953 o lab_sea.hb87: modify the domain & update output.hb87.txt :
2954 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
2955 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
2956 process. Fixed here by closing the domain at the Northern boundary.
2957 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
2958 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
2959 a set of consecutive levels in/from a 3-D array.
2960 o pkg/ptracers:
2961 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
2962 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
2963
2964 checkpoint59j (2007/11/09)
2965 o in pkgs: dic, obcs, offline, rbcs:
2966 standard way to compute coeff. for time interpolation between 2 time reccords
2967 which retains full precision (& make results less dependent on compiler).
2968 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
2969 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
2970 packages instead of reading ice cover and wind speed separately
2971 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
2972 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
2973 to allow to compile customized code before the update)
2974 o cleaning-up:
2975 - fix CPP instruction syntax in pkg/obcs
2976 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
2977 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
2978 - fix some threads issue in IO parts.
2979 o pkg/dic:
2980 - add tons of "_d 0" (--> much better testreports !)
2981 and then update outputs of tutorial_global_oce_biogeo
2982 o pkg/mom_fluxform:
2983 add a special version of momentum advection intended to conserve momentum
2984 next to a bathymetry step or a coastline edge. (default = off = #undef)
2985 o new read/write pickup version:
2986 - for now, only implemented for main (mdsio) pickup file.
2987 - write out only what is needed to restart; merge pickup_nh , pickup_ph
2988 and main pickup together.
2989 - read meta file; read only what is needed to restart; stop if a field
2990 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
2991 if it make sense (even if the restart is not perfect).
2992 - if no meta file, assume that pickup to read corresponds exactly to
2993 a pickup that would currently be written.
2994 - read pickup written in the old format (until checkpoint59i) if it
2995 recognizes an old meta file (no field-list).
2996 - add a meta file in exp. which starts from a pickup: 2 cases:
2997 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
2998 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
2999 b) a meta file describing the content of the associated pickup file
3000 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
3001 o pkg/mdsio & pkg/rw:
3002 - new routine to read a meta file ; new set of routine to read
3003 Multiple-fields file (with meta file).
3004 o added open boundary conditions capability for seaice
3005 HSNOW, HSALT, UICE, and VICE
3006
3007 checkpoint59i (2007/10/21)
3008 o adjoint:
3009 * fix multiDimAdvection adjoint
3010 (partial recomputation problem by TAF for fVerT(:,:,kDown)
3011 and comlev1 size definition (maxpass vs. max. number of tracers)
3012 * verification/global_ocean.90x45x15 adjoint now tests
3013 NLFS and multiDimAdvection using DST3 (=30)
3014 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
3015 o pkg/kpp: add "_d 0" to real constant (if missing);
3016 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
3017 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
3018 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
3019 for internal parameters related to restart process (formerly from PARAMS.h)
3020 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
3021 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
3022 as argument. (only atm2d & obcs write_pickup have not yet been updated)
3023 o pkg/monitor:
3024 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
3025 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
3026 - account for deep Atmosphere factor and density factor (anelastic)
3027 o added open boundary conditions capability for seaice HEFF and AREA
3028 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
3029 thermodynamics
3030 - requires a little reorganization, which affects the testreport results
3031 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
3032 so that now the conservative form is tested
3033 - add a few comments
3034 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
3035 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
3036 o add new diagnostics to seaice: advective, diffusive fluxes (only for
3037 multidim-advection, for scheme 2 they are not filled) and transports,
3038 thermodynamic growth rates
3039 o change units of EmPmR (inside the code, + within coupling interface)
3040 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
3041 Affects results @ truncation level (cg2d match) and update output of
3042 experiments: lab_sea(6), global_ocean.90x40x15(10),
3043 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
3044 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
3045 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
3046 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
3047
3048 checkpoint59h (2007/09/29)
3049 o pkg/exf:
3050 - improve vectorization by moving if-statement out of loops in
3051 exf_mapfields, exf_radiation
3052 - exf_bulkformulae.F: introduce 2D fields and vectorize code
3053 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
3054 o testreport:
3055 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
3056 monitor & update offline_exf_seaice exp. output.
3057 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
3058 o pkg/seaice:
3059 - bug fix in the evp solver: boundary conditions were affected be
3060 masking of zMax/zMin (changes results)
3061 - minor bug fix in boundary conditions in seaice_calc_strainrates
3062 (changes results for no_slip)
3063 - seaice_lsr.F: make interpolation of eta dependent on boundaries
3064 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
3065 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
3066 stress formulation and no-slip boundary conditions
3067 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
3068 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
3069 o pkg/seaice: a first HSALT time stepping equation has been checked in
3070 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
3071 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
3072 without requiring DO-IF statements
3073 o pkg/thsice:
3074 use continuous power-law function for partition of energy between lateral
3075 melting/freezing and thinning/thickening ; old code using step function
3076 still available with #undef THSICE_FRACEN_POWERLAW
3077 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
3078 o testreport: change AD testing : check against results/output_adm.txt
3079 using same scripts as for forward test.
3080
3081 checkpoint59g (2007/09/17)
3082 o adjoint testing: in preparation for changing testreport:
3083 - output format: cost and grad written on separated lines
3084 - ad output results in directory "results" (instead of "results_ad")
3085 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
3086 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
3087 o pkg/ecco: allow user defined cost function contributions
3088 o testreport:
3089 Allow to choose (per experiment) the list of tested output variables
3090 and the main variable (used to issue a pass/FAIL ) ;
3091 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
3092 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
3093 Also modify printing of summary:
3094 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
3095 b) echo the list of tested variables in the individual summary.txt of
3096 each experiment.
3097 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
3098 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
3099 (but still depend on the tile decompostion of the domain).
3100 o pkg/seaice: change a discretization detail to make the B-grid code
3101 "more symmetric". This change is likely to remove all "ridges/leads" that
3102 where quasi-aligned with the grid in B-grid solutions. It may also be
3103 the solution to the stress coupling issues with the B-grid.
3104 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
3105 remove .cvsignore from input dir. (since testreport no longer run here).
3106 o pkg/thsice:
3107 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
3108 - fix reshaping of sea-ice just after advection:
3109 melt all the ice only if ice-volume is too small.
3110 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
3111 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
3112 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
3113 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
3114 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
3115 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
3116 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
3117 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
3118 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
3119 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
3120 -> update output.txt
3121 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
3122 this affects truncation error: -> update output.txt of exp:
3123 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
3124 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
3125
3126 checkpoint59f (2007/08/21)
3127 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
3128 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
3129 a bounded range (in forward mode)
3130 o pkg/ecco, ctrl, autodiff and mom_common:
3131 internal parameter controls, completements of implementations
3132 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
3133 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
3134 (not seem any difference in testing results).
3135 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
3136 at face corners.
3137 o pkg/generic_advdiff:
3138 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
3139 loop range indices for computing vertical advection tendency
3140 and do the calculation in the interior only (no overlap) ;
3141 for now, only implemented for SOM advection (to save CPU time).
3142 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
3143 o exch2 adjoint
3144 First set of changes:
3145 - add exch2 hand-written adjoint templates
3146 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
3147 This will require cleanup in pkg/autodiff/*.F
3148 (changed routines currently kept separate in verif. code/)
3149 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
3150 that used to hide exch2 or cubed-sphere specific code
3151 (commented via 'cph-exch2')
3152 o pkg/seaice
3153 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
3154 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
3155 output of global_ocean.cs32x15.thsice .
3156
3157 checkpoint59e (2007/07/26)
3158 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
3159 for B-grid vector (not yet tested) and C-grid vector (<- only used
3160 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
3161 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
3162 (#ifdef ALLOW_SALT_PLUME)
3163 o gather_2d/scatter_2d: removed halo regions
3164 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
3165 scheme and the corresponding test case (under front_relax dir). For now,
3166 only available with Skew-flux form and not yet tested in realistic set-up.
3167 adjoint: store directives updated, but gradient checks deteriorated,
3168 so maybe GM/Redi adjoint is now broken.
3169 o seaice adjoint
3170 * add AREA, HEFF, HSNOW as control variable
3171 (should not change lab_sea results)
3172 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
3173 o pkg/seaice:
3174 * added computation of saltFlux in seaice_growth;
3175 For time being, sea ice salinity is assumed constant
3176 contribution of snow flooding to freshening of sea ice is neglected.
3177 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
3178 defaults to 0.0 in order to maintain backward compatibility.
3179 Typical values for SEAICE_salinity are 4 to 10 g/kg.
3180 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
3181 * added SEAICE_availHeatFrac, which specifies fraction of surface level
3182 heat content used to melt or grow ice
3183 * commented out cap of HICE: it helps keep ice thinner
3184 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
3185 * applied OBCS T/S mask to HEFFM sea ice mask
3186
3187 checkpoint59d (2007/06/21)
3188 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
3189 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
3190 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
3191 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
3192 and change default value of parameter "GM_Small_Number";
3193 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
3194 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
3195 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
3196 o pkg/ecco: cost function when applying pkg/smooth to controls
3197 o pkg/ctrl: add forcingPrecond run time parameter
3198 o pkg/seaice:
3199 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
3200 - fix bug in metric terms of u-equation in LSR solver (implicit part),
3201 changes verification/lab_sea
3202 - rearrange implicit part of u-equation in LSR solver to make it easier to
3203 read, understand, and debug. This causes changes at the truncation level.
3204 - fix (serious) bug in the boundary conditions (sign error in the implicit
3205 part) of the LSR solver. Changes all LSR results.
3206 - fixed problem with HSNOW initialization to avoid thick snow when AREA
3207 is initilized with small values - does not change lab_sea results.
3208 - added HsnowFile initialization capability
3209 o pkg/smooth: addition to model/src and pkg/ctrl so allow
3210 initialization of pkg/smooth and application to control vector
3211 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
3212 o dependencies: pkg/profiles requires pkg/cal
3213 o pkg/profiles:
3214 - added option ALLOW_PROFILES_GENERICGRID
3215 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
3216 that interpolation information (grid points and coefficients) is provided
3217 within the netcdf input files.
3218 -> sample matlab scripts can be found in MITgcm_contrib/gael
3219 that allow you to prepare netcdf input files.
3220 - also modified: cleaner include statements, cleaner error print statements,
3221 cleaner stops when error, and more tests of the netcdf input files consistency.
3222 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
3223 o pkg/seaice:
3224 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
3225 requires a new routine: seaice_diagnostics_fill.F
3226 - make sure that seaice does not move if not forced (pressure replacement
3227 method, Hibler and Ip, 1995), changes results
3228 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
3229 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
3230 It is turned off by default (=-1.), because it changes the results.
3231 - make it possible to read AREA from a file, too.
3232
3233 checkpoint59c (2007/06/04)
3234 o add S/R and diagnostics for oceanic mixed-layer depth
3235 o move GMRedi call after all vertical mixing schemes (including KPP)
3236 o pkg/thsice:
3237 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
3238 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
3239 o pkg/obcs:
3240 - bug fix for balance code
3241 o pkg/seaice:
3242 - allow values of SEAICE_elasticParm > 1
3243 - add new parameter SEAICE_evpTauRelax as an alternative
3244 to SEAICE_elasticParm
3245 - make lsr boundary conditions free slip (by default), changes result
3246 - add code for no slip boundary conditions for lsr
3247 - set minimum of zeta to zero (and not 4e8) (changes results)
3248 - add a cap on AREA after advecting AREA if seaice_growth is not called
3249 o change calculation of Visbeck K:
3250 - no longer depend on tapering scheme; instead, compute slope (limited
3251 by GM_maxSlope). this is equivalent to what was comuted before with
3252 clipping or linear tappering.
3253 - fix vertical averaging (wrong by 1/2 level)
3254 - leave the old version (but will not be maintained) within
3255 #ifdef OLD_VISBECK_CALC / #endif
3256 - update output of exp. ideal_2D_oce
3257 o change error catch in calc_r_star to improve vectorization
3258 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
3259 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
3260 o adjoint:
3261 Re-organized adjoint checkpointing according to Matt Mazloff
3262 (but with modifs/completions/cleanups)
3263 Storing is now bundled into large arrays to optimized I/O
3264 (and second step in cleanup of the_main_loop)
3265
3266 checkpoint59b (2007/05/16)
3267 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
3268 - export/import (between ocean & coupler) fields needed for ocean DIC.
3269 o pkg/seaice:
3270 - get rid of three more exchanges seaice_calc_viscosities (required
3271 different loop boundaries in seaice_lsr and seaice_ocean_stress)
3272 - bug fix in seaice_ocean_stress (update of lab_sea required)
3273 - reduce loop boundaries to necessary minimum also in seaice_evp
3274 - go back to the old way of computing deltaC/Z as the adjoint likes that
3275 better
3276 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
3277 passive tracer to an Age Tracer) + update output.txt
3278 o pkg/exf:
3279 - implement A-grid / C-grid selection for wind-stress input files.
3280 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
3281 for now, in exf_bulk_largeyeager04.F only :
3282 - change implementation for case where windspeed + 2. components wind-stress
3283 are read-in. AND use rhoConstFresh to convert evap.
3284 o pkg/seaice:
3285 - use correct EXCH_UV for wind-forcing (on A-grid).
3286 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
3287 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
3288 o pkg/exf:
3289 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
3290 EXF_INTERPOLATION:
3291 - merge global_with_exf/code version of exf_interp_read.F
3292 to the main code ;
3293 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
3294 reading the file ; Important: This options needs to be defined to recover
3295 previous code.
3296 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
3297 - no longer loose real*8 precision along the way when using exf_iprec=64.
3298 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
3299 - change discretisation of evp-solver in order to avoid another exchange
3300 (changes lab_sea) and clean up a little
3301 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
3302 help the adjoint (this also changes the results slightly)
3303 - add a few "_d 0" where they had been missing in seaice_evp.F
3304 - cleaning up: remove unused seaice_calc_rhs.F
3305 o pkg/exf: some cleaning-up:
3306 - change various "constants" into runtime parameters
3307 - cleaned-up Large&Yeager04 routine which should eventually
3308 replace exf_bulkformulae.F (changed names of S/R and CPP)
3309 and merged various ALLOW_ATM_WIND options
3310 only used with thsice pkg (in thsice_get_exf.F):
3311 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
3312 which are used when useStabilityFct_overIce=TRUE (= the default)
3313 - change default values of ice & snow emissivity and scale downward LW
3314 by ice & snow emissivity.
3315 o pkg/thsice:
3316 fix few little problems, in thsice_calc_thickn.F:
3317 - growth vertically (and not laterally) if iceFrac == iceMaskMax
3318 - melt only laterally if hIce < hThinIce (as the comments say)
3319 and in thsice_extend.F:
3320 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
3321 - start to form ice as soon as the minimum ice-volume is reachable.
3322 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
3323 and cpl_aim+ocn
3324 o pkg/kpp
3325 - move computation of surface related input fields to KPP into a new
3326 subroutine kpp_forcing_surf.F
3327 - remove wrong (within bi,bj loops) EXCH calls.
3328 - little cleaning (add argument myThid in last position, cvs header ...)
3329 - for now, fix conservation problem by exchanging KPPviscAz (may not
3330 be the best fix)
3331 o pkg/seaice
3332 - check for inconsistent evp parameter/cpp-flag combination
3333 - remove leftover errIO flat for obsolete name list error handling
3334 o OpenAD
3335 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
3336
3337 checkpoint59a (2007/05/01)
3338 o pkg/seaice: some parameter clarifications and a little bit of clean up
3339 o pkg/thsice: rename run-time parameters:
3340 himin -> hIceMin
3341 himin0 -> hThinIce
3342 hihig -> hThickIce
3343 i0 -> i0swFrac
3344 transCoef -> bMeltCoef
3345 frac_energy -> fracMelting
3346 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
3347 with default values (for now) that do not change the results.
3348 remove old version of thsice vars advection in pkg/seaice.
3349 o in FFIELDS.h:
3350 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
3351 - make pLoad & sIceLoad always available (but still only used if
3352 ATMOSPHERIC_LOADING is #define).
3353 o pkg/kpp: replaced _KPP_RL with _RL
3354 o bug fixes for vertical diffusivity computations when both KPP and
3355 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
3356 are no longer updating the vertical diffusivity array
3357 (passed as argument) but are (re-) setting those arrays.
3358 o pkg/seaice: fix bug in evp solver, while doing that
3359 - change (improve?) discretization of stress computations for both
3360 cgrid-lsr and evp solver
3361 - add a new routine to compute strain rates
3362 - the above changes lab_sea results
3363 - add no slip conditions for evp solver (off by default), lsr-version
3364 may follow
3365 - fix exchange for shear at Z-points (does not change lab_sea)
3366 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
3367 (to force the user to pick a time step since there is not "safe" way
3368 of choosing it)
3369 - add principal stress diagnostics
3370 - rearrange fields for evp a little to avoid having to call a: too many
3371 exchanges and b: exchanges for stress trensor components which we do
3372 not have.
3373 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
3374 of evp, complete rewrite for lsr case (latter is does not yet work
3375 in all cases)
3376 o pkg/kpp: add code to have mixing in shelf ice caverns
3377 - add myThid to all kpp routines (long overdue)
3378
3379 checkpoint59 (2007/04/19)
3380 o pkg/exf:
3381 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
3382 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
3383 - move exf header files from lower_case.h to UPPER_CASE.h ;
3384 add missing cvs Header & Name
3385 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
3386 - add namelist param. selectStressGridPosition, exf_monFreq
3387 - retire many _CLIM routines, and remove data.exf_clim
3388 + params moved to data.exf
3389 + climsst, climsss now handled by exf_set_gen, i.e.
3390 climss?period=0 refers to constant field,
3391 climss?period=-12 to monthly forcing
3392 - split up namelists in data.exf
3393 o pkg/seaice:
3394 - remove seaice_exch and seaice_exch_uv
3395 - remove superfluous exchange of theta
3396 - add myThid to seaice_budget_ocean/ice
3397 - add new interface for atmospheric wind forcing (C-grid only)
3398 + new routine
3399 + two new field (taux, tauy for stress over ice)
3400 + removed one global field (DAIRN) for C-grid case only
3401 o pkg/thsise
3402 - 2nd set of modifs for thsice adjoint in conjunction with exf
3403 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
3404
3405 checkpoint58y_post (2007/04/15)
3406 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
3407 vertical diffusivity, similar to that in MOM4; turned on using
3408 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
3409 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
3410 o Added capability for 3D specification of background vertical diffusion
3411 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
3412 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
3413 "data" file that contains the 3D vertical diffusivity coefficients.
3414 o ice dynamics (pkg/seaice) with thsice thermodynamics:
3415 - add code within pkg thsice to advect & diffuse sea-ice fields
3416 similar to (and will replace) what has been added in seaice_advdiff.F,
3417 but: - conserving Mass, Heat & Salt.
3418 - better when using non-linear advection scheme (not yet fully tested)
3419 - can also be used in atmospheric set-up (for now, only the diffusion).
3420
3421 checkpoint58x_post (2007/04/04)
3422 o IO option for global-file compact format:
3423 - add options when generating topology (utils/exch2/matlab-topology-generator)
3424 - add I/O capability (pkg/mdsio).
3425 - adapt utils/matlab/rdmds.m to read this format.
3426 for now long-line format not yet supported by pkg/mdsio (& exch2).
3427 o shelfice: add a few diagnostics
3428
3429 checkpoint58w_post (2007/03/13)
3430 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
3431 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
3432 (and replace horiVertRatio in NH code).
3433 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
3434 and tutorial_plume_on_slope (sensitive to truncation)
3435 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
3436 directly to drive seaice model (C-grid only)
3437 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
3438 - reintroduce computation of wind from stress,
3439 - compute tau (in exf_bulkformulae.F) from windstress averaged to
3440 mass points to avoid tau = 0
3441 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
3442 o rdmnc.m: make it work with "global" files created with gluemnc
3443 o rdmnc.m : some improvements in dealing with singleton dimension
3444 (tested on all testreport mnc output files).
3445 o genmake2: disable pkg/profiles if netcdf test fails.
3446 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
3447 o move call to cal_readparms up to make calendar parameters/variable available
3448 to all packages
3449
3450 checkpoint58v_post (2007/02/08)
3451 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
3452 useDynP_inEos_Zc tested.
3453 o pkg/exf: changes to properly interpolate/mask/scale initial fields
3454 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
3455 and portions thereof. See read_cs.txt for description and examples.
3456 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
3457 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
3458 following the great-circle arc between those 2 points.
3459 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
3460 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
3461 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
3462 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
3463 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
3464 - still needs work (not working with some options ; efficiency to improve)
3465 and serious testing.
3466 - use this scheme for temperature & salinity in 2 advection test exp.:
3467 advect_xy & advect_xz, respectively.
3468
3469 checkpoint58u_post (2007/01/12)
3470 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
3471 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
3472 o testreport: add option "-skipdir" to skip some test.
3473 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
3474 momentum calculation.
3475 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
3476 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
3477 remove checkpoint.F and the_correction_step.F (no longer used);
3478 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
3479 o add option (linFSConserveTr) to correct for tracer source/sink due to
3480 Linear Free surface
3481 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
3482 o pkg/thsice: fix reading mnc-pickups
3483
3484 checkpoint58t_post (2006/12/30)
3485 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
3486 o pkg/mdsio:
3487 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
3488 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
3489 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
3490 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
3491 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
3492 either MDS_READ_FIELD or MDS_WRITE_FIELD )
3493 - new S/R (to replace MDSWRITEMETA), which allows to write more
3494 informations (variable names, time ...) to meta files.
3495 - modify rdmds.m to give back the meta file content.
3496 o pkg/diagnostics: change vertical interpolation to be safer, and more
3497 flexible (define p-levels to interpolate to in data.diagnostics);
3498 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
3499 diagnostic pointer.
3500 o pkg/seaice: more cleaning up of seaice_growth, added many comments
3501 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
3502 o fix multi-category seaice:
3503 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
3504 SEAICE_MULTICATEGORY
3505 - fix short wave heat flux
3506 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
3507 and allow to use EVP solver. Change forward lab_sea: test both EVP
3508 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
3509 o Initial check-in of lab_sea adjoint
3510 (very similar to natl_box_adjoint/code_seaice)
3511 * used C-grid and EVP solver
3512 * used KPP, GM/Redi
3513 * uses inAdExact=.TRUE.
3514 * gradient checks fail for both ADM and TLM
3515 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
3516 f.d. gradients actually seem more problematic than ADM, TLM gradients;
3517 issue is related to forward mismatch between g77 an ifort
3518 o pkg/seaice: overhaul of thermodynamics
3519 - growth.F and groatb.F are replaced by new routine seaice_growth.F
3520 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
3521 - move a few global fields out of SEAICE.h into seaice_growth.F and
3522 make them 2D (FICE/QNETO/ ...)
3523 - remove FO (it is the same as QNETO)
3524 - introduce a few local fields to avoid modifying external fields such
3525 as atemp, etc.
3526
3527 checkpoint58s_post (2006/12/11)
3528 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
3529 changed exf_set_gen.F so that
3530 genperiod=0 means input file is one time-constant field and
3531 genperiod=-12 means input file contains 12 monthly means
3532 o CG2D: use pre-computed solver main-diagonal (stored in common block);
3533 this affects truncation error ; generate new output file for exp. which
3534 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
3535 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
3536 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
3537 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
3538 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
3539 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
3540 o start implementation of deep-atmosphere and anelastic formulation
3541 o verification: remove 2nd copy of input files and use script "prepare_run"
3542 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
3543 o mom_common/vecinv/fluxform: fix a few initialisation isssues
3544 o profiles: fix for multithreaded case
3545
3546 o diagnostics: rename few diags:
3547 s/'PRESSURE'/'RCENTER '/g
3548 s/'TICE '/'oceFreez'/g
3549 s/'TAUX '/'oceTAUX '/g
3550 s/'TAUY '/'oceTAUY '/g
3551 s/'SWFLUX '/'oceQsw '/g
3552 s/DIFx/DFxE/g
3553 s/DIFy/DFyE/g
3554 and add few ocean-forcing diagnostics:
3555 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
3556 o modifications to pkg/seaice/growth.F and budget.F, which change results of
3557 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
3558 as actual snow thickness. It now refers everywhere to effective snow
3559 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
3560
3561 checkpoint58r_post (2006/11/17)
3562 o modifications to pkg/seaice/growth.F, which change results of
3563 lab_sea experiment: fixes pertain to melting snow over open water, to
3564 masking EVAP under sea ice, and to using the correct AREA variable for
3565 computations of EVAP, PRECIP, HSNOW, and GHEFF
3566 o add ability to read bathy, salt, and theta using MNC (off by def)
3567 o add flooding algorithm and advection of HSNOW for pkg/seaice;
3568 both are turned off by default and do no change any results
3569 o seaice advection with pkg/thsice: a step toward the use of non-linear
3570 advection scheme, but #ifdef or commented out for now (requires more EXCH).
3571 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
3572 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
3573 in natl_box (affects results @ truncation level: update output.txt)
3574 o multi-threading and IO:
3575 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
3576 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
3577 (needed to work with SingleCpuIO): tested in all verif. exp.
3578 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
3579 affects the results (but none of the verification test uses this scheme).
3580 o Adding some pkg/diagnostics capability to pkg/seaice
3581 (will certainly be subject to changes)
3582 o ctrl: adding new control variables:
3583 lwflux, lwdown, evap, snowprecip, apressure, runoff
3584
3585 checkpoint58q_post (2006/10/20)
3586 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
3587 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
3588 high_res_cube configuration by 4% on Columbia.
3589 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
3590 add (in global_with_exf/code) a version of EXF_INTERP_READ without
3591 dynamical allocation (seems to work in multi-threaded).
3592 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
3593 single CPU io) so that TAF does not have to see EESUPPORT.h
3594 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
3595
3596 checkpoint58p_post (2006/09/08)
3597 o obcs: stop if obcs is used with useCDscheme = .true.
3598 o shelfice:
3599 - fix a sign error so that no slip at shelfice interface works
3600 - remove stop for combination non-hydrostatic code and shelfice. That does
3601 not mean, that the results are correct, but at least they are numerically
3602 stable
3603 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
3604 o added adjoint exch routined for all exch*3d* routines
3605 and updated flow directives
3606
3607 checkpoint58o_post (2006/08/28)
3608 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
3609 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
3610 o change controling S/R for writing pickup file (new S/R do_write_pickup)
3611 and clean-up reading/writing of pickup files.
3612 o fix local version of read/write pickup (NH part) in rotating_tank/code
3613 o simplify EXCH interface:
3614 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
3615 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
3616 o added the regrid package
3617 o shelfice:
3618 - add a simple boundary layer scheme to reduce noise
3619 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
3620
3621 checkpoint58n_post (2006/08/14)
3622 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
3623 local variable (not in common block).
3624 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
3625 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
3626 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
3627 to work with SingleCpuIO.
3628 o add "_d 0" to real constant of pkg/cfc subroutines ;
3629 update exp. cfc_exemple & tutorial_cfc_offline output files.
3630 o multi-threading and IO:
3631 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
3632 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
3633 - barrier before and after reading.
3634 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
3635 - avoid using MDS_WRITELOCAL for LAND pkg output.
3636 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
3637 common-block variables ; Allows multi-threading with master-thread IO.
3638 o change default MAX_NO_THREADS from 32 to 4 ;
3639 and stop cleanly when MAX_NO_THREADS is too small.
3640 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
3641
3642 checkpoint58m_post (2006/07/17)
3643 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
3644 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
3645 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
3646 keep global_ocean.90x40x15 (for AD testing) with former secondary test
3647 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
3648 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
3649 add MITgcm_tutorials (= code + all the tutorials)
3650 o ecco, option to compute cost for total ssh (mean+anom)
3651 o consistent with addition of ptracer and ssh in pkg/profiles
3652 o profiles: adding ptracer and ssh
3653 o testreport: change multi-test output-file name
3654 (from output.txt.{name} to output.{name}.txt)
3655 o profiles: now ok for mutli-tiles case
3656 o seaice: add 4 parameters for different advection schemes for area,
3657 (effective) seaice thickness, enthalphy, and snow height. Their default
3658 is the standard parameter SEAICEadvScheme
3659 o calc_gw:
3660 - add cosFacU in zonal viscous flux (harmonic.visc.).
3661 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
3662 of tutorial_plume_on_slope.
3663 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
3664 o calc_gw: true flux-form, account for horizontal grid spacing.
3665 update rotating_tank results, but not plume_on_slope (affected at
3666 truncation level, 11 digits).
3667
3668 checkpoint58l_post (2006/07/12)
3669 o calc_gw:
3670 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
3671 - remove side-drag for now (need to fix it); update plume_on_slope results.
3672 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
3673 o commit code to make SST/SSS weights spatially variable
3674 (based on either variable in-situ or variable initial T/S weights)
3675 o pkg/ecco:
3676 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
3677 now based on horizontally varying weights wthetaLev, wsaltLev
3678 * cost_averagesflags now returns year indices in addition to day, month
3679 * sflux balance is performed on annual basis
3680 (sflxumm, sfluxmm2, bal_sfluxmm)
3681 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
3682 including separate counting and multipliers
3683 o pkg/rbcs
3684 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
3685
3686 checkpoint58k_post (2006/07/06)
3687 o testreport:
3688 - always build in dir. "build" (if not there, mkdir build instead of building
3689 & running in input)
3690 - run in dir run (if it exists), in build otherwise.
3691 - call prepare_run (if input/prepare_run exists)
3692 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
3693 o pkg/exf modifications to interpolation and rotation routines for more
3694 reasonable treatment of North Pole singularity: for tracers North Pole
3695 value is set to northernmost zonal-mean value, for zonal velocity it is
3696 set to zero, and for meridional velocity it is set to northernmost value.
3697 o pkg/exf/exf_check_range.F
3698 - add tile index to diagnostics and move stop statement to the very
3699 end of the routine.
3700 o pkg/diagnostics: (diagnostics_main_init.F)
3701 define title of isomorphic variables according to the current config.
3702 o pkg/thsice with pkg/seaice dynamics:
3703 - fix domain of computation (interior only, required for exf) and do exchanges
3704 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
3705 o towards a standard way of dealing with multi-threading in MONITOR
3706 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
3707 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
3708 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
3709 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
3710 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
3711 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
3712 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
3713 o tracer advection:
3714 - clean-up and simplify calc_common_factors.F
3715 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
3716 advection subroutine (but still not used within DST advection S/R)
3717 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
3718
3719 checkpoint58j_post (2006/06/15)
3720 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
3721 from file (collects calls previously in FORWARD_STEP)
3722 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
3723 o adjoint store dir. adjusted accordingly
3724 o genmake2
3725 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
3726
3727 checkpoint58i_post (2006/06/14)
3728 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
3729 on wind stress (SEAICEstressFactor defaults to 1.)
3730 o Total number of Timers is finite (<=40): comment out 2 non-essential one
3731 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
3732 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
3733 on CS-grid: no longer loosing mass.
3734 o exf & curvilinear-grid: no longer modify longitude xC & xG.
3735 o pkg/ggl90: fix sloppy output and fix a bug
3736 o pkg/seaice: added SEAICEuseEVPpickup parameter
3737 - Set to false in order to start EVP solver with
3738 non-EVP pickup files when using SEAICEuseEVP
3739 - fix sign error in diffusion in seaice_calc_rhs
3740
3741 checkpoint58h_post (2006/06/07)
3742 * Modifications for bottom topography control
3743 o replace hFacC by _hFacC at various places
3744 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
3745 o add non-self-adjoint cg2d_nsa
3746 o update autodiff support routines
3747 o re-initialise hfac after ctrl_depth_ini
3748 o works for 5x5 box, doesnt work for global_ocean.90x40x15
3749 * Adding verification for 5x5 box (4-layer) bottom topography control
3750
3751 checkpoint58g_post (2006/06/07)
3752 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
3753 used for mean seasonal cycle, mean diurnal cycle); add an example
3754 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
3755 o pkg/ggl90:
3756 - add parameter (minimum surface kinetic energy)
3757 - fix bug (avoiding division by zero)
3758 o couple pkg/thsice to pkg/seaice:
3759 - modify advection in seaice to accomodate new scalar fields to be advected
3760 - only muliDimAdection scheme work with seaice/thsice
3761 - mapping of thsice-variables to seaice-variables, back and forth
3762 - does not break the verification experiments, but does not give the
3763 desired results either
3764 o pkg/seaice
3765 - make (default) second order advection a bit less confusing?
3766
3767 checkpoint58f_post (2006/06/05)
3768 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
3769 to pkg/seaice):
3770 - new routines thsice_map_exf and thsice_get_exf provide the interface
3771 - add an additional formal parameter to thsice_solve4temp
3772 o pkg/exf:
3773 - add new fields wspeed, snowprecip (to be able to couple to thsice)
3774 - correct Stefan-Boltzmann constant
3775 - new parameter for longwave surface emittance
3776 - separate some stuff from exf_bulkformulae into new routines
3777 exf_radiation, exf_wind
3778 - add new parameters and constants: longwave emissivity for ocean, ice
3779 and snow, evaporation parameters over ice
3780 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
3781 either wind from stress or stress from wind
3782 o pkg/thSIce:
3783 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
3784 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
3785 and THSICE_CALC_THICKN
3786 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
3787 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
3788 to make debugging easier.
3789 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
3790 o pkg/bulk_force:
3791 - clean-up comments and parameters ;
3792 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
3793 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
3794 generate new output for test-experiment: aim.5l_cs.thSI
3795 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
3796 testreport accordingly
3797
3798 checkpoint58e_post (2006/05/17)
3799 o SEAICE_CGRID adjoint done
3800 o R_STAR adjoint implemented.
3801 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
3802 * need to sort out init. of h0facc, etc.
3803 o Make pkg/profile fully independent of ecco,cost, etc. stuff
3804 to be able to use it in pure forward.
3805
3806 checkpoint58d_post (2006/04/21)
3807 o upgrade simple test-experiment to tutorial example:
3808 step.1: duplicate the experiment and (step.2) will remove the old copy.
3809 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
3810 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
3811 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
3812 tutorial_global_oce_biogeo <- copy of dic_example
3813 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
3814 tutorial_plume_on_slope <- copy of plume_on_slope
3815 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
3816 tutorial_global_oce_optim <- empty for now (David ?)
3817 tutorial_global_oce_in_p <- copy of global_ocean_pressure
3818 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
3819 o correct a sign problem in cost_scat.F
3820 o obcs and ptracers: fix boundary conditions for advections schemes
3821 with larger stencil
3822 o thsice adjoint: start
3823 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
3824 completeness
3825 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
3826 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
3827 o ptracers adjoint:
3828 * avoid extensive recomputatations
3829 * fix missing re-init. of gptr (missed by TAF)
3830 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
3831 me to turn off the excessive output to STDOUT that this package produces
3832 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
3833 and add those terms in Vector-Invariant formulation.
3834 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
3835 if the control period (xx_hfluxperiod etc) is 0
3836 o in profiles pkg, clean routines and fix details
3837 o in ecco pkg, reading ssh data:
3838 fix problem in case the model does not start at iter0=0
3839 o fix mnc-pickup/restart for ptracers
3840 o new package prifiles:
3841 code to compute profile-based cost by Gael Forget
3842 (modifs in ecco, ctrl, autodiff)
3843 o Benign bug fix in initialization (spotted by M. Mazloff) of
3844 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
3845
3846 checkpoint58c_post (2006/03/23)
3847 o adjoint: finish NLFS adjoint and provide reference output in
3848 verification/global_ocean.90x40x15/results_ad_nlfs
3849 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
3850 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
3851 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
3852 with SEAICE_CGRID defined.
3853 o move calendarDumps from "data" to "data.cal" and clean-up the code
3854 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
3855 o add useEXF & useCAL flags (for now, set in hard-coded way)
3856 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
3857 (were missing in NH mode, and wrong in quasihydrostatic mode).
3858 waiting for Chris updated version of calc_gw to add those CALLs.
3859 o fix bug in quasihydrostatic S/R ;
3860 add a test for this option: global_ocean.90x40x15.qshyd
3861 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
3862 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
3863 o add on/off flag useOffLine for package OFFLINE
3864 o seaice:
3865 - modify advection so that it works also on the C-grid
3866 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
3867 problem in multi-tile runs with C-grid
3868 - add flags for clipping ice velocities and/or masking solver forcing
3869 - fix drag (ocean on ice) formulation and a bug that caused noise in the
3870 C-grid solver
3871 - added a few comments to seaice_diffusion.F
3872 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
3873 are now exclusive)
3874 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
3875 required re-ordering the code a little:
3876 + make DAIRN global variable (defined in SEAICE)
3877 + move computation of the viscosities eta and zeta into a new separate
3878 routine (because I need to recompute them in seaice_ocean_stress.F)
3879
3880 checkpoint58b_post (2006/03/13)
3881 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
3882 update output.txt of exp. aim.5l_cs.thSI
3883 o various mnc cleanups and improvements:
3884 + shrink lookup tables by factor of ~4
3885 + better error reporting when running out of lookup space
3886 + able to handle longer path/file names (up to 500 chars)
3887 o adjoint:
3888 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
3889 - TBD: "hidden" mom_vecinv recomp. in dynamics
3890 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
3891 (allow to differentiate between forcing components using new integer flags:
3892 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
3893 and add new flag to put Dissipation tendency out of Adams-Bashforth.
3894 o ecco
3895 - enable trend removal from SSH anomaly obs.
3896 o adjoint
3897 - a fix for PmEpR when #undef EXACT_CONSERV
3898 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
3899 - try to fix "hidden" recomp. in forward_step for NLFS
3900 (NLFS seems broken sometimes after I checked it in)
3901 o seaice:
3902 - add c-grid version of the dynamic solver:
3903 + three new routines that are the c-grid substitute lsr, dynsolver
3904 and ostres
3905 + put a few fields that were local to dynsolver into global common
3906 blocks, so that I can move the computation of stresses etc into
3907 seaice_lsr (saves coding but may break the adjoint).
3908 - replace more hardwired parameters by runtime parameters
3909 - add ice masks that mask the rhs of the implicit solvers where there
3910 is no ice (commented out in seaice_dynsolver, because i am not sure
3911 if this works properly), eventually this should replace the clipping
3912 of ice velocities in seaice_dynsolver to +/-40cm/s.
3913 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
3914 include it only where its needed
3915 o move balancing of fluxes before the call of external_forcing_surf
3916 o seaice:
3917 - correct units of turning angles (now they are really in degrees)
3918 - move computation of GWATX/Y out of main routine into dynsolver
3919 - initialize GWATX/Y in seaice_init
3920 o Apply mask on Fresh-Water flux (needed for SSH forcing).
3921 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
3922 o seaice: add runtime flags for turning angles (default to zero)
3923 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
3924 and trend from exf forcing and ctrl control adjustments
3925 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
3926 (since checkpoint57x_post)
3927 o change the default rotation period to 86164.s = the Earth rotation
3928 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
3929 and based on a reference stratification. Tested within hs94.cs-32x32x5.
3930 o seaice advection: add code for choosing between the default (2nd order
3931 central differences) and multiDim advection schemes provided by
3932 pkg/generic_advdiff
3933 o seaice:
3934 - removed all references to SEAICE_GRID.h fields from
3935 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
3936 (cubed-sphere configuration will change a little)
3937 - grid computations in seaice_init are obsolete now.
3938 - cleaned up code a little so that is easier to read (hopefully).
3939 - added new (better?) discretizations of default advection and diffusion
3940 (turn on with SEAICEuseFluxForm)
3941 - replace 1 in 3d global fields by kSurface in growth.F
3942
3943 checkpoint58a_post (2006/02/13)
3944 o seaice:
3945 - bug fix in advect.F
3946 o shelfice:
3947 - separate shelfice load anomaly from pload (breaks with time
3948 dependent forcing), => introduce constant field shelficeLoadAnomaly.
3949 Its default is 0., but it may be computed more cleverly from (unknown)
3950 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
3951 done offline. A good approximation of the pressure load anomaly is
3952 necessary to avoid large initial adjustment processes underneath
3953 deep-reaching shelfice.
3954 - small fix in ISOMIP shelfice_thermodynamics
3955 - add more sophisticated thermodynamics of Hellmer (1989), this is
3956 now the default
3957 - give a few constants more intuitive names
3958 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
3959 if bulk formulae are used in long integration (especially EmPmR). Turn
3960 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
3961 if balancePrintMean, the imbalance that is substracted is printed to
3962 STDOUT.
3963 o fix bug (typo) in obcs_apply_eta.F
3964 o add a new package shelfice which enables us to model the circulation
3965 underneath shelf-ice with draughts of hundreds of meters.
3966 - works
3967 - to do: + include improved thermodynamics
3968 + check whether kSurfC (from model/inc/SURFACE.h) can be used
3969 instead of new field kTopC
3970 + can we use topoFile, Ro_surf and existing code in ini_depth.F
3971 instead of new field R_shelfIce and new code in ini_depth.F
3972 and ini_mask_etc.F?
3973 + adjust vertical mixing schemes?
3974 o seaice pkg:
3975 - add a cpp-flag to include a simple formula for a salinity dependent
3976 freezing point of sea water at the surface
3977 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
3978 meridional stresses are now different (and hopefully correct)
3979 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
3980 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
3981 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
3982 o pkg/diagnostics: add options and parameters for regional-statistics
3983 diagnostics ; define regions by reading a region-mask from a file
3984 (might add other options later)
3985 o pkg/bulk_force:
3986 - add option and parameters to use AIM surface-flux formulae.
3987 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
3988 others forcing fields (defined in PARM05, parameter file "data") are loaded
3989 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
3990 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
3991 - use the right EXCH call for uwind,vwind (to work on CS-grid).
3992 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
3993 and parameters (note: calcWindStress replaces .NOT.readwindstress).
3994 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
3995
3996 checkpoint58 (2006/01/12)
3997 o add "--embed-source" option to genmake2 which, when the supporting
3998 tools can be compiled (as determined by genmake2) will turn on the
3999 embed_files package which then embeds the entire MITgcm source code
4000 (*.[fFhc] + Makefile) used for the build within the executable
4001 - requested by CNH but off by default
4002 - adds a paltry <9MB to the mitgcmuv executable in most cases
4003 - only writes the output when useEMBEDSRC in eedata is true
4004 o clean up 3-dim. relaxation codes:
4005 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
4006 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
4007 * Thanks to Tom Haine for testing!
4008
4009 checkpoint57z_post (2005/12/31)
4010 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
4011 affects output (@ truncation level) of exp. plume_on_slope ; updated.
4012 o fix the pickup behavior for obcs in combination with ptracers
4013 o fix a bug in ptracers_external_fields_load
4014 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
4015 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
4016 o transfered surface NH pressure to eta field (if exactConserv).
4017 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
4018 and update lab_sea output.txt file.
4019 o completing 3-dim. relaxation code: additional term
4020 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
4021 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
4022 * At compile time, in "EXF_OPTIONS.h" set
4023 #define ALLOW_CLIMTEMP_RELAXATION
4024 #define ALLOW_CLIMSALT_RELAXATION
4025 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
4026 tauThetaClimRelax3Dim = 15552000.0,
4027 tauSaltClimRelax3Dim = 15552000.0,
4028 * 3 cases:
4029 1) Use a constant-in-time 3-dim. field
4030 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
4031 3) Real-time relax. to time-evolving prescribed field
4032 o Adding Laplacian-type smoothness constraint on
4033 initial and boundary (forcing) controls (ic, bc)
4034 * enable at compile-time via
4035 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
4036 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
4037 * Absolute scale somewhat unclear so far
4038 * no area weighting was included since no other cost term does so far
4039
4040 checkpoint57y_post (2005/12/08)
4041 First step for a NLFS adjoint
4042 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
4043 o new init. routines for calc_r_star, calc_surf_dr
4044 o still need to deal with ini_masks_etc
4045 o testreport seemed happy
4046 checkpoint57y_pre (2005/12/08)
4047
4048 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
4049 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
4050 o add new offset feature to offline pkg (plus minor cleanup)
4051 o cfc fixes for final year of integration
4052 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
4053 be in GCHEM_OPTIONS).
4054
4055 checkpoint57x_post (2005/12/04)
4056 o fix testreport Pb in multiple test experiment.
4057 o cleanup our namelist syntax in verification:
4058 - make it more F95 standards compliant (some work still needed)
4059 - allows the vast majority of our tests to work with gfortran
4060 o Non-Hydrostatic:
4061 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
4062 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
4063 o Allow to apply AB on T,S rather than on AB(gT,gS):
4064 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
4065 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
4066 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
4067 - need a "clever" read_pickup to restart from the other AB formulation
4068 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
4069 o remove some unused variables (reduces number of compiler warnings)
4070 o adjoint
4071 * Disable useVariableViscosity for adjoint for time being
4072 (there are a number of extensive recomputations)
4073 * Initialize certain variables needed for adjoint
4074
4075 checkpoint57w_post (2005/11/03)
4076 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
4077 fix the singleCpuIO RS version of MDSWRITEFIELD
4078 and add a WARNING if using globalFiles=T with multi-processors.
4079 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
4080 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
4081 o tracer advection scheme:
4082 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
4083 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
4084 was not very convenient).
4085 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
4086 (further tests needed for the implicit DST & Flux-Limiter schemes).
4087 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
4088 and sRef for convenience, handy, when you want to initialize
4089 ptracers in a large domain with a constant non-zero value. Also,
4090 untangle ptracers_init.F a little.
4091
4092 checkpoint57v_post (2005/10/13)
4093 o change dome exp. to use variable viscosity in side-drag terms.
4094 o remove all the files from the cfc_offline test since they are now
4095 incorporated into tutorial_cfc_offline which has been producing
4096 identical results for a few days of testing
4097 o add new parameter: sideDragFactor to enable half-slip-side BC
4098 and change side-drag S/R to use viscosity from mom_calc_visc
4099 (can switch back by setting sideDragFactor=0.); affects results at
4100 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
4101 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
4102 o vorticity & strain are now computed without masking, to account for
4103 no-slip-side BC in variable viscosity calculation ; mask is applied
4104 anyway later on, before computing advection/coriolis terms.
4105 o modify exp4 to test new obcs support for reading from external files
4106 and for passive tracers
4107 o fix behavior of ptracers_monitor when monitor output is written to a
4108 netcdf-file; still not independent of monitor.F (writes in the same
4109 file).
4110 o change default value of tRef (put a uniform, meaningful value for ocean
4111 & atmos) and initialize sRef (was missing, as Martin mentioned).
4112 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
4113 to be proportional to enstrophy dissipation length. Thus,
4114 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
4115 This is now consistent with Smagorinsky and with the manual.
4116
4117 checkpoint57u_post
4118 o OBCS and PTRACERS: add open boundary support for passive tracers
4119 - either use homogenous (pseudo) v.Neumann conditions or prescribe
4120 OB-values from file; this is not different from the way theta and salinity
4121 are treated
4122 - however, Orlanski-radiation conditions are not supported, and the model
4123 will stop if you use pTracers and Orlanski at the same time.
4124 - beefed up the rountine obcs_external_fields_load: now only those open
4125 boundary values are overwritten with values from files for which there
4126 are really files, otherwise the OB-fields remain untouched. This makes
4127 it possible to use different OBs at different ends of the domain (as
4128 with EXF)
4129 o reduce number of exch calls in shap_filt (s2).
4130 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
4131 truncation level) 4/5 MLAdjust test results (11&12 digits match).
4132
4133 checkpoint57t_post (2005/10/03)
4134 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
4135 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
4136 same truncation, independent of the face number: affects affects several
4137 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
4138 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
4139 note that biharmonic viscosity + no-slip was not tested in any experiment.
4140 o fix bug in non-linear free-surf side-drag ; generate new output for
4141 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
4142 o make mnc honor the writeBinaryPrec flag for most kinds of output
4143 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
4144 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
4145 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
4146 o add brackets in multi-terms sum to get same truncation, independent of
4147 the face number (manage to get exactly same value of gU,gV at the cs-edge)
4148 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
4149 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
4150 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
4151 a maximum grid-scale Reynolds number. Also, changes all length calculations
4152 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
4153 Suggested values of viscosity parameters found in mom_calc_visc.
4154 Many new viscosity diagnostics available.
4155
4156 checkpoint57s_post (2005/09/20)
4157 o Add clearing-house for viscosity calculations, mom_calc_visc and
4158 correct numerous bugs in LeithD and Smagorinsky discretizations.
4159 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
4160 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
4161 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
4162 and with Strain-Tension viscous term calculation (mom_hdissip.F).
4163 The Strain-Tension form is now called with useStrainTensonVisc=.true.
4164 ViscAhStrain and viscAhTension are now retired.
4165 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
4166 o In response to JMC's bug report, genmake2 now ignores any soft-links
4167 that it finds in the *current* directory when searching for files.
4168 Soft-links found in any other source directories will still work as
4169 they did before.
4170 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
4171 a C routine to unlimit the stack size
4172 o mnc-ify pkg/aim snapshot vars
4173 o mnc-ify pkg/land as requested by Daniel
4174 o various changes to mnc including:
4175 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
4176 - output can now be grouped so that all files within a group
4177 change the ITER portion of their names in lock-step together
4178 - can now read ("global") PER-FACE (in addition to PER-TILE) files
4179 and works with both EXCH1 and EXCH2 (but needs more testing)
4180 - writing works for all verification test cases w/ g77 on Linux
4181
4182 checkpoint57r_post (2005/09/07)
4183 o make MNC variable initialization happen earlier
4184 o add diagnostics for (almost) each term of the momentum Eq.
4185 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
4186 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
4187 o remove MINIMAL_TAVE_OUTPUT option ;
4188 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
4189 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
4190 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
4191 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
4192 o add time-dependent SST, SSS control
4193 o cost terms in ecco/ modularized (new cost_generic.F)
4194 o cost_averages routines are modularized (new cost_averagesgeneric.F)
4195 o new infrastructure for seaice model vs. obs misfits in seaice/
4196 * driver from the_main_loop.F is seaice_cost_driver.F
4197 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
4198 * gradient check in Exp. 6a of natl_box_adjoint/
4199 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
4200 (see README file)
4201
4202 checkpoint57q_post (2005/08/19)
4203 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
4204 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
4205 - bug was reported by Jean-Michel and Ian Fenty
4206 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
4207 update exp. cpl_aim+ocn output.
4208 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
4209 Needed for high-res. runs with large global files
4210 to be able to limit tapelev size
4211 o Changed some tests for adjoint:
4212 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
4213 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
4214 * global_ocean.90x40x15/ back to default 3-level checkpointing
4215 o Modifications to enable scripted COMMON to MODULE conversion
4216 * verification/OpenAD/code/ has necessary scripts and description;
4217 * converts, compiles and runs successfully;
4218
4219 checkpoint57p_post (2005/08/01)
4220 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
4221 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
4222 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
4223 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
4224 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
4225 (was already the case for dissipation with mom_vecinv,
4226 and also the case for grad.PhiHyd when staggered-timeStep)
4227 This will allow to put dissipation out-off the AB time-stepping.
4228 Unfortunately, affects truncation error. Update output of exp. that "fails"
4229 (cg2d matching number) and leave the others for later: front_relax(10),
4230 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
4231 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
4232
4233 checkpoint57o_post (2005/07/30)
4234 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
4235 (2) its ready to be documented during the 20050801 DocFest
4236 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
4237 for ideal_2D_oce and lab_sea on linux_ia32_g77
4238 o set to #undef CTRL_SET_OLD_MAXCVARS_30
4239 in global1x1_tot/code_seaice_adj to access indices 32, 33
4240 (worth another tag)
4241
4242 checkpoint57n_post (2005/07/29)
4243 o adding precip control xx_precip 32
4244 o adding swflux control xx_swflux 33
4245 o Replacing 10 forcing penalty cost routines by 1 generic.
4246 o Implementing partitioning in time-mean and variable adjustment
4247 for atmos. state.
4248 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
4249 o in natl_box_adjoint:
4250 * updated exp 1 to 10
4251 (but does not have time-mean vs. variable split results yet)
4252 o updated global1x1/*_seaice_adj/
4253 to incorporate latest changes
4254 o enable useSingleCpuIO for mdsio vector routines
4255 (applies in particular to tapelev I/O)
4256 o removed inefficient K-loop in all active_file*control*.F
4257
4258 checkpoint57m_post (2005/07/28)
4259 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
4260 and advect_cs (use EXCH-2 and standard cs-32 grid files).
4261 o pkg/exch2: filling of face-corner halo regions is optional
4262 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
4263
4264 checkpoint57l_post (2005/07/14)
4265 tag before updating tutorials (pre-release-2)
4266 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
4267 for output and interpolation of input fields onto model grid)
4268 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
4269 Affects results of exp. rotating_tank ; update output.txt.
4270 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
4271 and taking the square quantity and/or using a fraction-weight field.
4272 o fix aim_diagnostics_init.F mate numbers.
4273 o add mnc output capability to diagnostics/diagstat and update
4274 our cvsignore files for the ACSII output generated
4275
4276 checkpoint57k_post (2005/07/02)
4277 o lab_sea now uses diagnostics package and provides a suite of
4278 new EXF diagnostics output.
4279
4280 checkpoint57j_post (2005/06/30)
4281 o exf
4282 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
4283 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
4284 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
4285 * extended diagnostics output
4286 - now includes all EXF variables
4287 - hs, hl moved to common block
4288 - separate S/R for diagnostics, called after ctrl vector is added
4289 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
4290 - EXFqnet contains true Qnet (i.e. includes qsw)
4291 * updated verif. lab_sea, global_with_exf
4292 * Rearranging hflux (exf_mapfields -> exf_getforcing)
4293 to ensure that diagnostics sees a true EXFqnet
4294 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
4295 o diagnostics pkg: change pointers so that 1 diagnostic can be used
4296 several times with different frequencies.
4297 o mnc-ify the thsice package as requested by Daniel Enderton
4298 - the monitor--MNC output needs work
4299 - many attributes need to be added (most are currently blank)
4300 o mnc-ify theaim_v23 package as requested by Daniel Enderton
4301 - many attributes need to be added (most are currently blank)
4302 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
4303 o add Sadourny like discretization to the 4th.O vorticity advection scheme
4304 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
4305 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
4306 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
4307 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
4308 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
4309
4310 checkpoint57i_post (2005/06/19)
4311 o Diagnostics package was changed: diagnostic allocation is now deactivated
4312 by setting an empty file name in the namelist (used to be by setting 0 frequency)
4313 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
4314 add 1rst Order upwind vertical Shear.
4315 o add a quick fix for A/B checkpointing in OFFLINE mode
4316 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
4317 end-run around the C/Fortran linking horror in eesup/src/timers.F
4318 o added pkg/runclock: allows user to terminate run based on wall clock
4319 o added non-hydrostatic scaling parameter: nh_am2
4320 o pkg/my82: futile attempt to make results compiler-independent by adding
4321 some "_d 0", etc. no effect.
4322 o for mnc output, fill the 'T' coordinate var with myTime and create a
4323 separate 'iter' variable for iteration count
4324 o pkg/diagnostics:
4325 add new capability: output of Global/Regional & per-level statistics ;
4326 tested against monitor output (including land & thSIce) on various exp.
4327 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
4328
4329 checkpoint57h_done (2005/05/19)
4330 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
4331 data.diagnostics, data.gchem, data.ptracers) is done.
4332
4333 o pkg/diagnostics: prepare for Global/Regional statistics.
4334 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
4335 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
4336 and rename it: DIFFERENT_MULTIPLE
4337
4338 checkpoint57h_post (2005/05/14)
4339 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
4340 o pkg/diagnostics: change output frequency, now in seconds (instead
4341 of Nb of iterations). This requires to change data.diagnostics.
4342 checkpoint57h_pre (2005/05/12)
4343
4344 o in mnc, let the user create the output dir if both mnc_outdir_date
4345 and mnc_outdir_num are false
4346 o add fflags() to pkg/diagnostics which allows one to specify, on a
4347 per-file basis, the file precision [default behavior is unchanged]
4348 o added diagnostics to pkg/kpp, including computation of mixed layer
4349 depth based on a temperature/density criterion
4350 o updated verification/natl_box to test the new pkg/kpp diagnostics
4351 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
4352 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
4353 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
4354 not mnc -- this mistake was found by JMC and is now corrected
4355
4356 checkpoint57g_post (2005/04/15)
4357 o add Adams-Bashforth 3rd Order time stepping:
4358 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
4359 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
4360 checkpoint57g_pre (2005/04/15)
4361
4362 o make lambda[Theta,Salt]ClimRelax spatially varying
4363 (default remains spatially uniform constant based on tau)
4364 o added new control variables
4365 * init. uVel, vVel, etanN
4366 * lambda[Theta,Salt]ClimRelax
4367 o separate masks used for ctrl_pack/unpack 'from write_grid' output
4368 (suggested by G. Forget)
4369
4370 checkpoint57f_post (2005/04/06)
4371 o add parameter "baseTime" = model base time = time at iteration zero
4372 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
4373 account for baseTime shift
4374 o move Coriolis arrays from PARAMS.h to GRID.h
4375 checkpoint57f_pre (2005/04/06)
4376
4377 o mnc-ifying the seaice package
4378 o introduced an alternative length scale calculation for use in the limiting
4379 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
4380 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
4381 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
4382 as well as grad(vort3). Made it compatible with both approximate form
4383 for the cubed sphere and full form of these gradients. Added flag
4384 useFullLeith to select between approximate and full form.
4385 o add "d0" in getcon.F to reduce differences between compilers/platforms
4386 update output.txt of exp. fizhi-gridalt-hs
4387 o change port_rand funtion to allow to set the seed.
4388 o fix obscure MNC bug involving conversion between reals and integers
4389 - it caused no problems with certain (eg. gcc, ifc) compilers but the
4390 new version is now more standards-compliant
4391 o adjoint-related modifications
4392 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
4393 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
4394 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
4395
4396 checkpoint57e_post (2005/02/28)
4397 o Adding eddy stress controls a la Ferreira et al.
4398 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
4399
4400 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
4401 update output.txt of exp. fizhi-gridalt-hs
4402 o add more "Z" dimensions and associated coordinate vars to MNC
4403 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
4404 o parameter calendarDumps: when set, approximate months (30-31 days) and years
4405 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
4406 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
4407 months and years. Requires pkg/cal.
4408 o diagnostics: add pickup functionality
4409 - off by default for backwards compatibility
4410 - current version only uses MDSIO -- MNC will be added
4411 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
4412 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
4413
4414 checkpoint57d_post (2005/02/11)
4415 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
4416 o modify verification/ideal_2D_oce so that it tests the creation of mnc
4417 output from the diagnostics package
4418 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
4419 o make genmake2 more portable by using ".$FS" instead of ".f" for more
4420 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
4421 o add coordinate variables to the MNC output from the diagnostics package
4422 o change MNC-flags default value: true when useMNC=TRUE
4423 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
4424 the ability (off by default) to read the grid information using MNC
4425 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
4426 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
4427 o do snap-shot diagnostics at the middle of the time-interval (instead of
4428 at the end).
4429 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
4430 new test for AIM with thSIce + slab-ocean
4431 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
4432 o move state variable diagnostics to the beginning of the time step ;
4433 (note: still needs some work specially for snap-shot diagnostics)
4434 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
4435
4436 checkpoint57c_post (2005/01/27)
4437 o Change testing option (-ieee) to get closer agreement between g77 & ifort
4438 o generate new output.txt files on faulks with g77 & the new -ieee option
4439 checkpoint57c_pre (2005/01/27)
4440
4441 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
4442 update output.txt of exp. global_ocean.90x40x15
4443 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
4444 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
4445 o add saltFlux(+File) forcing capability with periodicExternalForcing
4446 o allow to use pkg diagnostics for GM-Redi & ThSIce output
4447 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
4448 o improvements for the MNC output from DIAGNOSTICS:
4449 - correct handling of the unlimitied dimension
4450 - all dims now have associated coordinate variables
4451 - variables located at U, V, and Corner ("Z") points are now written
4452 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
4453 *all* data points are output
4454 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
4455 o added pkg/seaice/seaice_monitor.F
4456 o mdsio_readfield.F can now read files visible only to master MPI process.
4457 o pkg/seaice: some test code for ice-modified ocean stress
4458 o exf_getffields interpolation defaults to bilinear for all scalar forcing
4459 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
4460 spurious negative numbers for precipitation and humidity. Will cause
4461 some small numerical differences for integrations using pkg/exf/exf_interp.F.
4462 o pkg/ctrl/
4463 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
4464 May be enabled via doPackDiag
4465 * introduce z-scaling of
4466 + gradient (doZscalePack) and
4467 + control (doZscaleUnpack)
4468 o pkg/mdsio/
4469 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
4470 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
4471
4472 checkpoint57b_post (2004/12/20)
4473 o simplify options in diagnostics_fill arguments (remove weird combinations)
4474 o fix MNC coordinate variables so that they now contain per-face index
4475 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
4476 general, EXCH2 grids are only aligned to a "local" coordinate system
4477 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
4478 o Implement instantaneous output within pkg diagnostics:
4479 setting a negative frequency in data.diagnostics produces
4480 "snap-shot" output (as opposed to time-average if freq > 0)
4481 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
4482 NOTE: change ptracer diagnostics name: use 2 characters to work with
4483 more than 9 tracers. Add also diagnostics of advect & diffus flux.
4484 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
4485 becomes the coordinate variable for the 'T' dimension
4486 o add CF-style coordinate variables to MNC
4487 - just a first cut: numbers are meaningless on the cubesphere and
4488 missing along the T axis but otherwise it works!
4489 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
4490 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
4491 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
4492 this is based directly on what the model compute, so that the content of
4493 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
4494 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
4495 o clean up build options files for SunOS, in particular
4496 - remove -traditional from xmakedepend
4497 - change -xarch=v9 to -xarch=native for f77
4498 - restore use of make (not gmake)
4499 - add CC=gcc if using g77
4500 o changes per discussion of AM, JMC, & EH3 today:
4501 - move redundant "grid" variables out of "state" -- in preparation of
4502 creating proper CF-style coordinate variables and in recognition
4503 that any/all grid variables can be easily copied (eg. w/NCO) from
4504 the grid files into any of the other NetCDF files
4505 - *always* output grid variables with MDSIO (this will eventually be
4506 changed)
4507 - output MNC grid file if useMNC is true
4508 o every instance of _END_MASTER() has been found and replaced with
4509 _END_MASTER( myThid ) in order to satisfy certain picky Sun
4510 preprocessors
4511 o re-arrange diagnostics pkg initialisation:
4512 - allow each package to extend the available diagnostics list
4513 - add some checking and fix small problems (multi-threaded, ...)
4514 - new S/R diagnostics_fill (replace fill_diagnostics):
4515 look through the short list of active diag. (instead of the long list)
4516 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
4517
4518 checkpoint57a_post (2004/12/10)
4519 o this set of changes restores TAMC compatibility
4520 tested for global_ocean.90x40x15 adjoint on trough
4521 (what a pain)
4522
4523 checkpoint57a_pre (2004/12/10)
4524 o some modifs in tools/build_options for sunos
4525 o call ctrl_pack for ctrl at end for optimcycle=0
4526
4527 checkpoint57 (2004/12/09)
4528 o add horizontal bi-harmonic viscosity for vertical velocity
4529 - new parameter viscA4W (defaults to viscA4)
4530 - affects only non-hydrostatic code
4531 - to be done: no-slip lateral boundary conditions
4532 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
4533 o implement Implicit Vertical advection for pTracers
4534 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
4535 (implemented also for implicit vertical diffusion & advection)
4536 o OBCS: extend application of tracer open boundary conditions
4537 to a strip beyond the boundary of width Olx/Oly
4538 o add call monitor to TAF set of required calls (flow directives)
4539 and include in natl_box_adjoint
4540 o untangle a few ifdefs related to cost, ctrl, autodiff
4541 untangel a few ALLOW_ECCO_OPTIMIZATION
4542 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
4543 (theta2, salt2 in ecco_cost_weights)
4544
4545 checkpoint56c_post (2004/12/03)
4546 o OBCS as control variables
4547 - update ctrl_ad_diff.list, obcs_ad_diff.list
4548 - remove balance of obcs controls from default
4549 - fix index bug nobcs in ctrl_init
4550 - fix dummy fields filen in ctrl_pack
4551 - add dummy weights for obcs
4552 o lsopt: comment out fort.94 output
4553 o optim:
4554 - remove unnecessary header files
4555 - adjusted namelists
4556 - add xerbla.F to Makefile
4557 o exf:
4558 - multiple modifications of exf_check_range
4559 - unit change in exf_init_runoff from [m/year] to [m/s]
4560 o mdsio:
4561 - i/o-vector change debugLevel from debLevA to debLevB
4562
4563 checkpoint56b_post (2004/12/01)
4564 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
4565 is called from DO_THE_MODEL_IO
4566 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
4567 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
4568 - clean up PTRACERS_WRITE_TIMEAVE a little
4569 o add another verification experiment that tests both the cfc-pkg and
4570 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
4571 reactive tendencies treated inline with regular timestepping
4572 o testreport previously did a lousy job of comparing small numbers, so
4573 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
4574 implemented in the little c-progam tmp_cmpnum.c which is embedded in
4575 testreport.
4576 o ptracers_monitor: bug fix for MPI
4577
4578 checkpoint56a_post (2004/11/28)
4579 o GCHEM: finish reorganizating the package
4580 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
4581 (introduces another 3D-array for each passive tracer, but only if
4582 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
4583 gchemTendency is not needed because the timestep is done separately)
4584 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
4585 - GCHEM is now---more or less cleanly---separate from PTRACERS
4586 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
4587 so clear to me how that should be done in a general way.
4588 o CFC: improve formatting of output in CFC_ATMOS
4589 o PTRACERS:
4590 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
4591 that ALL experiments with ptracers enable can be checked. This makes
4592 GCHEM_MONITOR obsolete.
4593 - include a runtime parameter PTRACERS_monitorFreq that defaults to
4594 monitorFreq
4595 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
4596 o add PTRACERS (PTR0[1-5]) to testreport output
4597 o exf_check_range:
4598 * default changed to .TRUE.
4599 * will check values for niter0 if debLevA, every timestep if debLevB
4600 * STOP in exf_check_range if 'out of range'
4601 * range chosen generous to allow for potential extema
4602 TBD: a version with stricter range
4603 permitted range would be runtime parameters
4604 o GMredi:
4605 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
4606 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
4607 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
4608 o GCHEM:
4609 - move call to GCHEM_FORCING_SEP, so that it is now called before
4610 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
4611 - introduced a useGCHEM runtime flag and applied it everywhere.
4612 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
4613 this flag is now only visible within GCHEM-pkg routines.
4614 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
4615 be replaced by a 3D array that is computed before thermodynamics; for
4616 this, the tracer ID iTracer had to be included into the parameter list
4617 of ptracers_forcing
4618 - set up forward_step to call gchem_forcing, that will replace
4619 gchem_forcing_int in ptracers_forcing
4620 - cleaning up
4621 o small cleaning of exch2: remove files that are also in eesupp/src
4622
4623 checkpoint56 (2004/11/17)
4624 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
4625 o mnc: cleanup "full" files--fixes out-of-memory problem
4626 o ECCO-GODAE
4627 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
4628 * fully merged and updated from SIO code
4629 windstress sign change affects
4630 - exf_inscal_[u/v]stress
4631 - sign of xx_tau[u/v] adjustments
4632 - signs in cost_scat
4633 * ctrl_get_gen: avoid update of tau[u/v] for first few days
4634 * natl_box_adjoint updated and compressed
4635 * 2-level checkpoint switch added
4636 (tested in EXP. 1 of natl_box_adjoint)
4637 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
4638 o SVD
4639 * first complete, non-hacked version for SVD calculations
4640 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
4641 performed via direct access files admtlm_vector.it????
4642 (via ctrl_[un]pack)
4643 * optimcycle is used for ARPACK iteration counter
4644 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
4645 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
4646 and add linear transforms where necessary
4647 * controls are initial/final SST, SSS (can be extended; need to check
4648 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
4649 o mdsio: filename info to both stderr, stdout
4650 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
4651 from sign change
4652
4653 checkpoint55j_post (2004/11/10)
4654 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
4655 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4656 o add consistent build directories and .cvsignore files to verification
4657 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
4658 o make all subroutines 30 or less characters in length for certain older
4659 compilers to work (a thorough search only turns up two routines in
4660 pkg/ptracers)
4661 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
4662 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
4663
4664 checkpoint55i_post (2004/10/28)
4665 o change arrays for total vertical diffusivity (2.D if explicit,
4666 3.D if implicit) ; each ptracer uses its own background value.
4667 o added mnc/NetCDF output capability to ocn_compon_interf
4668 - added bits to verification/cpl_aim+ocn so that it can run on
4669 ITRDA and other clusters without the mpirun "-wd" option
4670 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
4671 configuration
4672 o give MNC the ability to create additional files rather than
4673 exceeding a specified file size limit "MNC_MAX_FILESIZE"
4674 - the default is just less than 2GB which is a practical limit
4675 on many systems
4676 o Compute the non-local term using either KPP vertical diffusivity (=default)
4677 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
4678
4679 checkpoint55h_post (2004/10/20)
4680 o add verification test "vermix"
4681 o remove all the *_ioinc flags and replace with the single global
4682 outputTypesInclusive flag
4683 o allow to set a vertical profile of vertical diffusivity for T & S
4684 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
4685 o useMNC moved from data.mnc to data.pkg
4686
4687 checkpoint55g_post (2004/10/14)
4688 o Renaming carbon AD experiments to comply with testreport conventions
4689 o Updating adjoint of Held-Suarez hs94.1x64x5
4690 o Fixing directives for non-ECCO forward_step, after ECCO directives
4691 have been fixed to avoid recomp. of do_oceanic_phys
4692 Works well for global_ocean.90x40x15,
4693 but recomp. issue remains for carbon
4694 o Updating adjoint output for natl_box_adjoint after
4695 pkg/ecco has been modified (see taga c55d_post)
4696
4697 checkpoint55f_post (2004/10/13)
4698 o rename to timeave_init_fixed
4699
4700 checkpoint55e_post (2004/10/13)
4701 o some delicate re-shuffle of store directives to avoid one
4702 extra call of do_oceanic_physics
4703 affects ecco_the_main_loop.F, do_oceanic_physics.F
4704 checkpoint_lev1_directives.h
4705 o NB: this may break global_ocean adjoint temporarily,
4706 but it is clear how to fix it. Will do later, need this now.
4707
4708 checkpoint55d_post (2004/10/11)
4709 o ECCO specific cost function terms (up-to-date with 1x1 runs)
4710 o ecco_cost_weights is modified to 1x1 runs
4711 o modifs to allow observations to be read in as
4712 single file or yearly files
4713 o enable to read exf forcing fields as either
4714 single file or yearly files (flag useExfYearlyFields)
4715 checkpoint55d_pre (2004/10/08)
4716
4717 o switch between 2-level and 3-level checkpointing
4718 o add ability of MNC to write local and "partial" (eg. 2D slices where
4719 the full 3D field is never actually stored) arrays to NetCDF files
4720 with the correct (that is, the complete multi-dimensional) set of
4721 array indicies
4722 - used in mom_vecinv() to write the diagFreq output
4723 - tested (demonstrated) in verification/aim.5l_cs
4724 o further mnc-ification
4725 - add verification/lab_sea to the list with mnc setups
4726 - fix undefined mnc v-names in cd_code
4727 - add kpp to mnc output (both snapshot and timeave)
4728 o non-hydrostatic code
4729 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
4730 in calc_gw.F
4731 - defaults to viscAh
4732 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
4733 friction or Leith) in non-hydrostatic mode, as long as there is
4734 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
4735 o pkg/cost
4736 extend simple cost functions to treat time mean quantities
4737 (T,U,V) via cost_accumulate_state from cost_tile
4738 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
4739 be 2 times larger than the minimum size the advection scheme requires.
4740 now get a perfect conservation of salt in advect_cs test-exp (updated)
4741 o GGL90 (Gaspar's TKE mixed layer)
4742 - add horizontal diffusion of TKE, requires exchanges in
4743 do_fields_blocking_exchanges, horizontal diffusivity is zero by
4744 default. In OPA there is no horizontal diffusion of TKE but the
4745 mixing coefficients are computed from a horizontal average of TKE of
4746 6 points or so. I think that diffusion has a little more physical
4747 justification.
4748 - clean up ggl90_calc in the hope of reducing memory usage (this hope
4749 was in vain)
4750 - mask tke-variable in ggl90_init
4751 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
4752 o fix biharmonic diffusion on CS-grid.
4753 o more obcs stuff
4754 - added obcs_external_fields_load as an alternative to the EXF-pkg option
4755 for reading boundary values. This routine is called from
4756 obcs_prescribe_read
4757 - updated obcs_check
4758 - changed sponge layer relaxation parameter units for days to seconds
4759 - turned off sponge layer by default
4760 - changed argument list of OBCS_CALC to myTime+deltaTclock
4761 - fixed about 35 bugs in obcs_external_fields_load
4762
4763 checkpoint55c_post (2004/09/23)
4764 o obcs stuff
4765 - new runtime flags useOBCSprescribe, useOBCSbalance
4766 - re-arranged obcs_calc
4767 - moved exf_getobcs to obcs_prescibe_read
4768 obcs_prescibe_read is called after ORLANSKI stuff
4769 and independent of it (executable can contain all).
4770 - updated obcs_check
4771 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
4772 These may be necessary only if tangential velocities are
4773 prescribed at OB, not sure, needs testing.
4774 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
4775 which simplifies the calls and passes the ifc check-bounds test
4776
4777 checkpoint55b_post (2004/09/22)
4778 o add a 2D scalar, Z location, exchange_2 routine.
4779 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
4780 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
4781 affects advect_cs results (for the wrong reason): update output.txt
4782 o use a more standard discretization for biharmonic viscosity ;
4783 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
4784 affects results of dome set-up: update output.txt
4785 o fix gad_advection.F (CubedSphere part), back to version 1.23
4786 o fix bug in mom_vi_del2uv.F (CubedSphere part).
4787
4788 checkpoint55a_post (2004/09/20)
4789 o merged code to
4790 * prescribe/read time-dependent open boundaries
4791 (works in conjunction with exf, cal)
4792 * sponge layer code for open boundaries
4793 * each boundary N/S/E/W now has its own CPP option
4794 (healthy for the adjoint)
4795
4796 checkpoint55 (2004/09/17)
4797 o up-to-date adjoint of previous breaks
4798 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
4799 - global_ocean_ebm: adjoint still needs fix (TLM ok)
4800 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
4801 - carbon: * remove tr1-related adjoint verification
4802 * add ptracer as control variable
4803 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
4804 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
4805
4806 checkpoint54f_post (2004/09/16)
4807 o in verification/carbin/ remove experiment related to
4808 ALLOW_PASSIVE_TRACER (array tr1 etc)
4809 code_ad/ input_ad/ results_ad
4810
4811 o add two new packages
4812 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
4813 + subject to optimization (memory)
4814 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
4815 + subject to reordering (many GOTOs in the original code)
4816 + so far opps is called for every (i,j) point, and then operates in
4817 the vertical; one may want to reorder the scheme in order operate in
4818 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
4819 fields)
4820 o overhaul of IO so that we now have flags for MDSIO and/or MNC
4821 - all verification tests compile and run with linux_ia32_g77
4822 - defaults are compatible with current input files--nothing
4823 should change if you were not previously using MNC
4824 - MNC output has been added in numerous places (eg. timeave)
4825 but there are still a few writes not yet do-able with MNC
4826 (this is in progress)
4827 - flags now allow for either/or/both use of MDSIO and MNC and
4828 documentation will soon follow
4829 - numerous small formatting cleanups for ProTeX
4830 o add version info (via BUILD_INFO.h) to MNC and stdout
4831
4832 checkpoint54e_post (2004/09/02)
4833 o add two new packages
4834 - pp81 (Packanowski and Philander, 1981), Richardson number and
4835 stratification dependent mixing
4836 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
4837 - these scheme operate in a similar manner as KPP (without ghat, of
4838 course), however there is only one diffusivity that is used for both
4839 temperature and salinity (and passive tracers)
4840 o add offline package
4841 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
4842 provided by Stephanie Dutkiewicz
4843 o genmake2: add ability to search for C compilers and cleanup test output
4844 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
4845
4846 checkpoint54d_post (2004/07/27)
4847 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
4848 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
4849 leading to additional shift by 5 days each year of integration
4850 (i.e. leading to considerable offset over the years)
4851 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
4852 o start with no AB and no initial filtering (staggerTimeStep):
4853 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
4854 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
4855 (external loading & cpl import/export stay in forward_step.F)
4856 o update coupling interface to work with new staggerTimeStep
4857 o change MDSIO ptracers_pickup.
4858 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
4859 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
4860 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
4861
4862 checkpoint54c_post (2004/07/18)
4863 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
4864 this affects (truncation error) output.txt of test-exp:
4865 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
4866 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
4867 o change Qnet to always be the net heat flux, (+upward).
4868 affects (truncation error) output of natl_box exp.: updated
4869 o define the max number of passive tracers in PTRACERS_SIZE.h
4870 o start to test mnc routinely in exp0
4871 o add sea-ice loading (sIceLoad) as a new forcing field.
4872
4873 checkpoint54b_post (2004/07/08)
4874 o add testreport "-j JOBS" option for parallel builds (tested and pretty
4875 impressive on Altix and Opteron systems)
4876 o diagnostics can now write NetCDF files through the mnc package
4877 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
4878 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
4879 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
4880 affects (truncation error) output of lab_sea & natl_box exp.: updated
4881 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
4882
4883 checkpoint54a_post (2004/07/06)
4884 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
4885 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
4886 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
4887 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
4888 + internal_wave (shift in writing cg2d_ini_res)
4889 checkpoint54a_pre (2004/07/05)
4890
4891 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
4892 - modified verification/lab_sea and natl_box_adjoint accordingly
4893
4894 checkpoint54 (2004/07/02)
4895 checkpoint53g_post (2004/07/02)
4896 o prepare splitting of thermodynamics: store convect.counter in common block
4897 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
4898 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
4899 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
4900 o new parameter "nShapS": allow to treat differently S from T (nShapT)
4901 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
4902 o restore adjointability
4903
4904 checkpoint53f_post (2004/06/25)
4905 o modifications that affect AIM experiment results (update output.txt):
4906 - no advection of S at top interface Nr (pkg/generic_advdiff)
4907 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
4908 o AIM pkg:
4909 - include stability function into surf.Flux derivative relative to Tsurf
4910 - calculate clear-sky radiation & surface temp. change (for diagnostics)
4911
4912 checkpoint53e_post
4913 o merged cylindrical coord configuration
4914 o added rotating_tank experiment
4915 checkpoint53e_pre
4916
4917 checkpoint53d_post (2004/06/14)
4918 o faulks upgraded: re-generate output.txt that have changed:
4919 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
4920 o Added Bryan and Lewis, 1979, vertical diffusivity profile
4921 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
4922 o added Sadourny discretization of Coriolis
4923 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
4924 - re-enabled use of omega3 (useAbsVorticity)
4925 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
4926 vector-invariant equations
4927 - note: does *NOT* yet use same variable visc. for no-slip BC's.
4928 o recoded the lateral boundary conditions for non-hydrostatic w, this time
4929 hopefully without new bugs
4930 - still to do: biharmonic friction for non-hydrostatic w
4931 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
4932 o regenerated output for global_ocean_ebm (using -ieee)
4933 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
4934 of mom_common/
4935 - simple re-arrangement of instructions within computing loop
4936 checkpoint53d_pre (2004/05/21)
4937
4938 checkpoint53c_post (2004/05/21)
4939 o new version of coupler for AIM+thSIce and Ocean models
4940 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
4941 - land: change Evaporation of snow
4942 - aim with thSIce: fix bug in snow-precip.
4943 o changes to calc_gw.F
4944 - bug fix for w^2 term near the bottom boundary
4945 - (hopefully) improve the lateral slip boundary condtions for use with
4946 partial/looped cells
4947 - because the bug fix changes two verification experiments anyway (exp5
4948 and plume on slope), change the lateral boundary condition from half slip
4949 to the value of no_slip_sides
4950 o ebm package wasnt quite up to the parallel task. Fixed that.
4951 o Adjoint of EBM package + verification
4952 * TLM OK
4953 * ADM not sufficient accuracy yet (needs further testing)
4954
4955 checkpoint53b_post (2004/05/14)
4956 o Commiting new energy balance model to repository
4957 * package is pkg/ebm
4958 * verif. is verification/global_ocean_ebm
4959 * references are in ebm_driver.F
4960 C * X. Wang, P. Stone and J. Marotzke, 1999:
4961 C Global thermohaline circulation. Part I:
4962 C Sensitivity to atmospheric moisture transport.
4963 C J. Climate 12(1), 71-82
4964 C * X. Wang, P. Stone and J. Marotzke, 1999:
4965 C Global thermohaline circulation. Part II:
4966 C Sensitivity with interactive transport.
4967 C J. Climate 12(1), 83-91
4968 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
4969 C Destabilization of the thermohaline circulation
4970 C by atmospheric eddy transports.
4971 C J. Climate 7(12), 1870-1882
4972 o Will need long integration testing.
4973 checkpoint53b_pre (2004/05/14)
4974
4975 o created pkg/mom_common in preparation for variable viscosity code
4976 o renamed and split ini_mnc_io
4977 o pkg/land: only liquid water can diffuse or run-off
4978 o AIM using land: soil wetness availability account for snow
4979 o added printMapIncludesZeros to EEPARMS namelist
4980
4981 checkpoint53a_post (2004/05/11)
4982 o restore TAMC compatiility for exf_constants.h
4983 (no usage of _d in .h)
4984 o Additional storing in KPP in an attempt to fix
4985 TAMC problem with adjoint of KPP code.
4986 (no success...)
4987 Identical code works fine with TAF.
4988 o Fixed verification/natl_box_adjoint experiments.
4989 Initial conditions for Experiments 4 and 5 are now
4990 set to "SEAICE_initialHEFF=0", which is more reasonable,
4991 and hence gives results closer to that of Experiment 2.
4992 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
4993
4994 checkpoint53 (2004/05/06)
4995 o stable checkpoint with up to date adjoint
4996 TLM tests only run for 1st grdchk at the moment. Its unclear if
4997 this is a code problem or a problem with resetting code for g_
4998 variables that is being autogenerated wrong.
4999 Otherwise:
5000 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
5001 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
5002 are both still in chaos following their security messes.
5003
5004 checkpoint52n_post (2004/05/06)
5005 o various build (mostly genmake2) changes including:
5006 - ability to build/run more easily within Cygwin and MacOS X
5007 - more complicated Makefiles with a stronger dependence on Gnu Make
5008 o pkg/seaice modifications
5009 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
5010 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
5011 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
5012 - changed proxy for geostrophic velocity and updated
5013 verification/lab_sea/results/* accordingly
5014 - removed ADI dynamic solver from pkg/seaice
5015 - replaced all occurrences of 1/CSTICE or 1/CSUICE
5016 they caused a segmentation fault under certain circumstances
5017 - removed unused field WATR
5018 o bug fix in exf-package:
5019 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
5020 now reflect that.
5021 o small fixes in the cal-package:
5022 - set reference date to first of January for the 'model'-calendar
5023 - failing of cal_CheckDate in cal_FullDate now actually results in a
5024 warning
5025 o small modifications in exf-package to increase flexibility:
5026 - change climtempfreeze from a constant to a runtime parameter that
5027 is specified in data.exf_clim (default = -1.9)
5028 - introduce runtime parameter windstressmax (default = 2.0) that is
5029 specified in data.exf
5030 o fix in pkg/thsice:
5031 - update Evap (Tsf changes) to be consistent with Latent heat flux
5032 - maintain snow precipitation unchanged (even if Tsf >=0).
5033 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
5034
5035 checkpoint52m_post (2004/04/18)
5036 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
5037 this does not change any of the results, because myIter=0 in swfrac always
5038 lead to jwtype=2 (the default anyway), but the call makes little sense
5039 as a default
5040 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
5041 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
5042 atmospheric model (AIM) to use it ; add a "slab ocean" component.
5043 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
5044 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
5045 o extending useSingleCpuIO option to work with new exch2 I/O format
5046 - old-style, missing-tile I/O is still accessible by defining CPP
5047 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
5048 o monitor package can write to NetCDF files and/or STDOUT
5049 o fix re-definition bug in MNC_GRID_INIT_ALL()
5050 o doc/api_reference added
5051 - a framework for building an API Reference Manual using all
5052 the "protex" comments embedded in the code
5053 - see pkg/generic_advdiff, pkg/mnc for examples
5054 o MNC:
5055 - make myThid the last argument for all subroutines
5056 - new default for the grid files: NO halos
5057 - add useMNC and other run-time flags
5058 - separate per-file-group handling of the unlimited dimension
5059 - early initialization of MNC w/ flags read at the eeboot stage
5060 and lookup tables set in initialize_fixed
5061 - write all MNC output to a freshly-created directory
5062 o thermodynamics sea-ice (thsice) is now tested with testreport.
5063 o test exp. advect_cs: use the standard cs32 grid ; update output.
5064 o Added functionality to grdchk:
5065 pick global i,j,k position (or nearest wet) where to perform check.
5066
5067 checkpoint52l_post (2004/03/11)
5068 o new land formulation:
5069 a) use ground enthalpy as prognostic variable to ensure exact
5070 energy conservation.
5071 b) account for water temperature and for latent heat of freezing
5072 in all processes (rain, run-off, ground storage)
5073 c) compute surface and ground temperature implicitly.
5074 o aim_v23 modification for new land model:
5075 a) Treat separately land / ocean / sea-ice surface fluxes
5076 to allow implicit computation of land & sea-ice surface temp.
5077 b) add snow precipitation.
5078 checkpoint52l_pre (2004/03/11)
5079
5080 o fix problem (when 1 tile is empty) in min/max monitor.
5081 o fix bug in timeAve (u,vZetatave in common block)
5082 o no restoring terms under ice for pkg/seaice
5083 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
5084 o bug fix for pkg/seaice pickups
5085 o change MNC call locations and add coordinate attributes
5086 o mask vorticity at the corner ; affects global_ocean.cs output
5087 o fix ini_curvilinear_grid ; test CS experiments with mpi
5088 o aim.5l_cs: modify sea-ice fraction input file ; update output
5089 o exf: Adding simple range check routine for exf fields after read
5090
5091 checkpoint52k_post (2004/02/23)
5092 o removed top-level directory "diags"
5093 - we migrated these functions to pkg/timeave a long time ago
5094 o fixed bug introduced in pkg/monitor
5095 o accuracy ctrlprec = 32 insuffient for gradient checks using
5096 averaged fields (I/O via cost_averages)
5097 -> use ctrl.h in active_file*.F to control I/O precision.
5098 o paramter list of CALL ADTHE_MAIN_LOOP
5099 o added initial do_the_model_io to ecco
5100 o set all ...Freq to zero after cost_final
5101 taveFreq, dumpFreq, pChkptFreq
5102 o MAIN and ECCO differentiability restored
5103
5104 checkpoint52j_post (2004/02/18)
5105 o fix nchklev in tamc.h for global_ocean...
5106 o Bringing flow and store directives up-to-date
5107 o Really weird thing!
5108 call do_the_model_io from the_main_loop with parameters
5109 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
5110 TAF places a faulty re-call of initialise_varia
5111 after cost_final call which should not be there!
5112 checkpoint52j_pre (2004/02/03)
5113
5114 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
5115 error messages
5116 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
5117 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
5118 debug output
5119 o modfied mdsio_writefield.F to handle non-global files under exch2
5120 o update AIM Cubed-Sphere exp (aim.5l_cs):
5121 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
5122 o update AIM Equatorial Channel exp:
5123 use standard aim_v23 pkg and change the SST fields to be more realistic.
5124 o globalFile now works with exch2
5125 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
5126 mon_vort3.F to make exch2 friendly with >1 tile per cube face
5127 o limit timeave output for hi-res integrations
5128
5129 checkpoint52i_post (2004/01/21)
5130 o removed CPP_EEOPTIONS.h from verification/*/code
5131 o updated the tiling for global_ocean_pressure
5132 checkpoint52i_pre (2004/01/20)
5133
5134 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
5135 the old pkg/aim).
5136
5137 checkpoint52h_pre (2004/01/20)
5138 o shortened offending lines in exch2_send_rx?.template
5139 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
5140 o genmake2: add build & execute test for NetCDF code
5141 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
5142 old grid files, moved CPP_EEMACROS.h to pkg/exch2
5143 o added useSingleCPUIO flag to monitor.F and mon_out.F
5144 o added temporary hack for sea-ice dynamics on the cube:
5145 metric terms are ignored and it is assumed that
5146 there is no sea-ice on cube faces 1, 2, 4, and 5.
5147
5148 checkpoint52f_post (2004/01/09)
5149 o added exch2 cube routines to pkg/exch2
5150 o modified hs94.cs-32x32x5 to use it
5151 o added new grid files to hs94.cs-32x32x5
5152 checkpoint52f_pre (2004/01/07)
5153
5154 checkpoint52e_post (2004/01/07)
5155 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
5156 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
5157 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
5158 to work with implicit vertical advection and AB ;
5159 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
5160 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
5161 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
5162 checkpoint52e_pre (2004/01/02)
5163
5164 o fix bug in impldiff when Nr=1 or Nr=2.
5165 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
5166 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
5167 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
5168 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
5169 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
5170 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
5171 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
5172
5173 checkpoint52d_post (2003/12/16)
5174 o re-tiled many expts to allow comparison in multi-processor mode
5175 - updated output accordingly
5176 - changed hs94.128x64x5 to use intial T from file rather than use the
5177 random number generator
5178 o add infrastructure in model routines for fizhi and gridalt packages
5179 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
5180 o changes to permit hi-res, cubed-sphere, configuration
5181 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
5182 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
5183 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
5184 of surface winds for the cube
5185 (A verification experiment, based on global_ocean.cs32x15, but with
5186 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
5187 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
5188 complete with example surface forcing files and matlab scripts to look
5189 at the output and compare it with that of global_ocean.cs32x15.)
5190 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
5191 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
5192 to conform to the common rule.
5193 o check-in the first version of the coupler + interfaces for multi-components
5194 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
5195 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
5196 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
5197 - ocean and atmos. share the same horizontal grid (no interpolation).
5198 - exchanges between component and coupler is done in forward_step
5199 o new verification experiment, cpl_aim+ocn:
5200 coupled ocean - AIM atmosphere on cs32 grid.
5201
5202 checkpoint52d_pre (2003/12/06)
5203 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
5204 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
5205
5206 checkpoint52c_post (2003/11/25)
5207 o Fixing OPTIONS files for use of exf:
5208 - ALLOW_ECCO not needed
5209 - ECCO_CPPOPTIONS.h should not be included from
5210 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
5211 as has been the case in the past
5212 - All cal/exf related options are currently set in
5213 single header file. Should remain so until we
5214 agree on a consistent new policy.
5215 o Removed all CPP options for cal package.
5216 cal has no more CPP options.
5217 o modified STOREs in GAD_ADVECTION
5218 o corrected key comp. for passkey
5219
5220 checkpoint52b_post (2003/11/23)
5221 o new version: "thsice" of thermodynamic sea-ice pkg:
5222 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
5223 - modify fluxes but do not change theta directly;
5224 - light cleaning of bulk_force pkg (still needed with thsice).
5225 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
5226 + output_thsice.txt to test thsice & bulk_force pkgs.
5227 o put back grid & coriolis monitor output.
5228 checkpoint52b_pre (2003/11/23)
5229
5230 o call "do_the_model_io" at the beginning (=> dump initial state)
5231 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
5232 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
5233 (need info on NUMBER_OF_PTRACERS)
5234 o missing PTRACERS headers in some routines
5235 o default tamc.h in pkg/autodiff supposed to crash
5236 to ensure proper customization
5237
5238 checkpoint52a_post (2003/11/17)
5239 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
5240 - moved surfaceTendencyTice from pkg/seaice to main code
5241 - subroutine FREEZE_SURFACE now limits only surface temperature
5242 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
5243 => new output.txt for global_ocean.cs32x15 & global_with_exf
5244 - keep the old version of FREEZE for backward compatibility;
5245 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
5246 - corresponding modifs for TAF directives
5247 o added surface flux output variables to TIMEAVE_STATVARS
5248 o time-averaged output for pkg/ptracers
5249 o fix problem with ECCO-related divided adjoint
5250 snapshot file was missing some ad-variables,
5251 but no warning issued by TAF
5252
5253 checkpoint52a_pre (2003/11/12)
5254 o some bug fixes for #undef REAL4_IS_SLOW
5255
5256 checkpoint52 = ecco_c52_e35
5257 o after testing adjoints of checkpoint51u_post
5258
5259 checkpoint51u_post (2003/11/06)
5260 o this is the post-merge tag of the ecco-branch
5261 (needs another clean checkout and re-testing)
5262 o various natl_box_adjoint configs and results
5263 but no input fields
5264 o obcs adjoint not yet merged!
5265 o adding ECCO global 1x1 and 2x2 degree configs
5266 o updated/extended some store directives for seaice
5267 o pkg/ecco now containes ecco-specific part of cost function
5268 o top level routines the_main_loop, forward_step
5269 supersede those in model/src/
5270 previous input data.cost now in data.ecco
5271 (new namelist ecco_cost_nml)
5272 o in ctrl/ cleaned some cross-dependencies and updated CPP options
5273
5274 checkpoint51t_post (2003/11/04)
5275 o this is the pre-merge tag of the ecco-branch
5276
5277 checkpoint51s_post (2003/11/04)
5278 o cleanup: removed various obsolete #define-s
5279 o pkg/grdchk
5280 - renamed 'ph-grd 3' to 'grad-res'
5281 - merged from ecco-branch
5282 (remaining bug fixes for obcs gradient checks)
5283 - additional high-precision output for testreport
5284 (grep for 'precision_grdchk_result')
5285
5286 checkpoint51r_post (2003/11/03)
5287 o cleaned up or removed CPP_OPTIONS.h files
5288 o updated results for some of the tests to reflect the new
5289 optfiles (-ieee: -O0 instead of -O3)
5290
5291 checkpoint51q_post (2003/10/30)
5292 o cd_code:
5293 - moved cd_scheme.F -> cd_code_scheme.F
5294 - separate read_checkpoint from cd_code_ini_vars.F
5295 - separated cd_code part from write_checkpoint
5296 - updated AD_SOURCE, generated .flow
5297 - added CD_CODE_VARS.h to the_main_loop
5298 - Moving cd_code specific store dir.s to pkg/cd_code
5299 o ctrl package totally restructured
5300 - pack/unpack now optional and decoupled from
5301 xx_/adxx_ I/O
5302 - ctrl_pack/unpack cleaned
5303 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
5304 - confined inclusion of AD_CONFIG.h to where necessary.
5305 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
5306
5307 checkpoint51p_post (2003/10/30)
5308 o create initial cd_code package
5309 - WARNING: the initialization of fields within packages
5310 is broken because INI_FIELDS (where READ_CHECKPOINT is
5311 called) is called *before* PACKAGES_INIT_VARIABLES.
5312 This seems to be backwards since
5313 1) its important to initially zero the entire field including
5314 the "halo" region
5315 2) zeroing needs to be done *before* reading pickup info
5316 and the pickup call might or might not happen in any
5317 particular run
5318 - this needs an overhaul for R2
5319 o cleanup verification/*/code/GMREDI_OPTIONS.h
5320 o cleanup testreport
5321
5322 checkpoint51o_post (2003/10/27)
5323 o bringing AD-related verif's up to date with genmake2
5324 - carbon/
5325 - global_ocean.90x40x15/
5326 - hs.94.1x64x5/
5327 - (front_relax/ )
5328 o (more) consistent directory structure for AD-related verif.'s
5329 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
5330 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
5331 o bug fix in find_alpha.F for MDJWF:
5332 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
5333 change rho -> rho-rhoConst
5334 - replace call find_rho to find_rhonum
5335 o initialisation of rFlx extended to full array (required by TAF)
5336 and shifted to thermodynamics
5337 o removed PTRACERS.h in ptracers routine
5338 o added surfacetendencyPtr to S/R parameter list pracers_forcing
5339 o Correcting initialisations for fVerU, fVerV.
5340 o helping TAF to recognize dependency on kUp for
5341 fVerU, fVerV
5342 o Replacing delZ by delR in pkg/ctrl/
5343 checkpoint51o_pre (2003/10/24)
5344
5345 o undid all of cp51 pending some cleanups and discussion
5346 o added the [#include "AD_CONFIG.h"] statement to all files that need
5347 it for adjoint/tl #defines
5348 o re-worked the build logic in genmake2 to support AD_CONFIG.h
5349 o removed tools/genmake since it no longer works
5350
5351 checkpoint51n_post (2003/10/23)
5352 o modifications to make FREEZE flux visible to pkg/kpp
5353 - moved surfaceTendencyTice from pkg/seaice to main code
5354 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
5355 - subroutine FREEZE now limits only surface temperature
5356 (this means new output.txt for global_ocean.90x40x15,
5357 global_ocean.cs32x15, and global_with_exf)
5358 o added surface flux output variables to TIMEAVE_STATVARS
5359
5360 checkpoint51n_pre (2003/10/23)
5361 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
5362 o added [#include "AD_CONFIG.h"] to all files that use the following
5363 defines:
5364 - ALLOW_ADJOINT_RUN
5365 - ALLOW_TANGENTLINEAR_RUN
5366 - ALLOW_ECCO_OPTIMIZATION
5367
5368 checkpoint51m_post (2003/10/21)
5369 o incorporating changes to get TAMC/TAF working in genmake2
5370 - added new TAMC/TAF targets to the Makefile
5371 - various cleanups related to package handling
5372 - these changes should have no impact on the forward model
5373
5374 checkpoint51l_post (2003/10/20)
5375 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
5376 - faster algorithm for cal_addtime.F
5377 - higher precision arithmetic, where needed
5378 - pkg/exf *startdate variables changed from calendar date to
5379 model integration time
5380
5381 checkpoint51l_pre (2003/10/17)
5382 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
5383 o enable to apply restoring on S & T only in a latitude band.
5384 o update output (external_forcing_surf modif. change truncation errors)
5385 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
5386
5387 checkpoint51k_post (2003/10/16)
5388 o change default to: useNHMTerms=.FALSE.
5389 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
5390 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
5391 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
5392 exp1, ideal_2D_oce
5393 - change data file of oceanic exp (leave the results unchanged for now)
5394 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
5395 o set gravitySign automatically according to the vertical coordinate used
5396 (and change sign: back to "logical" value: +1 when R increases downward)
5397 o added an include barrier to the default CPP_OPTIONS.h and
5398 removed the #include "PACKAGES_CONFIG.h" from it
5399 o fix a bug in mom_fluxform (from chk51j_post)
5400
5401 checkpoint51j_post (2003/10/10)
5402 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
5403 o adjusted some flow directives (dynamics, thermodynamics)
5404 o added cubed-sphere case to test cost function
5405 o heckpoint_lev?_directives.h now include
5406 pkg-specific directives, whenever those are enabled.
5407 o Moving pkg-specific flow directives to corresponding pkg
5408 Moving pkg-specific differentiation list to corresponding pkg
5409 Moving pkg-specific checkpoint-lev storing to corresponding pkg
5410 ---> conventions are
5411 - pkg_ad.flow
5412 - pkg_ad_diff.list
5413 - pkg_ad_check_lev?_dir.h
5414
5415 checkpoint51i_post (2003/10/09)
5416 o merge of the branch-genmake2
5417 - knowingly breaks the older genmake
5418 - automatic generation of all ALLOW_${PKG_NAME} defines
5419 - new testreport supersedes older testscript
5420 o large number of package inclusion and header cleanups
5421 checkpoint51i_pre (2003/10/08)
5422
5423 o new output for adjoin of global ocean vector invariant
5424 o fix for checkpoint of thermodynamic seaice and bulk_force
5425 o Steph gchem various cleanups
5426
5427 checkpoint 51h_pre
5428 o fixed some single quotes
5429 o modify gchem pkg to be more versatile
5430 o modifications to clean up dic pkg
5431 o add pkg/cfc
5432
5433 checkpoint51g_post (2003/10/02)
5434 o provide links for ARPACK and ADM*TLM
5435 o start removing verification/vero/
5436 o update AD-related stuff
5437 (in particular some IF-statements in model/src/ routines)
5438 o adding to verification/global_ocean.90x40x15/ adjoint of
5439 vector invariant setup
5440
5441 checkpoint51f_post (2003/10/02)
5442 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
5443 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
5444 of tracer Green's fucntions for ocean inversion project.
5445
5446 checkpoint51f_pre (2003/08/07)
5447 o Added on-the-fly spatial interpolation capability
5448 "USE_EXF_INTERPOLATION" to pkg/exf.
5449 - This is a temporary Cartesian-grid hack until
5450 the super-duper ESMF coupler becomes available.
5451 - See verification/global_with_exf/README for usage example.
5452 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
5453 flags and modified pkg/seaice accordingly.
5454 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
5455 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
5456 non-local transport term.
5457
5458 checkpoint51e_post (2003/08/03)
5459 o pkg/mom_vecinv:
5460 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
5461 - add time-ave diagnostic of vorticity advection.
5462 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
5463 o atmospheric geopotential: - include water vapor effect;
5464 - use p^kappa in p* scaling.
5465 o land pkg: read initial state from files.
5466 o AIM : add stratospheric drag in the upper level
5467
5468 checkpoint51d_post (2003/07/18)
5469 o change function ILNBLNK (=> last non-blank char.) to return zero
5470 (instead of the string length) when the string. char is empty
5471 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
5472 o modif's to restore TAMC compatibility
5473 - avoid "_d" constructs in PARAMETER declarations
5474 - avoid interrupting lines by comment lines
5475 o Use cluster local disks for purely local I/O
5476 vs. globally visible disks needed for ctrl stuff
5477 (merged from ecco-branch)
5478 - new active_file_loc... and mdsio_..._loc routines
5479 - affected packages: autodiff, ctrl, grdchk, mdsio
5480
5481 checkpoint51c_post (2003/07/08)
5482 o introducing integer flag debugLevel
5483 - debLevZero: suppress all output
5484 - debLevA: standard
5485 - debLevB: equivalent to current debugMode=.TRUE.
5486 o introducing pathname variable mdsioLocalDir for mdsio
5487 that can be specified at runtime
5488 (relevant for cluster I/O to local disk)
5489 `
5490 >>>checkpoint51b_post
5491 adjoint of ptracers
5492 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
5493 o extended state in checkpoint_lev?, etc.
5494 o alternative ctrl/cost with tr1 or ptracer
5495 o new comlev1_bibj_ptracers
5496 o new ptracers.flow
5497 o made ptracers_forcing same as external_forcing_s
5498 o added verification for adjoint with ptracers
5499 - adm. grdchk fail so far
5500 - tlm. grdchk OK
5501 - checked tapelev/comlev recomputations: OK
5502 <<<checkpoint51b_pre
5503
5504 checkpoint51a_post (2003/06/25)
5505 o added code for biogeochemistry package
5506 - new pkgs: dic, gchem
5507 - new subroutine in ptracers
5508 o modify code for biogeo packages
5509 - in model/src and pkg/ptracers
5510
5511 checkpoint51 (2003/06/24)
5512 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
5513 - autodiff, ctrl, exf, grdchk, seaice
5514 kept separate packages
5515 - cost, ecco, obcs
5516 o updating verification/internal_wave, verification/lab_sea
5517 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
5518
5519 checkpoint50i_post (2003/06/23)
5520 o Preparing next differentiable checkpoint and sync
5521 of MAIN vs. ecco-branch
5522 - 1st step: this one is differentiable
5523 - 2nd step: next(! not this) checkpoint will have updated packages
5524 from ecco-branch)
5525
5526 checkpoint50h_post (2003/06/20)
5527 o new package "land": provide surface BC for AIM.
5528 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
5529 o AIM: use true log-P extrapolation for near surface temp (= as in
5530 F.Molteni paper) ; update aim.5l_cs output.
5531 o New variable in PARM03 for more flexible pickups
5532 o somewhat cleaned package initialisation sequence for
5533 ctrl/ cost/ ecco/ in packages_... routines
5534
5535 checkpoint50g_post (2003/05/23)
5536 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
5537 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
5538 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
5539 made the default because of faster convergence than ADI
5540
5541 checkpoint50f_post (2003/05/23)
5542 o exf totally restructured
5543 - replaced all exf_set_ routines by one generic exf_set_gen.F
5544 and made sure it's still differentiable
5545 - split exf_getffields.F into new exf_bulkformulae.F
5546 - exf_inscal_/exf_outscal_ suffixes consistent with field names
5547 - updated adjoint/makefile and relevant verif. accordingly
5548
5549 checkpoint50f_pre (2003/05/23)
5550 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
5551 + change Evap over land. (update aim.5l_cs output)
5552 o added missing .cvsignores and made uniform across expts
5553 o changed configuration of tidal_basin_2d expt
5554 o added pkg/debug functions for tracing code in fatal crashes
5555 o tidied pkg/monitor to use MONITOR_OPTIONS.h
5556 o new fn in pkg/monitor to stop model if solution grows too big
5557 o removed lots of single quotes from comments
5558
5559 checkpoint50e_post (2003/05/14)
5560 o make KPP work with PTRACERS
5561 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
5562 nearly a copy of kpp_transport_s
5563 - there is no analogue to SurfaceTendencyS, so I have to use
5564 gPtr(of the surface layer) instead
5565 o add a new platform SunFire+mpi (SunFire 15000) to genmake
5566 checkpoint50e_pre (2003/05/13)
5567
5568 checkpoint50d_post (2003/05/13)
5569 o change kpp output from multiple-record state files to single-record state
5570 files analogous to write_state.F
5571 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
5572 analogous to the cg2d-related output.
5573 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
5574 so that writing to internal file fn (with length 512) fails.
5575 checkpoint50d_pre (2003/05/12)
5576
5577 checkpoint50c_post (2003/05/12)
5578 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
5579 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
5580 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
5581 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
5582 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
5583
5584 checkpoint50c_pre (2003/04/30)
5585 Merging from release1_p13:
5586 o bug fix for pkg/seaice dynamic solver
5587 o Added SEAICE_initialHEFF to pkg/seaice
5588
5589 checkpoint50b_post (2003/04/17)
5590 o store u*,v* in gU,V instead of in guNm1,gvNm1
5591 o in order to put the momForcing out of the Adams-Bashforth:
5592 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
5593 to timestep.F
5594 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
5595 o re-generate output for highly sensitive test-exp:
5596 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
5597
5598 checkpoint50b_pre (2003/04/17)
5599 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
5600 o corrected CPP option mismatch in exf_Bulk... functions for case
5601 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
5602
5603 checkpoint50a_post (2003/03/21)
5604 o Bug fix for merging between c50 and KPP.
5605 ikey was passed from thermodynamics to kpp_calc via
5606 common block rather than being recomputed in kpp_calc,
5607 in contradiction with new key itdkey.
5608 New key ikppkey created, and tamc.h headers updated.
5609
5610 checkpoint50 (2003/03/08)
5611 - 2nd step of merge with ecco-branch:
5612 merge changes in ecco-branch back into main trunk
5613 - bug fix in find_alpha
5614 - more storing in gmredi_calc_tensor.F, kpp_routines.F
5615 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
5616 - merged some sliced AD support routines
5617
5618 checkpoint49 (2003/03/06)
5619 merged from ecco-branch:
5620 o exf:
5621 - Enable initialisation of forcing fields to constant
5622 (runtime) values.
5623 - in exf_getffields.F
5624 Reduce i-/j-loop to interior domain, discarding overlaps.
5625 That also fixes wrong TAF-key computations for key_1, key_2
5626 with bulf formulae.
5627 - exf_init.F modify #ifdef for exf_init_evap
5628 - exf_getffieldrec.F, ctrl_getrec.F
5629 The following INT-usages are not safe:
5630 fldsecs = int(fldsecs/fldperiod)*fldperiod
5631 fldcount = int(fldsecs/fldperiod) + 1
5632 and were modified.
5633 o autodiff: checkpoint_lev...
5634 - updated storing for bulk formulae (some arrays were missing)
5635 - added state for seaice package
5636 - synchronized with main branch
5637 o DIVA:
5638 Modif.s in
5639 - the_main_loop.F
5640 - the_model_main.F
5641 and added cost_final_restore.F cost_final_store.F
5642 o With these changes, it is possible to fully separate
5643 the first forward run to compute the cost function (mdthe_main_loop)
5644 and adjoint runs over individual DIVA intervals (adthe_main_loop)
5645 into separate model executions.
5646 This enables better tuning of DIVA to given queue sizes.
5647 o Loss of cost function value in consecutive DIVA runs is
5648 fixed by storing to 'costfinal' file.
5649 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
5650 beginning/end of adjoint integration is accounted for.
5651 The current changes apply to TAF-1.4.26.
5652 TAF has one remaining bug, requiring one manual change
5653 (see MITgcm manual).
5654 o cal: synchronized between MAIN and ecco-branch
5655
5656 checkpoint48i_post (2003/03/05)
5657 o Changes to restore differentiability of code w.r.t. previous tag
5658 (mostly adding new routines to make list and replacing
5659 pressure by totPhiHyd).
5660 o Updated and merged grdchk package
5661 - has both ADM and TLM checks
5662 - works for single- and multi-proc.
5663 - output cleaned
5664 - worked successfully for parallel DIVA
5665 o genmake:
5666 - Adding -platform=SP4
5667 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
5668 o Modif. for DIVA:
5669 ctrl_unpack should not be called in intermediate DIVA interval.
5670 (similar thing would apply for active files such as
5671 tbar, sbar, psbar, which should not be reinitialised;
5672 only relevant for ecco-branch)
5673
5674 checkpoint48h_post (2003/02/28)
5675 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
5676 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
5677 o Added SEAICE_initialHEFF to pkg/seaice
5678 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
5679
5680 checkpoint48g_post (2003/02/18)
5681 --- EOS:
5682 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
5683 store total Potential in totPhyHyd for diagnostics & EOS.
5684 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
5685 --- Pressure/geopotential gradient:
5686 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
5687 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
5688 ( changes results of global_ocean_pressure )
5689 o NLFS + z-coord.: add eta*Rho' contribution.
5690 o accurate phiHyd when using interface-W at the middle between 2 centers
5691 ( changes results of ideal_2D_oce )
5692 o includes r* 2nd term in potential gradient.
5693
5694 checkpoint48f_post (2003/02/18)
5695 Merging from release1_p12:
5696 o Modifications for using pkg/exf with pkg/seaice
5697 - improved description of the various forcing configurations
5698 - added basic radiation bulk formulae to pkg/exf
5699 - units/sign fix for evap computation in exf_getffields.F
5700 - updated verification/global_with_exf/results/output.txt
5701 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
5702 (SBO) core products, including oceanic mass, center-of-mass,
5703 angular, and bottom pressure (see pkg/sbo/README.sbo).
5704 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
5705 to avoid negative values in shallow regions.
5706 - updated verification/natl_box/results/output.txt
5707 - updated verification/lab_sea/results/output.txt
5708 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
5709 o Added useSingleCpuIO option (see PARAMS.h).
5710 o Updated useSingleCpuIO option in mdsio_writefield.F to
5711 work with multi-field files, e.g., for single-file pickup.
5712 o pkg/seaice:
5713 - bug fix in growth.F: QNET for no shortwave case
5714 - added HeffFile for specifying initial sea-ice thickness
5715 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
5716 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
5717 kpp_transport_t.F, forward_step.F, and the_main_loop.F
5718 o pkg/seaice:
5719 - adjoint-friendly modifications
5720 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
5721
5722 checkpoint48e_post (2003/02/12)
5723 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
5724 o dynamics: change definition of computational domain & adapt mom_fluxform
5725 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
5726 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
5727 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
5728 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
5729 global_ocean.90x40x15 global_with_exf global_ocean_pressure
5730 inverted_barometer solid-body.cs-32x32x1
5731 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
5732
5733 checkpoint48d_post (2003/02/09)
5734 o in preparation for r*:
5735 a) use pre-computed gradient of hydrostatic potential:
5736 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
5737 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
5738 => affects results of glob_oce_pressure (different truncation error)
5739 update output.txt of ideal_2D_oce & global_ocean_pressure
5740
5741 checkpoint48d_pre (2003/02/08)
5742 o in preparation for r*:
5743 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
5744 pass the 2 comp. of the grad. as arguments to momentum S/R.
5745 but for the moment, only used if it does not change the results.
5746 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
5747
5748 checkpoint48c_post (2003/02/06)
5749 Modifications in treatment of initial flux forcing controls
5750 to avoid extra storing of flux fields.
5751
5752 checkpoint48c_pre (2003/01/21)
5753 o Added tidal_basin_2d experiment (currently 1D!)
5754 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
5755
5756 checkpoint48b_post (2003/01/27)
5757 o r* coordinate added in #ifdef NONLIN_FRSURF block.
5758 (modification to pressure gradient not yet implemented)
5759 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
5760 (for U & V) that are used for vertical advection of momentum.
5761
5762 checkpoint48a_post (2003/01/24)
5763 o In preparation for r*, use temp. array to compute vertical transport
5764 in flux-form momentum pkg. => change results of few test-exp.
5765 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
5766 lab_sea, natl_box & plume_on_slope
5767
5768 checkpoint48 (2003/01/23)
5769 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
5770
5771 checkpoint47j_post (2003/01/21)
5772 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
5773 o moved adexch from forward_step to addummy_in_stepping
5774 o added exch in ctrl_map_...
5775 o aveFreq.=0. at end of cost_final to avoid overwrite in
5776 reverse checkpointing loop
5777 o Yet more changes in gmredi:
5778 * adgmredi_calc_tensor
5779 avoiding all recomputation of gmredi_slope_limit
5780 * adgmredi_x/y/rtransport
5781 added flag for excessive storing to avoid recomp. of
5782 u/v/rtans, dTdx/y/z
5783 -> this is not really necessary and very memory-consuming
5784 * adgmredi_slope_psi:
5785 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
5786 * gmredi_slope_limit
5787 re-activated full calculation of taperfct for case 'ac02'
5788 o updating verification/ adjoints of carbon, global_ocean.90x40x15
5789
5790 checkpoint47i_post (2003/01/13)
5791 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
5792 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
5793 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
5794 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
5795 o gmredi: fix few bugs.
5796
5797 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
5798 This will be a good checkpoint to plug into the ecco-branch.
5799 o few modif.'s to get latest version adjointed
5800 (mainly kick out code in ini_linear_phisurf)
5801 o modif's to run adjoint with exactConserv
5802 o case GM_BOLUS_ADVEC should be cleaned
5803 S/R gmredi_slope_psi should be cleaned
5804 o verification/carbon now has exactConserv=.TRUE.
5805
5806 checkpoint47g_post (2003/01/10)
5807 o time-average AIM output: becomes independent from statvars time-average
5808 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
5809 o After TAF bug fix:
5810 Tested adjoint of gmredi package.
5811 Tests were done with checkpoint47 rather than with latest
5812 checkpoint47f_post since the latter is broken for the adjoint
5813 verification/carbon/ contains both ADM and TLM gradient checks.
5814 Here they are, before they get changed/lost/stolen.
5815 Mostly modif.'s to fix numerical sensitivities.
5816 Gradient checks OK for
5817 - GM_taper_scheme:
5818 * clipping
5819 * ac02
5820 * linear
5821 * glw91
5822 * dm95
5823 * ldd97
5824 - GMREDI_OPTIONS:
5825 * GM_VISBECK_VARIABLE_K
5826 * GM_NON_UNITY_DIAGONAL
5827 * GM_EXTRA_DIAGONAL
5828 * GM_BOLUS_ADVEC
5829 in conjunction with data.gmredi parameters to be checked in
5830 in a few minutes under verification/carbon/code/
5831
5832 checkpoint47f_post (2002/12/28)
5833 Merging from release1_p10:
5834 o modifications for using pkg/exf with pkg/seaice
5835 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
5836 and SEAICE_EXTERNAL_FLUXES
5837 - pkg/exf CPP options EXF_READ_EVAP and
5838 EXF_NO_BULK_COMPUTATIONS
5839 - usage examples are Experiments 8 and 9 in
5840 verification/lab_sea/README
5841 - verification/lab_sea default experiment now uses
5842 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
5843
5844 checkpoint47e_post (2002/12/27)
5845 o created a tag prior to creating a branch
5846
5847 checkpoint47d_post (2002/12/16)
5848 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
5849 at the bottom boundary had an erroneous half slip boundary condition
5850 o added bottom drag and no slip boundary condition capabilities to
5851 oceanic pressure coordinates code
5852 o added new verification experiment global_ocean_pressure, this experiment is
5853 also described in the tutorial section of the manual
5854 checkpoint47d_pre (2002/12/16)
5855
5856 checkpoint47c_post (2002/12/16)
5857 o Added a verification experiment for a global cubed-sphere ocean run
5858 - verification/global_ocean.cubed32x32x30
5859 - uses pkg/therm_seaice and pkg/bulk_forcing
5860
5861 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
5862 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
5863 when using P-coordinate; only implemented for atmospheric config.
5864 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
5865 NOTES: requires option NONLIN_FRSURF to be "#define".
5866 o update advect_xz/results/output.txt (left from checkpoint44g_post)
5867
5868 checkpoint47b_post (2002/12/05)
5869 Merging from release1_p9:
5870 o pkg/seaice
5871 - removed GOTO's and added taf directives
5872 - double precision constants to reduce the g77 (Linux)
5873 to F77 (SGI) differences reported in release1_p8
5874 o tools/genmake
5875 - added SGI options
5876 o verification/testscript
5877 - updated to that of checkpoint47a_post
5878 o verification/global_ocean.90x40x15/input/eedata
5879 - modified for SGI f77 compatibility
5880 o verification/lab_sea
5881 - added description of sea-ice model
5882 - added missing matlab routines
5883 - added test of thermodynamics parallelization
5884
5885 checkpoint47a_post (2002/11/23)
5886 o new pkg: aim_v23
5887 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
5888 for now, keep the same surface forcing as before.
5889 - Part-Cell implemented into AIM; check that Heat & Water are conserved
5890 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
5891 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
5892 o add diagnostic of surface correction term in monitor output
5893
5894 o bulk_force and therm_seaice
5895 - Two packages: bulk_force (Bulk forcing)
5896 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
5897 - Earlier integration from Stephaine Dutkiewicz
5898 and Patrick Heimbach.
5899 - Two ifdef statements for compile time,
5900 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
5901
5902 checkpoint47 (2002/11/15)
5903 differentiable version of checkpoint46n_post
5904 o bug fix in quasihydrostaticterms
5905 o * "clean" adjoint code (in terms of extensive recomputations)
5906 can now be obtained for all GMREDI options (i.e. for
5907 - GM_VISBECK_VARIABLE_K
5908 - GM_NON_UNITY_DIAGONAL
5909 - GM_EXTRA_DIAGONAL
5910 - GM_BOLUS_ADVEC )
5911 * However, wrong gradient check problem remains unsolved.
5912 * New CPP options have been introduced for different
5913 tapering schemes
5914 o external_fields_load now part of differentiation list
5915 o pressure needs multiple storing;
5916 would be nice to have store_pressure at beginning or
5917 end of forward_step, e.g. by having phiHyd global (5-dim.)
5918 (NB: pressure is needed for certain cases in find_rho,
5919 which is also invoked through convective_adjustment).
5920 o recomputations in find_rho for cases
5921 'JMD95'/'UNESCO' or 'MDJWF' are OK.
5922 o #define ATMOSPHERIC_LOADING should be differentiable
5923 o ini_forcing shifted to begining of initialise_varia
5924 o Incorporating QNVS line search routines into MITgcm
5925 (this is separate code, and therefore not under pkg)
5926 lsopt/, optim/
5927 o Updated verification/carbon/
5928 - #define GM_VISBECK_VARIABLE_K
5929 - GM_taper_scheme = 'ldd97'
5930
5931 checkpoint46n_post (2002/11/12)
5932 Merging from release1_p8:
5933 o verification/natl_box:
5934 updating new external_fields_load routine
5935 o New package: pkg/seaice
5936 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
5937 The sea-ice code is based on Hibler (1979-1980).
5938 Two sea-ice dynamic solvers, ADI and LSR, are included.
5939 In addition to computing prognostic sea-ice variables and diagnosing
5940 the forcing/external data fields that drive the ocean model,
5941 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
5942 The implied surface heat flux is then stored in variable
5943 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
5944 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
5945 non-local transport term. Because this call precedes model
5946 thermodynamics, temperature under sea-ice may not be "exactly" at
5947 the freezing point by the time theta is dumped or time-averaged.
5948 N.B.: fairly large differences in accuracy occur across
5949 different platforms/compilers; comparison between
5950 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
5951 generated output gives:
5952 T S U V
5953 C D M c m s m s m s m s
5954 n p a R g m m e . m m e . m m e . m m e .
5955 f n k u 2 i a a d i a a d i a a d i a a d
5956 g d e n d n x n . n x n . n x n . n x n .
5957
5958 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
5959 o GAD:
5960 - generated new common blocks to account for call of
5961 same gad routines with differing traceridentities
5962 (needed to modify tracerIdentity indices in GAD.h)
5963 - generated separate common blocks for case useCubedSphereExchange
5964 (Department of Futurology)
5965 - parameter lists to gmredi_?transport: added tracerIdentity
5966 - added new key indices to tamc.h
5967 o external_fields_load:
5968 - added this routine to TAF list
5969 - needed to make some common blocks global and additional storing
5970 along the same lines as exf package (checkpoint_lev?_directives.h)
5971 o exf:
5972 updated external forcing package
5973 - bug fixes carried over from ecco-branch
5974 (missing OBCS_OPTIONS.h in two routines)
5975 - enable easy to use "no forcing".
5976 - added exf I/O for atmospheric loading
5977 - added exf I/O for runoff data
5978 - transfered scaling between exf <-> MITgcm to exf namelist
5979 o Adding new verification experiment global_with_exf.
5980 This verification experiment is almost identical to the
5981 global_ocean.90x40x15 experiment, except that it uses
5982 the exf (and cal) package instead of the
5983 external_fields_load routine (cf README file).
5984
5985 checkpoint46m_post (2002/11/07)
5986 o modified testscript to return -- when there are no lines of "%MON" output
5987 o added new flag "quasiHydrostatic" for QH mode
5988 and new routine quasihydrostaticterms()
5989 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
5990 New routine: mom_u_coriolis_nh()
5991 o fixed sign of non-hydrostatic metric terms in u and v equations.
5992 Depend on correct sign of gravitySign.
5993 o added work.pc* to .cvsignore in aim directories using ifc
5994 o introduced flag for controllin non-hydrostatic metric terms
5995 o removed gravitySign from PARM04
5996 o switched to g77/ifc from pgf77 in aim experiments
5997
5998 checkpoint46l_post (2002/11/01)
5999 o made convective adjustment work with pressure coordinates:
6000 - changed the direction of k-loop in convective_adjustment.F for the
6001 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
6002 - adjusted the reference pressure k-index in convective_adjustment.F
6003 - adjusted the convection condition in convect.F (in analogy to
6004 calc_ivdc.F)
6005 - convective_adjustment no longer computes anything on the halos
6006 - removed the warnings about negative salinity from find_rho.F and
6007 find_alpha.F; instead the new routine look_for_neg_salinity, called
6008 at the beginning of find_rho, find_alpha, and find_beta, does a
6009 check of the entire slice, if CPP-option
6010 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
6011 checkpoint46l_pre (2002/10/23)
6012
6013 checkpoint46k_post (2002/10/23)
6014 o fixed the verification/global_ocean.90x40x15 experiment:
6015 - new bathymetry (the world according to A., JMC, and M.)
6016 - new initial fields and forcing fields (*.bin files)
6017 - new POLY3.COEFFS (for the next release one should switch to a full
6018 equation of state: JMD95P or MDJWF)
6019 - fixed several errors and redundancies in the data file
6020 - experiment uses looped cells
6021 - added matlab directory with diagnostic scripts for plotting of output
6022
6023 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
6024 - read AIM physics parameters from a file (data.aimphys)
6025 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
6026
6027 checkpoint46j_post (2002/10/07)
6028 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
6029 o move wVel computation at the end of the time step, in S/R integr_continuity
6030 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
6031 o update timeave pkg for wVel diagnostic.
6032 checkpoint46j_pre (2002/09/27)
6033
6034 checkpoint46i_post (2002/09/25)
6035 o Clean up AIM package (and keep the results unchanged):
6036 include CPP_OPTION and use IMPLICT NONE in all routines ;
6037 declare all the variables _RL ; use _d 0 for all numerical constants.
6038 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
6039
6040 checkpoint46h_post (2002/09/25)
6041 o cleaned up the use of rhoNil and rhoConst.
6042 - rhoNil should only appear in the LINEAR equation of state, everywhere
6043 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
6044 and the dynamical equations are all divided by rhoConst
6045 o introduced new parameter rhoConstFresh, a reference density of fresh
6046 water, to remove the fresh water flux's dependence on rhoNil. The default
6047 value is 999.8 kg/m^3
6048 o cleanup up external_forcing.F and external_forcing_surf.F
6049 - can now be used by both OCEANIC and OCEANICP
6050 checkpoint46h_pre (2002/09/18)
6051
6052 Added code to convert surface volume flux (fresh water) into
6053 a mass flux when using P coordinates in the ocean (OCEANICP).
6054 Note: It assumes you have set rho0=rhoConst=density of fresh water.
6055
6056 checkpoint46g_post (2002/09/18)
6057 o Include a new diagnostic variable phiHydLow for the ocean model
6058 - in z-coordinates, it is the bottom pressure anomaly
6059 - in p-coordinates, it is the sea surface elevation
6060 - in both cases, these variable have global drift, reflecting the mass
6061 drift in z-coordinates and the volume drift in p-coordinates
6062 - included time averaging for phiHydLow, be aware of the drift!
6063 o depth-dependent computation of Bo_surf for pressure coordinates
6064 in the ocean (buoyancyRelation='OCEANICP')
6065 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
6066 Theta, Salinity, and Pressure in the parameter list. This routine is
6067 presently contained in find_rho.F. This routine does not give the
6068 correct density for 'POLY3', which would be a z-dependent reference
6069 density.
6070 o cleaned up find_rho
6071 - removed obsolete 'eqn' from the parameter list.
6072 o added two new verification experiments: gop and goz
6073 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
6074 checkpoint46g_pre (2002/09/16)
6075
6076 checkpoint46f_post (2002/09/16)
6077 o Enable tangent linear (forward mode) gradient checks:
6078 - extended active file handling to g_... files
6079 - added TANGENT_SIMULATION to theSimulationMode
6080 - extended grdchk package accordingly
6081 o added tangent linear setup in verification/carbon/code_ftl
6082 o added adjoint setup in verification/front_relax/code_ad
6083
6084 checkpoint46e_post (2002/09/05)
6085 o Added new equation of state -> MDJWF
6086 - EOS of McDougall et al., 2002, JAOT, submitted
6087 - caveat: the equation of state is only valid for a smaller (more
6088 realistic?) range of values than JMD95P/Z and UNESCO
6089 - added masks to the calculation of pressure in store_pressure
6090 - added more check values for density in check_eos (ini_eos.F), some of
6091 the old check values are out of the range of the MDJWF-eos, so don't
6092 expect perfect matches for those
6093 checkpoint46e_pre (2002/08/19)
6094
6095 checkpoint46d_post (2002/08/19)
6096 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
6097 'OCEANICP', also initialised field pressure correctly in ini_eos in the
6098 case of pressure coordinates. eosType='JMD95Z' in
6099 combination with buoyancyRelation='OCEANICP' now causes an error.
6100 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
6101 in find_alpha/beta.
6102 checkpoint46d_pre (2002/08/15)
6103
6104 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
6105 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
6106
6107 checkpoint46c_post (2002/08/15)
6108 o Changes necessary for ocean in p-coordinates
6109 - Added new buoyancy relation = 'OCEANICP'
6110 - Added new parameters = gravitySign (this used to be contained inside
6111 the factor dRdZ which I added when we first switched to R coordinates).
6112 X GM/Redi is not compatible (yet)
6113 X bottom drag and no-slip need to be debugged.
6114 checkpoint46c_pre (2002/08/07)
6115
6116 checkpoint46b_post (2002/08/07)
6117 o Added new equation of state -> JMD95Z and JMD95P
6118 - EOS of Jackett and McDougall, 1995, JAOT
6119 - moved all EOS parameters into EOS.h
6120 - new routines ini_eos.F, store_pressure.F
6121 o Added UNESCO EOS, but not recommended because it requires
6122 in-situ temperature (see JMD95)
6123 o Modified formatting for knudsen2.f in utils/knudsen2 and added
6124 unesco.f to be used with POLY3
6125 checkpoint46b_pre (2002/07/31)
6126
6127 checkpoint46a_post (2002/07/31)
6128 o Added (atmospheric) pressure loading
6129 - new field in FFIELDS.h, etc...
6130 - new cpp flag ATMOSPHERIC_LOADING
6131 o Changed hFacC to _hFacC in calc_phi_hyd.F
6132 o Added SHORTWAVE_HEATING to some files for consistency
6133 checkpoint46a_pre (2002/07/13)
6134
6135 checkpoint46 (2002/07/13)
6136 further merges from release1_p5
6137 o new ctrl package
6138 - adopted from ECCO environment to enable optimization
6139 - added Eliassen Palm fluxes to controls
6140 o added Eliassen Palm flux controls to gradient check package
6141 o cost package
6142 - Compatible with new ctrl package
6143 - added Eliassen Palm cost hooks
6144 - modif's of existing cost functions
6145 o Adjoint-related bug fixes in kpp:
6146 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
6147 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
6148 o autodiff package
6149 - flow directives:
6150 + new for S/R do_the_model_io
6151 + enhanced for S/R checkpoint
6152 + new gmredi.flow
6153 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
6154 disable adcommon.h/g_common.h by default.
6155 - fixed problem for adjoint of global_max
6156 o modified verification/carbon/
6157 o New setup for adjoint of global_ocean
6158 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
6159 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
6160 o incorporated hooks for sponge layer code (external_forcing.F)
6161
6162 checkpoint45d_post (2002/07/12)
6163 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
6164 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
6165 (affects plume_on_slope "cg2d" output)
6166 o add new parameter deltaTfreesurf for free-surface time stepping
6167 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
6168 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
6169 o change phiMin in exp1 (to agree with documentation)
6170 o add new flags:
6171 - T,S forcing inside/outside Adams-Bashforth
6172 - turn off temp,salt advection and/or forcing
6173 - for each tracer, define internal flag for multiDimAdvection & A-B
6174 o monitor: change definition of KE to check conservation of Energy
6175
6176 checkpoint45c_post (2002/05/30)
6177 o Removed f90 comments ("!")
6178 o Modified initialisations to enable exf package for MITgcm
6179 (without invoking ECCO_PACKAGE).
6180 o modifications to gradient check package (Martin Losch)
6181 - enable centered differences
6182 - modified format of standard output
6183
6184 checkpoint45b_post (2002/05/30)
6185 o cleaned exchange calls in cg2d
6186 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
6187 o included CPP option SINGLE_LAYER_MODE in thermodynamics
6188 to configure barotropic setup (Martin Losch)
6189 o moved some initialisations within bi,bj loop in dynamics
6190 (TAF flow dependency)
6191 o in initialise_varia, moved call packages_init_variables
6192 before convective_adjustment_init
6193 (corresponding adjustment of TAF tape initialisation).
6194 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
6195
6196 checkpoint45a_post (2002/05/01)
6197 o compute Rho over the whole domain (extend iMin,jMin indices)
6198 o specific exchange for X-slice domain (case Ny=1)
6199 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
6200 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
6201
6202 checkpoint44h_post = checkpoint45
6203 o Fix to restore differentiability:
6204 place at which packages_init_variables is called in
6205 initialise_varia is crucial for reverse control flow.
6206 o modifications in GMRedi to enable stable adjoint
6207 (corresponding modif's in thermodynamics, dynamics)
6208 o added missing hook for sponge layer code in external_forcing
6209 o modified test cost functions
6210 o storing in gad_advection (plus removal of write(0,*)!
6211 o missing headers TR1.h added in convective_adjustment routines
6212 o errorMessageUnit set non-equal zero in eeboot
6213 (conflict on some platforms, e.g. IBM SP3)
6214 o modified carbon verif.
6215
6216 checkpoint44h_pre (2002/03/14)
6217 o vertical grid option: allow to put the Interface at the middle between
6218 2 cell-centers ; replace delZ in pkg/kpp by drF.
6219 o GM Advective form: Tracers are advected using the residual transport (=
6220 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
6221
6222 checkpoint44g_post (2002/03/05)
6223 o fix surface correction term in multiDimAdvection (affects plume_on_slope
6224 results) ; ifdef missing in thermodynamics.F
6225
6226 checkpoint44f_pre,checkpoint44f_post
6227 o added PTRACERS package
6228 This allows an arbitrary number of passive tracers to be integrated
6229 forward simultaneously with the dynamicaly model.
6230 + Implemented so far:
6231 - basic forward algorithm (time-stepping, advection, diffusion, convection)
6232 - I/O and checkpointing
6233 - GM/Redi *but* using the GM/Redi coefficient of Salt
6234 + Not implemented so far:
6235 - KPP
6236 - OBCS
6237 + No specific example supplied (yet) but global_ocean.90x40x15 has the
6238 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
6239 line in data.pkg.
6240 + This package is disabled by default since it increases storage.
6241
6242
6243 o testscript: added -cleanup option
6244 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
6245 b) enable to filter 2D fields.
6246
6247 checkpoint44e_pre,post
6248 o re-wrote convective adjustment to use pre-calculated weights
6249 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
6250 Adds: model/src/convective_weights.F, convectively_mixtracer.F
6251 Original calls to convect() still in place.
6252
6253 chkpt44d_pre,post
6254 o added missing EXCLUDE_MONITOR flags
6255 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
6256 (incompatible typ in MIN/MAX expressions caused problems
6257 on IBM SP3)
6258 o in genmake added variable MAKEDEPEND
6259 plus resetting for case SunOS
6260 o added timer_stats.c routine for IBM SP3
6261 o removed variables in dynamics
6262 !!! I forgot to create tag chkpt44d_pre !!!
6263 !!! But chkpt44d_pre = chkpt44c_post !!!
6264
6265 o real fresh water flux implemented with non-linear free-surface.
6266
6267 chkpt44c_pre,post
6268 o few fix (mask in shap_s2, EmPmR in external_field_load,
6269 USE_NATURAL_BCS in solve_for_P);
6270 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
6271
6272 checkpoint44b_pre/_post
6273 o merge of relevant stuff from the ecco-branch:
6274 - genmake: removed $S64 overwrite for case SunOS
6275 - pkg/exf: update and corrections for field swapping and obcs
6276 - pkg/ecco: parameter lists for the_model_main, the_main_loop
6277 harmonized between ECCO and MITgcm
6278 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
6279 updated checkpointing_lev... lists for obcs
6280 - model/src: minor changes in forward_step, plot_field
6281 added directive for divided adjoint in the_main_loop
6282 - pkg/mdsio: added mdsio_gl_slice
6283
6284 o check parameters & config (chkpt44a_pre,post)
6285 o OBC and NonLin_FrSurf.
6286
6287 checkpoint44 (2002/01/18)
6288 o fix bug in mom_vi_del2uv
6289 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
6290 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
6291 o update AIM experiments (NCEP input files)
6292 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
6293 o added some stuff for AD
6294
6295 checkpoint43 (2001/09/28)
6296 o added two new advection tests
6297 o added global 4x4 degree ocean test
6298 o added test of H&S94 with free surface on cube
6299 o some final mods for gradient check, adjoint,...
6300
6301 checkpoint42 (2001/09/27)
6302 Fixed AD-related problems:
6303 o Store directives up-to-date with re-arranged Adams-Bashforth
6304 (mainly thermodynamics.F)
6305 o New store directives for multi-dim. advection schemes
6306 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
6307 * new common block and key passkey
6308 (mainly gad_advection.F)
6309 o Modified store directives for split of dynamics/thermodynamics
6310 for the case ALLOW_KPP
6311 o Cleaned argument list for timestep_tracer.F
6312
6313 checkpoint41 (2001/09/27)
6314 o re-formatted/added comments in prologues of key subroutines
6315 to work with protex
6316
6317 checkpoint40 (2001/09/27)
6318 o moved calc_gs, calc_gt and calc_tr1 back to model/src
6319 o added FLT (floats) package from Arne along with demo. experiment
6320 o re-arranged Adams-Bashforth scheme for tracers to allow easier
6321 implementation of forward-in-time forcing terms
6322 o more mods for non-linear free-surface including new variable
6323 o modified multi-dim method to work on cube
6324 o bug fix in KPP (from DM)
6325
6326 checkpoint40pre9 (2001/09/27)
6327 o added DST advection schemes
6328 o fix MPI bug on SGI's
6329 o modifications for non-linear free-surface
6330 o fixed conditionals for fixed flow/passive tracer only mode
6331 o added tension/strain form of stress tensor
6332 o changes to commenting of arguments for TAF/TAMC
6333 o added/updated many matlab scripts
6334 o added multi-dimensional advection method for tracers
6335
6336 checkpoint40pre8 (2001/09/05)
6337 o new package rw/
6338 Added method for dumping intermediate local arrays:
6339 mdsio_writetile - same as mdsio_writefield except works from inside
6340 bi,bj loop
6341 mdsio_writelocal - same as mdsio_writetile except works for local
6342 arrays
6343 write_local_r? - higher-level wrapper for mdsio_writelocal
6344 Controlled by diagFreq. Defaults to zero (ie. no dumps)
6345 Example given at end of mom_vecinv.F that dumps some local arrays.
6346 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
6347 control flux-form versus vector invariant code.
6348 Switch is runtime flag vectorInvariantMomentum (defaults to false)
6349 or genmake -DISABLE ...
6350 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
6351 (additional storing is now needed for case vecinv;
6352 currently nothing implemented to switch this storing off
6353 in case fluxform is used since no CPP flag available).
6354
6355 checkpoint40pre7 (2001/08/14)
6356 o bug fix in dynamics.F
6357 calc_viscosity called before k=1,Nr loop.
6358 o added some #ifdef's ALLOW_PASSIVE_TRACER
6359 o cleaned initialisations in ctrl_map_ini
6360 related to TAF
6361
6362 checkpoint40pre6 (2001/08/13)
6363 o split dynamics into thermodynamics & dynamics
6364 o corresponding split of calc_diffusivity into
6365 calc_diffusivity, calc_viscosity
6366 (kpp_calc_diff, kpp_calc_visc).
6367 o Added diffkr, kapgm to control variables
6368 o bug fix in gmredi_slope_limit for ldd97
6369
6370 checkpoint40pre5 (2001/07/31)
6371 o proper initialization of Adams-Bashforth time stepping
6372 + uses forward step for very first step of model (iter=0)
6373 o re-generated *all* output since almost all output is modified by this
6374 change (sorry but we've been putting this one off for about 2 years)
6375 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
6376 *not* regenerated since they are already out of date and I don't
6377 want to create the impression that they are suddenly working.
6378 o removed KAP stuff for DEC's
6379 o modified/added many .cvsignore files in */code and */input
6380 o added new expt "solid-body.cs-32x32x1"
6381 + this uses an alternative form of ini_curvilinear_grid.F which
6382 is not necessarily any better than the current one...
6383
6384 checkpoint40pre4 (2001/07/30)
6385 o added re-initialisations of utrans,vtrans,rtrans in
6386 calc_common_factors which are crucial for TAF.
6387 o extended iMin,jMin range for calc_common_factors,
6388 calc_diffusivity
6389 o added option ALLOW_PASSIVE_TRACER
6390 o a few minor updates and fixes
6391
6392 checkpoint40pre3 (2001/07/13)
6393 o created calc_gtr1.F for gad package
6394 o split the_main_loop and re-introduced forward_step
6395 o some recomputations of nIter0 for TAMC
6396
6397 checkpoint40pre2 (2001/07/13)
6398 o Updated to latest branch of AJA, JMC
6399 o Added gradient check package
6400 o Added routines for passive tracer handling
6401 o Added carbon sequestration sensitivity experiment
6402
6403 checkpoint39 (2001/05/14)
6404 o Modifications and fixes to support TAMC
6405 (mainly missing or wrong directives)
6406 o Corrected common blocks when fooling TAMC to produce adjoint I/O
6407 in addummy_in_stepping
6408 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
6409 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
6410 o Included following packages:
6411 cal: calendar
6412 exf: external forcing
6413 ecco: essential routines to control use of cal, exf
6414 (NB: this is not the full ECCO environment)
6415 o disabled some packages by default in genmake
6416
6417 checkpoint38 (2001/04/10)
6418 o see notes_c37_adj.txt
6419 o corrected wrong layer index in external_forcing_t
6420 o replaced the_main_loop/forward_step by the_main_loop
6421 o removed forceoutput from write_state
6422 (replaced criteria for initial/final state)
6423 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
6424
6425 checkpoint37 (2001/03/13)
6426 o mdsio.F routine split and packaged in pkg/mdsio
6427 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
6428 used unless genmake -disable=mdsio)
6429 o allow a more precise surface-geopotential gradient for the atmosphere
6430 taking into account the change in space of Alpha (=1/rho) at the surface.
6431 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
6432 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
6433 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
6434 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
6435 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
6436 o Time-Average diagnostics defined as a pseudo package "timeave".
6437 o pickup files : old pickup (before c35) did not work with new code (c35
6438 and after) unless activating 2 commented lines in initialise-varia.
6439 o Non-Hydrostatic pickup file Pb fixed.
6440 o bug with Rigid-lid version (since c35) fixed.
6441
6442 checkpoint36 (2001/02/20)
6443 o implement Crank-Nickelson barotropic time-stepping
6444 o recover Time-Average diagnostics
6445 o fix Pb in checkpoint (PR#19)
6446 o AIM become a standard package ; clean unused CPP_kees
6447
6448 checkpoint35 (2001/02/08)
6449 o subtantial rewrite of dynamics.f
6450 o allows staggered time-stepping
6451 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
6452 o added bottom drag (linear + quadratic)
6453
6454 checkpoint34 (2001/01/30)
6455 o Modified exchange routines for correct reverse simulation.
6456 o Added verification output to comply with bug fix in impldiff.F
6457 as of c33 (exp2, natl_box).
6458 o Corrected store directives in dynamics.F
6459 o Corrected array boundaries in impldiff.F
6460 o Corrected array dimensions in gmredi.
6461 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
6462 o Added routine GLOBAL_SUM_INT to global_sum.F
6463 o Added mdsio_gl.F for ECCO purposes.
6464
6465 checkpoint33 (2000/11/30)
6466 o Fixed bug in lower BC in impldiff.F
6467 o Fixed confusion about units of forcing arrays in FFIELDS.h
6468 namely Fu,Fv,Qnet,Qsw,EmPmR:
6469 - Removed verification/natl_box/code/external_fields_scale.F
6470 (did not differ from that in model/src)
6471 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
6472 (see FFIELDS.h for description)
6473 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
6474 kpp_calc.F and kpp_transport_t.F
6475 - Removed model/src/external_fields_scale.F and calls to it
6476 - verification/natl_box uses flux data with "atmospheric" sign so
6477 a special version of external_fields_load.F is used to
6478 change the data as it's read in. This way, the arrays
6479 have the right units and signs at all times tha a user could
6480 possibly use them.
6481 o Corrected genmake to delete a temporary file during configuration
6482
6483 checkpoint32 (2000/11/13)
6484 o Scaling of forcing fields moved from external_forcing.F to
6485 external_fields_scale.F, called directly after loading fields.
6486 o Surface relaxation terms added to surface tendency fields in
6487 extra subroutine.
6488 o impldiff.F changed to avoid storing by TAMC of huge intermediate
6489 fields.
6490 o Changes in GMRedi to comply with packaging structure.
6491 o Modifications and bug fixes in KPP package.
6492 o Verification experiment for KPP added (verification/nat_box/)
6493
6494 checkpoint31 (2000/09/11)
6495 o Packages interface brought in line with defined standard
6496 -> new routines packages_...F
6497 -> changes in initialise_fixed.F, initialise_varia.F
6498 -> enables initialisation interface for ECCO package
6499 o Rescaling of external forcing fields immediately after read
6500 (removed from external_forcing.F)
6501 -> new: surface_fields_scale.F
6502 -> affects ini_foorcing.F, external_fields_load.F
6503 o Computation of surface tendencies before tendency updates.
6504 -> new: external_forcing_surf.F
6505 o Change of variable names useGMRedi, useKPP, useECCO
6506 o Further changes in dynamics.F, impldiff.F for TAMC
6507 o Tested for experiments 0, 2, 4.
6508 - not yet tested for GMRedi.
6509 - not yet tested for KPP.
6510
6511 checkpoint30 (2000/07/13)
6512 o Updates for OBCs
6513 o New experiment for test OBCs (internal_wave)
6514 o New output.txt in verification/exp4/results/
6515 o Updates for KPP: calculation of viscosity corrected, new variables
6516 kpp_dumpFreq and kpp_taveFreq
6517 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
6518 and entry for T90 in genmake
6519
6520 checkpoint29 (2000/06/21)
6521 o packaged KPP and GM/Redi
6522
6523 checkpoint28 (2000/06/09)
6524 o Corrected initialization of hFacMin for difference vertical coordinates
6525 o Modified calculation of partial cell thickness to more robust algorithm
6526 o config_summary.F: replaced write_1D_... by write_0D_...
6527 read_write.F: added subroutines write_0D_...
6528 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
6529 included some initialisations required for TAMC.
6530 o routine calc_isoslopes: modified sqrt computation to make it
6531 differentiable for zero argument.
6532 o routines dynamics, impldiff:
6533 included store directives and tape key computations required for TAMC.
6534 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
6535
6536 checkpoint27 (2000/04/10)
6537 o fixed calc_isoslopes() to so that cancellation of terms in tensor
6538 formulation works properly with variable resolution.
6539 o restructured the calling tree between the_model_main() and dynamics()
6540 o split initialise() into initialise_fixed() and initialise_varia()
6541 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
6542 in new routine ini_psurf()
6543
6544 checkpoint26 (2000/04/05)
6545 o moved some #ifdef in optional routines to encompass everything
6546 except the argument declarations. This was using up some memory.
6547 o fixed macros like _ADT to work with both versions of Linux cpp
6548 o cleaned up some unused and uninitialized variables
6549 (helps when debugging with strict compile options)
6550 o split up CPP_EEOPTIONS.h into options and macros
6551 (macros are now in eesupp/inc/CPP_EEMACROS.h)
6552 o patch for 2 processor JAM mode
6553
6554 checkpoint25 (2000/03/15)
6555 o updates for OBCs and NH
6556 o dramatically reduced memory usage
6557 o added "JAM" routines for use on Artic network
6558 o parameterization of convection by implicit vertical diffusion
6559 o added a diagnostic of convective index
6560 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
6561 (this is was partly for OBCs and NH but also in anticipation of
6562 an explicit free-surface option)
6563 o initial state input files for U and V
6564
6565 checkpoint24 (1999/08/02)
6566 o Removed some spurious "REAL"s
6567 o Updated KPP to latest version from JPL
6568 o Added a COS(latitude) in horizontal viscosity
6569
6570 checkpoint23 (1999/05/26)
6571 o Added del^4 diffusion for salt and temperature
6572 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
6573
6574 checkpoint22 (1999/05/18)
6575 o Made many small changes: implicit none, format(i5), etc...
6576 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
6577
6578 checkpoint21 (1999/05/18)
6579 o Introduced new I/O package that supports direct-access records (mdsio.F)
6580 o Split-up mid-level I/O routines
6581 o Updated input data for experiments 0,1,2,4 and 5
6582 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
6583
6584 checkpoint20 (1999/03/22)
6585 o Tidied up open-boundaries some more
6586 o Added non-hydrostatic code
6587 o Fixed some input data
6588 o Modified MPI start-up to work in "coupled" context.
6589
6590 checkpoint19 (1998/12/15)
6591 o Tidied up directory structure for verification experiments.
6592 o Added new code for open boundaries.
6593 o Corrected advective terms near boundaries.
6594 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
6595 o Implemented free-slip/no-slip BCs and del^4 dissipation.
6596 o Split default parameters out of ini_parms.F into set_defaults.F.
6597
6598 checkpoint18 (1998/11/30)
6599 o Further changes for optional code generation with
6600 CPP - ugh!
6601
6602 checkpoint17 (1998/11/03)
6603 o Beginning to incorporating modularity
6604 for supporting atmos. and ocean configs.
6605 o Small changes for TAMC complinace
6606 o New ultra simple test case. Barotropic box
6607 configuration "exp0".
6608
6609 checkpoint16 (1998/10/28)
6610 o Minor changes to exchange routines to support
6611 accumulation in reverse mode. Adjoint of an
6612 assignment is an addition.
6613 o Changes to support compilation by TAMC (LR(1)
6614 syntax) and by g77 under Linux ( 72 character
6615 limit ).
6616
6617 checkpoint15 (1998/09/29)
6618 Rewrote exchange routines to allow
6619 o General tile <-> tile connectivity.
6620 o TAMC reverse mode flag ( is this really needed? )
6621 o Variable width overlap and exchange region widths.
6622 o Hooks for sharing data via DMA, Arctic, Memory Channel,
6623 shmput/shmget, VIA, SYSV shmem and every other cool
6624 communication method.
6625
6626 checkpoint14 (1998/09/09)
6627 Consistent isomorphism chages made. These allow dynamical core
6628 to support both pressure and meters as a vertical coordinate.
6629
6630 checkpoint13 (1998/07/17)
6631 Release which corrects global_max problem and a couple
6632 of KGM time-averaging diagnostic errors. Also contains
6633 a double-gyre experiment setup as well as the baseline
6634 4 degree global template. The double gyre template is
6635 organised to allow it to be applied automatically to
6636 the baseline configuration.
6637
6638 branch-point-rdot
6639 A few tidy-ups have been made bt the real point of this
6640 check-point (excuse the pun) is to allow a branch to be
6641 made for the purposes of adding the rDot alterations.
6642 I don't want to commit the rDot to the main-trunk until
6643 we've actually tested it...
6644
6645 checkpoint12 (1998/07/08)
6646 Tidy up and added generic genmake script (formerly
6647 configure script).
6648 Released to testers.
6649
6650 checkpoint11 (1998/07/02)
6651 Re-arranged initialise() and introduced ini_vertical_grid()
6652 and ini_masks_etc().
6653
6654 checkpoint10 (1998/07/01)
6655 Introduced the configure script.
6656 Separated out the diags package.
6657 Added template for writing time-averages of tile/intermediate quantities.
6658 Updated SIZE.h in exp2 and made the data big-endian.
6659
6660 checkpoint9 (1998/06/22)
6661 MPI fix. Filename changes (meta/data). salbin*y stuff.
6662 General tidy-up.
6663 SST.bin SSS.bin added to verification/exp2
6664
6665 checkpoint8 (1998/06/22)
6666 Inludes time-dependant forcing and time-averaging.
6667 Works at 4x4 and 2.8125x2.8125 global
6668
6669 checkpoint7-4degree-ref
6670 Branch from checkpoint7. Released for application to
6671 global modeling and general modeling - process studies, regional
6672 model etc..
6673 Configured for verification/exp2 - 4 degree global, two process.
6674
6675 checkpoint7 (1998/06/15)
6676 Created by cnh
6677 Simple 4 degree global simulation
6678 configuration.
6679 Includes climatological wind,
6680 hydrography, bathymetry etc
6681 Does not include Heat Flux and E-P
6682
6683 checkpoint6 (1998/06/08)
6684 Created by cnh
6685 merged checkpoint5 with CD and
6686 spherical polar code.
6687 Still some problems with GM Redi
6688 abd full topography.
6689
6690 checkpoint5 (1998/06/08)
6691 Created by AJA
6692 contains updates to GM Redi
6693 and reordered timestepping loop
6694 for Implicit Diffusion.
6695
6696 checkpoint4 (1998/05/30)
6697 Created by cnh
6698 Contains memory saving macros ( _rdxc etc..) for when
6699 grid variations are limited.
6700 Contains polynomial coeffs for EOS and knudsen program
6701 for generation.
6702
6703 checkpoint3 (1998/05/26)
6704 Created by cnh
6705 Added extra flags for runtime options
6706 Added this file
6707 Added implicit free-surface
6708 Added pre-conditioner
6709 Put compare01 into repository ( compare01/... )
6710 Put data and eedata into repository ( verification/exp1 )
6711
6712 checkpoint2
6713 Created by AJA
6714 Added GM/Redi
6715
6716 checkpoint1
6717 Created by AJA
6718 Restructured kloop in dynamics.F
6719 Added non-linear EOS
6720
6721 baseline
6722 Original checked in code

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