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Revision 1.862 - (show annotations) (download)
Tue Aug 21 14:39:43 2007 UTC (16 years, 6 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint59f
Changes since 1.861: +4 -1 lines
checkpoint59f

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.861 2007/08/20 17:44:38 gforget Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 checkpoint59f
8 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
9 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
10 a bounded range (in forward mode)
11 o pkg/ecco, ctrl, autodiff and mom_common:
12 internal parameter controls, completements of implementations
13 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
14 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
15 (not seem any difference in testing results).
16 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
17 at face corners.
18 o pkg/generic_advdiff:
19 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
20 loop range indices for computing vertical advection tendency
21 and do the calculation in the interior only (no overlap) ;
22 for now, only implemented for SOM advection (to save CPU time).
23 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
24 o exch2 adjoint
25 First set of changes:
26 - add exch2 hand-written adjoint templates
27 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
28 This will require cleanup in pkg/autodiff/*.F
29 (changed routines currently kept separate in verif. code/)
30 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
31 that used to hide exch2 or cubed-sphere specific code
32 (commented via 'cph-exch2')
33 o pkg/seaice
34 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
35 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
36 output of global_ocean.cs32x15.thsice .
37
38 checkpoint59e
39 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
40 for B-grid vector (not yet tested) and C-grid vector (<- only used
41 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
42 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
43 (#ifdef ALLOW_SALT_PLUME)
44 o gather_2d/scatter_2d: removed halo regions
45 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
46 scheme and the corresponding test case (under front_relax dir). For now,
47 only available with Skew-flux form and not yet tested in realistic set-up.
48 adjoint: store directives updated, but gradient checks deteriorated,
49 so maybe GM/Redi adjoint is now broken.
50 o seaice adjoint
51 * add AREA, HEFF, HSNOW as control variable
52 (should not change lab_sea results)
53 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
54 o pkg/seaice:
55 * added computation of saltFlux in seaice_growth;
56 For time being, sea ice salinity is assumed constant
57 contribution of snow flooding to freshening of sea ice is neglected.
58 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
59 defaults to 0.0 in order to maintain backward compatibility.
60 Typical values for SEAICE_salinity are 4 to 10 g/kg.
61 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
62 * added SEAICE_availHeatFrac, which specifies fraction of surface level
63 heat content used to melt or grow ice
64 * commented out cap of HICE: it helps keep ice thinner
65 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
66 * applied OBCS T/S mask to HEFFM sea ice mask
67
68 checkpoint59d
69 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
70 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
71 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
72 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
73 and change default value of parameter "GM_Small_Number";
74 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
75 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
76 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
77 o pkg/ecco: cost function when applying pkg/smooth to controls
78 o pkg/ctrl: add forcingPrecond run time parameter
79 o pkg/seaice:
80 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
81 - fix bug in metric terms of u-equation in LSR solver (implicit part),
82 changes verification/lab_sea
83 - rearrange implicit part of u-equation in LSR solver to make it easier to
84 read, understand, and debug. This causes changes at the truncation level.
85 - fix (serious) bug in the boundary conditions (sign error in the implicit
86 part) of the LSR solver. Changes all LSR results.
87 - fixed problem with HSNOW initialization to avoid thick snow when AREA
88 is initilized with small values - does not change lab_sea results.
89 - added HsnowFile initialization capability
90 o pkg/smooth: addition to model/src and pkg/ctrl so allow
91 initialization of pkg/smooth and application to control vector
92 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
93 o dependencies: pkg/profiles requires pkg/cal
94 o pkg/profiles:
95 - added option ALLOW_PROFILES_GENERICGRID
96 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
97 that interpolation information (grid points and coefficients) is provided
98 within the netcdf input files.
99 -> sample matlab scripts can be found in MITgcm_contrib/gael
100 that allow you to prepare netcdf input files.
101 - also modified: cleaner include statements, cleaner error print statements,
102 cleaner stops when error, and more tests of the netcdf input files consistency.
103 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
104 o pkg/seaice:
105 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
106 requires a new routine: seaice_diagnostics_fill.F
107 - make sure that seaice does not move if not forced (pressure replacement
108 method, Hibler and Ip, 1995), changes results
109 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
110 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
111 It is turned off by default (=-1.), because it changes the results.
112 - make it possible to read AREA from a file, too.
113
114 checkpoint59c
115 o add S/R and diagnostics for oceanic mixed-layer depth
116 o move GMRedi call after all vertical mixing schemes (including KPP)
117 o pkg/thsice:
118 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
119 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
120 o pkg/obcs:
121 - bug fix for balance code
122 o pkg/seaice:
123 - allow values of SEAICE_elasticParm > 1
124 - add new parameter SEAICE_evpTauRelax as an alternative
125 to SEAICE_elasticParm
126 - make lsr boundary conditions free slip (by default), changes result
127 - add code for no slip boundary conditions for lsr
128 - set minimum of zeta to zero (and not 4e8) (changes results)
129 - add a cap on AREA after advecting AREA if seaice_growth is not called
130 o change calculation of Visbeck K:
131 - no longer depend on tapering scheme; instead, compute slope (limited
132 by GM_maxSlope). this is equivalent to what was comuted before with
133 clipping or linear tappering.
134 - fix vertical averaging (wrong by 1/2 level)
135 - leave the old version (but will not be maintained) within
136 #ifdef OLD_VISBECK_CALC / #endif
137 - update output of exp. ideal_2D_oce
138 o change error catch in calc_r_star to improve vectorization
139 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
140 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
141 o adjoint:
142 Re-organized adjoint checkpointing according to Matt Mazloff
143 (but with modifs/completions/cleanups)
144 Storing is now bundled into large arrays to optimized I/O
145 (and second step in cleanup of the_main_loop)
146
147 checkpoint59b
148 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
149 - export/import (between ocean & coupler) fields needed for ocean DIC.
150 o pkg/seaice:
151 - get rid of three more exchanges seaice_calc_viscosities (required
152 different loop boundaries in seaice_lsr and seaice_ocean_stress)
153 - bug fix in seaice_ocean_stress (update of lab_sea required)
154 - reduce loop boundaries to necessary minimum also in seaice_evp
155 - go back to the old way of computing deltaC/Z as the adjoint likes that
156 better
157 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
158 passive tracer to an Age Tracer) + update output.txt
159 o pkg/exf:
160 - implement A-grid / C-grid selection for wind-stress input files.
161 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
162 for now, in exf_bulk_largeyeager04.F only :
163 - change implementation for case where windspeed + 2. components wind-stress
164 are read-in. AND use rhoConstFresh to convert evap.
165 o pkg/seaice:
166 - use correct EXCH_UV for wind-forcing (on A-grid).
167 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
168 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
169 o pkg/exf:
170 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
171 EXF_INTERPOLATION:
172 - merge global_with_exf/code version of exf_interp_read.F
173 to the main code ;
174 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
175 reading the file ; Important: This options needs to be defined to recover
176 previous code.
177 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
178 - no longer loose real*8 precision along the way when using exf_iprec=64.
179 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
180 - change discretisation of evp-solver in order to avoid another exchange
181 (changes lab_sea) and clean up a little
182 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
183 help the adjoint (this also changes the results slightly)
184 - add a few "_d 0" where they had been missing in seaice_evp.F
185 - cleaning up: remove unused seaice_calc_rhs.F
186 o pkg/exf: some cleaning-up:
187 - change various "constants" into runtime parameters
188 - cleaned-up Large&Yeager04 routine which should eventually
189 replace exf_bulkformulae.F (changed names of S/R and CPP)
190 and merged various ALLOW_ATM_WIND options
191 only used with thsice pkg (in thsice_get_exf.F):
192 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
193 which are used when useStabilityFct_overIce=TRUE (= the default)
194 - change default values of ice & snow emissivity and scale downward LW
195 by ice & snow emissivity.
196 o pkg/thsice:
197 fix few little problems, in thsice_calc_thickn.F:
198 - growth vertically (and not laterally) if iceFrac == iceMaskMax
199 - melt only laterally if hIce < hThinIce (as the comments say)
200 and in thsice_extend.F:
201 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
202 - start to form ice as soon as the minimum ice-volume is reachable.
203 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
204 and cpl_aim+ocn
205 o pkg/kpp
206 - move computation of surface related input fields to KPP into a new
207 subroutine kpp_forcing_surf.F
208 - remove wrong (within bi,bj loops) EXCH calls.
209 - little cleaning (add argument myThid in last position, cvs header ...)
210 - for now, fix conservation problem by exchanging KPPviscAz (may not
211 be the best fix)
212 o pkg/seaice
213 - check for inconsistent evp parameter/cpp-flag combination
214 - remove leftover errIO flat for obsolete name list error handling
215 o OpenAD
216 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
217
218 checkpoint59a
219 o pkg/seaice: some parameter clarifications and a little bit of clean up
220 o pkg/thsice: rename run-time parameters:
221 himin -> hIceMin
222 himin0 -> hThinIce
223 hihig -> hThickIce
224 i0 -> i0swFrac
225 transCoef -> bMeltCoef
226 frac_energy -> fracMelting
227 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
228 with default values (for now) that do not change the results.
229 remove old version of thsice vars advection in pkg/seaice.
230 o in FFIELDS.h:
231 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
232 - make pLoad & sIceLoad always available (but still only used if
233 ATMOSPHERIC_LOADING is #define).
234 o pkg/kpp: replaced _KPP_RL with _RL
235 o bug fixes for vertical diffusivity computations when both KPP and
236 3D diffusivity arrays are used.
237 o pkg/seaice: fix bug in evp solver, while doing that
238 - change (improve?) discretization of stress computations for both
239 cgrid-lsr and evp solver
240 - add a new routine to compute strain rates
241 - the above changes lab_sea results
242 - add no slip conditions for evp solver (off by default), lsr-version
243 may follow
244 - fix exchange for shear at Z-points (does not change lab_sea)
245 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
246 (to force the user to pick a time step since there is not "safe" way
247 of choosing it)
248 - add principal stress diagnostics
249 - rearrange fields for evp a little to avoid having to call a: too many
250 exchanges and b: exchanges for stress trensor components which we do
251 not have.
252 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
253 of evp, complete rewrite for lsr case (latter is does not yet work
254 in all cases)
255 o pkg/kpp: add code to have mixing in shelf ice caverns
256 - add myThid to all kpp routines (long overdue)
257
258 checkpoint59
259 o pkg/exf:
260 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
261 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
262 - move exf header files from lower_case.h to UPPER_CASE.h ;
263 add missing cvs Header & Name
264 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
265 - add namelist param. selectStressGridPosition, exf_monFreq
266 - retire many _CLIM routines, and remove data.exf_clim
267 + params moved to data.exf
268 + climsst, climsss now handled by exf_set_gen, i.e.
269 climss?period=0 refers to constant field,
270 climss?period=-12 to monthly forcing
271 - split up namelists in data.exf
272 o pkg/seaice:
273 - remove seaice_exch and seaice_exch_uv
274 - remove superfluous exchange of theta
275 - add myThid to seaice_budget_ocean/ice
276 - add new interface for atmospheric wind forcing (C-grid only)
277 + new routine
278 + two new field (taux, tauy for stress over ice)
279 + removed one global field (DAIRN) for C-grid case only
280 o pkg/thsise
281 - 2nd set of modifs for thsice adjoint in conjunction with exf
282 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
283
284 checkpoint58y_post
285 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
286 vertical diffusivity, similar to that in MOM4; turned on using
287 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
288 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
289 o Added capability for 3D specification of background vertical diffusion
290 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
291 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
292 "data" file that contains the 3D vertical diffusivity coefficients.
293 o ice dynamics (pkg/seaice) with thsice thermodynamics:
294 - add code within pkg thsice to advect & diffuse sea-ice fields
295 similar to (and will replace) what has been added in seaice_advdiff.F,
296 but: - conserving Mass, Heat & Salt.
297 - better when using non-linear advection scheme (not yet fully tested)
298 - can also be used in atmospheric set-up (for now, only the diffusion).
299
300 checkpoint58x_post
301 o IO option for global-file compact format:
302 - add options when generating topology (utils/exch2/matlab-topology-generator)
303 - add I/O capability (pkg/mdsio).
304 - adapt utils/matlab/rdmds.m to read this format.
305 for now long-line format not yet supported by pkg/mdsio (& exch2).
306 o shelfice: add a few diagnostics
307
308 checkpoint58w_post
309 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
310 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
311 (and replace horiVertRatio in NH code).
312 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
313 and tutorial_plume_on_slope (sensitive to truncation)
314 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
315 directly to drive seaice model (C-grid only)
316 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
317 - reintroduce computation of wind from stress,
318 - compute tau (in exf_bulkformulae.F) from windstress averaged to
319 mass points to avoid tau = 0
320 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
321 o rdmnc.m: make it work with "global" files created with gluemnc
322 o rdmnc.m : some improvements in dealing with singleton dimension
323 (tested on all testreport mnc output files).
324 o genmake2: disable pkg/profiles if netcdf test fails.
325 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
326 o move call to cal_readparms up to make calendar parameters/variable available
327 to all packages
328
329 checkpoint58v_post
330 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
331 useDynP_inEos_Zc tested.
332 o pkg/exf: changes to properly interpolate/mask/scale initial fields
333 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
334 and portions thereof. See read_cs.txt for description and examples.
335 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
336 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
337 following the great-circle arc between those 2 points.
338 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
339 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
340 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
341 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
342 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
343 - still needs work (not working with some options ; efficiency to improve)
344 and serious testing.
345 - use this scheme for temperature & salinity in 2 advection test exp.:
346 advect_xy & advect_xz, respectively.
347
348 checkpoint58u_post
349 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
350 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
351 o testreport: add option "-skipdir" to skip some test.
352 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
353 momentum calculation.
354 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
355 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
356 remove checkpoint.F and the_correction_step.F (no longer used);
357 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
358 o add option (linFSConserveTr) to correct for tracer source/sink due to
359 Linear Free surface
360 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
361 o pkg/thsice: fix reading mnc-pickups
362
363 checkpoint58t_post
364 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
365 o pkg/mdsio:
366 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
367 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
368 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
369 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
370 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
371 either MDS_READ_FIELD or MDS_WRITE_FIELD )
372 - new S/R (to replace MDSWRITEMETA), which allows to write more
373 informations (variable names, time ...) to meta files.
374 - modify rdmds.m to give back the meta file content.
375 o pkg/diagnostics: change vertical interpolation to be safer, and more
376 flexible (define p-levels to interpolate to in data.diagnostics);
377 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
378 diagnostic pointer.
379 o pkg/seaice: more cleaning up of seaice_growth, added many comments
380 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
381 o fix multi-category seaice:
382 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
383 SEAICE_MULTICATEGORY
384 - fix short wave heat flux
385 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
386 and allow to use EVP solver. Change forward lab_sea: test both EVP
387 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
388 o Initial check-in of lab_sea adjoint
389 (very similar to natl_box_adjoint/code_seaice)
390 * used C-grid and EVP solver
391 * used KPP, GM/Redi
392 * uses inAdExact=.TRUE.
393 * gradient checks fail for both ADM and TLM
394 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
395 f.d. gradients actually seem more problematic than ADM, TLM gradients;
396 issue is related to forward mismatch between g77 an ifort
397 o pkg/seaice: overhaul of thermodynamics
398 - growth.F and groatb.F are replaced by new routine seaice_growth.F
399 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
400 - move a few global fields out of SEAICE.h into seaice_growth.F and
401 make them 2D (FICE/QNETO/ ...)
402 - remove FO (it is the same as QNETO)
403 - introduce a few local fields to avoid modifying external fields such
404 as atemp, etc.
405
406 checkpoint58s_post
407 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
408 changed exf_set_gen.F so that
409 genperiod=0 means input file is one time-constant field and
410 genperiod=-12 means input file contains 12 monthly means
411 o CG2D: use pre-computed solver main-diagonal (stored in common block);
412 this affects truncation error ; generate new output file for exp. which
413 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
414 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
415 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
416 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
417 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
418 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
419 o start implementation of deep-atmosphere and anelastic formulation
420 o verification: remove 2nd copy of input files and use script "prepare_run"
421 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
422 o mom_common/vecinv/fluxform: fix a few initialisation isssues
423 o profiles: fix for multithreaded case
424
425 o diagnostics: rename few diags:
426 s/'PRESSURE'/'RCENTER '/g
427 s/'TICE '/'oceFreez'/g
428 s/'TAUX '/'oceTAUX '/g
429 s/'TAUY '/'oceTAUY '/g
430 s/'SWFLUX '/'oceQsw '/g
431 s/DIFx/DFxE/g
432 s/DIFy/DFyE/g
433 and add few ocean-forcing diagnostics:
434 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
435 o modifications to pkg/seaice/growth.F and budget.F, which change results of
436 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
437 as actual snow thickness. It now refers everywhere to effective snow
438 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
439
440 checkpoint58r_post
441 o modifications to pkg/seaice/growth.F, which change results of
442 lab_sea experiment: fixes pertain to melting snow over open water, to
443 masking EVAP under sea ice, and to using the correct AREA variable for
444 computations of EVAP, PRECIP, HSNOW, and GHEFF
445 o add ability to read bathy, salt, and theta using MNC (off by def)
446 o add flooding algorithm and advection of HSNOW for pkg/seaice;
447 both are turned off by default and do no change any results
448 o seaice advection with pkg/thsice: a step toward the use of non-linear
449 advection scheme, but #ifdef or commented out for now (requires more EXCH).
450 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
451 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
452 in natl_box (affects results @ truncation level: update output.txt)
453 o multi-threading and IO:
454 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
455 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
456 (needed to work with SingleCpuIO): tested in all verif. exp.
457 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
458 affects the results (but none of the verification test uses this scheme).
459 o Adding some pkg/diagnostics capability to pkg/seaice
460 (will certainly be subject to changes)
461 o ctrl: adding new control variables:
462 lwflux, lwdown, evap, snowprecip, apressure, runoff
463
464 checkpoint58q_post
465 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
466 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
467 high_res_cube configuration by 4% on Columbia.
468 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
469 add (in global_with_exf/code) a version of EXF_INTERP_READ without
470 dynamical allocation (seems to work in multi-threaded).
471 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
472 single CPU io) so that TAF does not have to see EESUPPORT.h
473 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
474
475 checkpoint58p_post
476 o obcs: stop if obcs is used with useCDscheme = .true.
477 o shelfice:
478 - fix a sign error so that no slip at shelfice interface works
479 - remove stop for combination non-hydrostatic code and shelfice. That does
480 not mean, that the results are correct, but at least they are numerically
481 stable
482 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
483 o added adjoint exch routined for all exch*3d* routines
484 and updated flow directives
485
486 checkpoint58o_post
487 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
488 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
489 o change controling S/R for writing pickup file (new S/R do_write_pickup)
490 and clean-up reading/writing of pickup files.
491 o fix local version of read/write pickup (NH part) in rotating_tank/code
492 o simplify EXCH interface:
493 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
494 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
495 o added the regrid package
496 o shelfice:
497 - add a simple boundary layer scheme to reduce noise
498 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
499
500 checkpoint58n_post
501 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
502 local variable (not in common block).
503 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
504 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
505 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
506 to work with SingleCpuIO.
507 o add "_d 0" to real constant of pkg/cfc subroutines ;
508 update exp. cfc_exemple & tutorial_cfc_offline output files.
509 o multi-threading and IO:
510 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
511 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
512 - barrier before and after reading.
513 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
514 - avoid using MDS_WRITELOCAL for LAND pkg output.
515 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
516 common-block variables ; Allows multi-threading with master-thread IO.
517 o change default MAX_NO_THREADS from 32 to 4 ;
518 and stop cleanly when MAX_NO_THREADS is too small.
519 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
520
521 checkpoint58m_post
522 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
523 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
524 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
525 keep global_ocean.90x40x15 (for AD testing) with former secondary test
526 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
527 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
528 add MITgcm_tutorials (= code + all the tutorials)
529 o ecco, option to compute cost for total ssh (mean+anom)
530 o consistent with addition of ptracer and ssh in pkg/profiles
531 o profiles: adding ptracer and ssh
532 o testreport: change multi-test output-file name
533 (from output.txt.{name} to output.{name}.txt)
534 o profiles: now ok for mutli-tiles case
535 o seaice: add 4 parameters for different advection schemes for area,
536 (effective) seaice thickness, enthalphy, and snow height. Their default
537 is the standard parameter SEAICEadvScheme
538 o calc_gw:
539 - add cosFacU in zonal viscous flux (harmonic.visc.).
540 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
541 of tutorial_plume_on_slope.
542 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
543 o calc_gw: true flux-form, account for horizontal grid spacing.
544 update rotating_tank results, but not plume_on_slope (affected at
545 truncation level, 11 digits).
546
547 checkpoint58l_post
548 o calc_gw:
549 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
550 - remove side-drag for now (need to fix it); update plume_on_slope results.
551 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
552 o commit code to make SST/SSS weights spatially variable
553 (based on either variable in-situ or variable initial T/S weights)
554 o pkg/ecco:
555 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
556 now based on horizontally varying weights wthetaLev, wsaltLev
557 * cost_averagesflags now returns year indices in addition to day, month
558 * sflux balance is performed on annual basis
559 (sflxumm, sfluxmm2, bal_sfluxmm)
560 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
561 including separate counting and multipliers
562 o pkg/rbcs
563 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
564
565 checkpoint58k_post
566 o testreport:
567 - always build in dir. "build" (if not there, mkdir build instead of building
568 & running in input)
569 - run in dir run (if it exists), in build otherwise.
570 - call prepare_run (if input/prepare_run exists)
571 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
572 o pkg/exf modifications to interpolation and rotation routines for more
573 reasonable treatment of North Pole singularity: for tracers North Pole
574 value is set to northernmost zonal-mean value, for zonal velocity it is
575 set to zero, and for meridional velocity it is set to northernmost value.
576 o pkg/exf/exf_check_range.F
577 - add tile index to diagnostics and move stop statement to the very
578 end of the routine.
579 o pkg/diagnostics: (diagnostics_main_init.F)
580 define title of isomorphic variables according to the current config.
581 o pkg/thsice with pkg/seaice dynamics:
582 - fix domain of computation (interior only, required for exf) and do exchanges
583 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
584 o towards a standard way of dealing with multi-threading in MONITOR
585 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
586 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
587 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
588 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
589 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
590 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
591 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
592 o tracer advection:
593 - clean-up and simplify calc_common_factors.F
594 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
595 advection subroutine (but still not used within DST advection S/R)
596 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
597
598 checkpoint58j_post
599 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
600 from file (collects calls previously in FORWARD_STEP)
601 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
602 o adjoint store dir. adjusted accordingly
603 o genmake2
604 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
605
606 checkpoint58i_post
607 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
608 on wind stress (SEAICEstressFactor defaults to 1.)
609 o Total number of Timers is finite (<=40): comment out 2 non-essential one
610 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
611 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
612 on CS-grid: no longer loosing mass.
613 o exf & curvilinear-grid: no longer modify longitude xC & xG.
614 o pkg/ggl90: fix sloppy output and fix a bug
615 o pkg/seaice: added SEAICEuseEVPpickup parameter
616 - Set to false in order to start EVP solver with
617 non-EVP pickup files when using SEAICEuseEVP
618 - fix sign error in diffusion in seaice_calc_rhs
619
620 checkpoint58h_post
621 * Modifications for bottom topography control
622 o replace hFacC by _hFacC at various places
623 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
624 o add non-self-adjoint cg2d_nsa
625 o update autodiff support routines
626 o re-initialise hfac after ctrl_depth_ini
627 o works for 5x5 box, doesnt work for global_ocean.90x40x15
628 * Adding verification for 5x5 box (4-layer) bottom topography control
629
630 checkpoint58g_post
631 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
632 used for mean seasonal cycle, mean diurnal cycle); add an example
633 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
634 o pkg/ggl90:
635 - add parameter (minimum surface kinetic energy)
636 - fix bug (avoiding division by zero)
637 o couple pkg/thsice to pkg/seaice:
638 - modify advection in seaice to accomodate new scalar fields to be advected
639 - only muliDimAdection scheme work with seaice/thsice
640 - mapping of thsice-variables to seaice-variables, back and forth
641 - does not break the verification experiments, but does not give the
642 desired results either
643 o pkg/seaice
644 - make (default) second order advection a bit less confusing?
645
646 checkpoint58f_post
647 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
648 to pkg/seaice):
649 - new routines thsice_map_exf and thsice_get_exf provide the interface
650 - add an additional formal parameter to thsice_solve4temp
651 o pkg/exf:
652 - add new fields wspeed, snowprecip (to be able to couple to thsice)
653 - correct Stefan-Boltzmann constant
654 - new parameter for longwave surface emittance
655 - separate some stuff from exf_bulkformulae into new routines
656 exf_radiation, exf_wind
657 - add new parameters and constants: longwave emissivity for ocean, ice
658 and snow, evaporation parameters over ice
659 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
660 either wind from stress or stress from wind
661 o pkg/thSIce:
662 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
663 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
664 and THSICE_CALC_THICKN
665 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
666 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
667 to make debugging easier.
668 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
669 o pkg/bulk_force:
670 - clean-up comments and parameters ;
671 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
672 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
673 generate new output for test-experiment: aim.5l_cs.thSI
674 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
675 testreport accordingly
676
677 checkpoint58e_post
678 o SEAICE_CGRID adjoint done
679 o R_STAR adjoint implemented.
680 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
681 * need to sort out init. of h0facc, etc.
682 o Make pkg/profile fully independent of ecco,cost, etc. stuff
683 to be able to use it in pure forward.
684
685 checkpoint58d_post
686 o upgrade simple test-experiment to tutorial example:
687 step.1: duplicate the experiment and (step.2) will remove the old copy.
688 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
689 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
690 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
691 tutorial_global_oce_biogeo <- copy of dic_example
692 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
693 tutorial_plume_on_slope <- copy of plume_on_slope
694 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
695 tutorial_global_oce_optim <- empty for now (David ?)
696 tutorial_global_oce_in_p <- copy of global_ocean_pressure
697 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
698 o correct a sign problem in cost_scat.F
699 o obcs and ptracers: fix boundary conditions for advections schemes
700 with larger stencil
701 o thsice adjoint: start
702 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
703 completeness
704 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
705 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
706 o ptracers adjoint:
707 * avoid extensive recomputatations
708 * fix missing re-init. of gptr (missed by TAF)
709 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
710 me to turn off the excessive output to STDOUT that this package produces
711 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
712 and add those terms in Vector-Invariant formulation.
713 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
714 if the control period (xx_hfluxperiod etc) is 0
715 o in profiles pkg, clean routines and fix details
716 o in ecco pkg, reading ssh data:
717 fix problem in case the model does not start at iter0=0
718 o fix mnc-pickup/restart for ptracers
719 o new package prifiles:
720 code to compute profile-based cost by Gael Forget
721 (modifs in ecco, ctrl, autodiff)
722 o Benign bug fix in initialization (spotted by M. Mazloff) of
723 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
724
725 checkpoint58c_post
726 o adjoint: finish NLFS adjoint and provide reference output in
727 verification/global_ocean.90x40x15/results_ad_nlfs
728 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
729 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
730 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
731 with SEAICE_CGRID defined.
732 o move calendarDumps from "data" to "data.cal" and clean-up the code
733 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
734 o add useEXF & useCAL flags (for now, set in hard-coded way)
735 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
736 (were missing in NH mode, and wrong in quasihydrostatic mode).
737 waiting for Chris updated version of calc_gw to add those CALLs.
738 o fix bug in quasihydrostatic S/R ;
739 add a test for this option: global_ocean.90x40x15.qshyd
740 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
741 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
742 o add on/off flag useOffLine for package OFFLINE
743 o seaice:
744 - modify advection so that it works also on the C-grid
745 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
746 problem in multi-tile runs with C-grid
747 - add flags for clipping ice velocities and/or masking solver forcing
748 - fix drag (ocean on ice) formulation and a bug that caused noise in the
749 C-grid solver
750 - added a few comments to seaice_diffusion.F
751 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
752 are now exclusive)
753 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
754 required re-ordering the code a little:
755 + make DAIRN global variable (defined in SEAICE)
756 + move computation of the viscosities eta and zeta into a new separate
757 routine (because I need to recompute them in seaice_ocean_stress.F)
758
759 checkpoint58b_post
760 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
761 update output.txt of exp. aim.5l_cs.thSI
762 o various mnc cleanups and improvements:
763 + shrink lookup tables by factor of ~4
764 + better error reporting when running out of lookup space
765 + able to handle longer path/file names (up to 500 chars)
766 o adjoint:
767 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
768 - TBD: "hidden" mom_vecinv recomp. in dynamics
769 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
770 (allow to differentiate between forcing components using new integer flags:
771 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
772 and add new flag to put Dissipation tendency out of Adams-Bashforth.
773 o ecco
774 - enable trend removal from SSH anomaly obs.
775 o adjoint
776 - a fix for PmEpR when #undef EXACT_CONSERV
777 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
778 - try to fix "hidden" recomp. in forward_step for NLFS
779 (NLFS seems broken sometimes after I checked it in)
780 o seaice:
781 - add c-grid version of the dynamic solver:
782 + three new routines that are the c-grid substitute lsr, dynsolver
783 and ostres
784 + put a few fields that were local to dynsolver into global common
785 blocks, so that I can move the computation of stresses etc into
786 seaice_lsr (saves coding but may break the adjoint).
787 - replace more hardwired parameters by runtime parameters
788 - add ice masks that mask the rhs of the implicit solvers where there
789 is no ice (commented out in seaice_dynsolver, because i am not sure
790 if this works properly), eventually this should replace the clipping
791 of ice velocities in seaice_dynsolver to +/-40cm/s.
792 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
793 include it only where its needed
794 o move balancing of fluxes before the call of external_forcing_surf
795 o seaice:
796 - correct units of turning angles (now they are really in degrees)
797 - move computation of GWATX/Y out of main routine into dynsolver
798 - initialize GWATX/Y in seaice_init
799 o Apply mask on Fresh-Water flux (needed for SSH forcing).
800 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
801 o seaice: add runtime flags for turning angles (default to zero)
802 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
803 and trend from exf forcing and ctrl control adjustments
804 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
805 (since checkpoint57x_post)
806 o change the default rotation period to 86164.s = the Earth rotation
807 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
808 and based on a reference stratification. Tested within hs94.cs-32x32x5.
809 o seaice advection: add code for choosing between the default (2nd order
810 central differences) and multiDim advection schemes provided by
811 pkg/generic_advdiff
812 o seaice:
813 - removed all references to SEAICE_GRID.h fields from
814 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
815 (cubed-sphere configuration will change a little)
816 - grid computations in seaice_init are obsolete now.
817 - cleaned up code a little so that is easier to read (hopefully).
818 - added new (better?) discretizations of default advection and diffusion
819 (turn on with SEAICEuseFluxForm)
820 - replace 1 in 3d global fields by kSurface in growth.F
821
822 checkpoint58a_post
823 o seaice:
824 - bug fix in advect.F
825 o shelfice:
826 - separate shelfice load anomaly from pload (breaks with time
827 dependent forcing), => introduce constant field shelficeLoadAnomaly.
828 Its default is 0., but it may be computed more cleverly from (unknown)
829 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
830 done offline. A good approximation of the pressure load anomaly is
831 necessary to avoid large initial adjustment processes underneath
832 deep-reaching shelfice.
833 - small fix in ISOMIP shelfice_thermodynamics
834 - add more sophisticated thermodynamics of Hellmer (1989), this is
835 now the default
836 - give a few constants more intuitive names
837 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
838 if bulk formulae are used in long integration (especially EmPmR). Turn
839 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
840 if balancePrintMean, the imbalance that is substracted is printed to
841 STDOUT.
842 o fix bug (typo) in obcs_apply_eta.F
843 o add a new package shelfice which enables us to model the circulation
844 underneath shelf-ice with draughts of hundreds of meters.
845 - works
846 - to do: + include improved thermodynamics
847 + check whether kSurfC (from model/inc/SURFACE.h) can be used
848 instead of new field kTopC
849 + can we use topoFile, Ro_surf and existing code in ini_depth.F
850 instead of new field R_shelfIce and new code in ini_depth.F
851 and ini_mask_etc.F?
852 + adjust vertical mixing schemes?
853 o seaice pkg:
854 - add a cpp-flag to include a simple formula for a salinity dependent
855 freezing point of sea water at the surface
856 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
857 meridional stresses are now different (and hopefully correct)
858 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
859 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
860 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
861 o pkg/diagnostics: add options and parameters for regional-statistics
862 diagnostics ; define regions by reading a region-mask from a file
863 (might add other options later)
864 o pkg/bulk_force:
865 - add option and parameters to use AIM surface-flux formulae.
866 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
867 others forcing fields (defined in PARM05, parameter file "data") are loaded
868 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
869 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
870 - use the right EXCH call for uwind,vwind (to work on CS-grid).
871 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
872 and parameters (note: calcWindStress replaces .NOT.readwindstress).
873 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
874
875 checkpoint58
876 o add "--embed-source" option to genmake2 which, when the supporting
877 tools can be compiled (as determined by genmake2) will turn on the
878 embed_files package which then embeds the entire MITgcm source code
879 (*.[fFhc] + Makefile) used for the build within the executable
880 - requested by CNH but off by default
881 - adds a paltry <9MB to the mitgcmuv executable in most cases
882 - only writes the output when useEMBEDSRC in eedata is true
883 o clean up 3-dim. relaxation codes:
884 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
885 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
886 * Thanks to Tom Haine for testing!
887
888 checkpoint57z_post
889 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
890 affects output (@ truncation level) of exp. plume_on_slope ; updated.
891 o fix the pickup behavior for obcs in combination with ptracers
892 o fix a bug in ptracers_external_fields_load
893 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
894 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
895 o transfered surface NH pressure to eta field (if exactConserv).
896 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
897 and update lab_sea output.txt file.
898 o completing 3-dim. relaxation code: additional term
899 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
900 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
901 * At compile time, in "EXF_OPTIONS.h" set
902 #define ALLOW_CLIMTEMP_RELAXATION
903 #define ALLOW_CLIMSALT_RELAXATION
904 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
905 tauThetaClimRelax3Dim = 15552000.0,
906 tauSaltClimRelax3Dim = 15552000.0,
907 * 3 cases:
908 1) Use a constant-in-time 3-dim. field
909 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
910 3) Real-time relax. to time-evolving prescribed field
911 o Adding Laplacian-type smoothness constraint on
912 initial and boundary (forcing) controls (ic, bc)
913 * enable at compile-time via
914 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
915 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
916 * Absolute scale somewhat unclear so far
917 * no area weighting was included since no other cost term does so far
918
919 checkpoint57y_post
920 First step for a NLFS adjoint
921 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
922 o new init. routines for calc_r_star, calc_surf_dr
923 o still need to deal with ini_masks_etc
924 o testreport seemed happy
925 checkpoint57y_pre
926
927 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
928 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
929 o add new offset feature to offline pkg (plus minor cleanup)
930 o cfc fixes for final year of integration
931 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
932 be in GCHEM_OPTIONS).
933
934 checkpoint57x_post
935 o fix testreport Pb in multiple test experiment.
936 o cleanup our namelist syntax in verification:
937 - make it more F95 standards compliant (some work still needed)
938 - allows the vast majority of our tests to work with gfortran
939 o Non-Hydrostatic:
940 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
941 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
942 o Allow to apply AB on T,S rather than on AB(gT,gS):
943 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
944 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
945 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
946 - need a "clever" read_pickup to restart from the other AB formulation
947 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
948 o remove some unused variables (reduces number of compiler warnings)
949 o adjoint
950 * Disable useVariableViscosity for adjoint for time being
951 (there are a number of extensive recomputations)
952 * Initialize certain variables needed for adjoint
953
954 checkpoint57w_post
955 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
956 fix the singleCpuIO RS version of MDSWRITEFIELD
957 and add a WARNING if using globalFiles=T with multi-processors.
958 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
959 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
960 o tracer advection scheme:
961 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
962 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
963 was not very convenient).
964 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
965 (further tests needed for the implicit DST & Flux-Limiter schemes).
966 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
967 and sRef for convenience, handy, when you want to initialize
968 ptracers in a large domain with a constant non-zero value. Also,
969 untangle ptracers_init.F a little.
970
971 checkpoint57v_post
972 o change dome exp. to use variable viscosity in side-drag terms.
973 o remove all the files from the cfc_offline test since they are now
974 incorporated into tutorial_cfc_offline which has been producing
975 identical results for a few days of testing
976 o add new parameter: sideDragFactor to enable half-slip-side BC
977 and change side-drag S/R to use viscosity from mom_calc_visc
978 (can switch back by setting sideDragFactor=0.); affects results at
979 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
980 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
981 o vorticity & strain are now computed without masking, to account for
982 no-slip-side BC in variable viscosity calculation ; mask is applied
983 anyway later on, before computing advection/coriolis terms.
984 o modify exp4 to test new obcs support for reading from external files
985 and for passive tracers
986 o fix behavior of ptracers_monitor when monitor output is written to a
987 netcdf-file; still not independent of monitor.F (writes in the same
988 file).
989 o change default value of tRef (put a uniform, meaningful value for ocean
990 & atmos) and initialize sRef (was missing, as Martin mentioned).
991 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
992 to be proportional to enstrophy dissipation length. Thus,
993 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
994 This is now consistent with Smagorinsky and with the manual.
995
996 checkpoint57u_post
997 o OBCS and PTRACERS: add open boundary support for passive tracers
998 - either use homogenous (pseudo) v.Neumann conditions or prescribe
999 OB-values from file; this is not different from the way theta and salinity
1000 are treated
1001 - however, Orlanski-radiation conditions are not supported, and the model
1002 will stop if you use pTracers and Orlanski at the same time.
1003 - beefed up the rountine obcs_external_fields_load: now only those open
1004 boundary values are overwritten with values from files for which there
1005 are really files, otherwise the OB-fields remain untouched. This makes
1006 it possible to use different OBs at different ends of the domain (as
1007 with EXF)
1008 o reduce number of exch calls in shap_filt (s2).
1009 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1010 truncation level) 4/5 MLAdjust test results (11&12 digits match).
1011
1012 checkpoint57t_post
1013 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1014 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1015 same truncation, independent of the face number: affects affects several
1016 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1017 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1018 note that biharmonic viscosity + no-slip was not tested in any experiment.
1019 o fix bug in non-linear free-surf side-drag ; generate new output for
1020 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1021 o make mnc honor the writeBinaryPrec flag for most kinds of output
1022 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1023 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1024 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1025 o add brackets in multi-terms sum to get same truncation, independent of
1026 the face number (manage to get exactly same value of gU,gV at the cs-edge)
1027 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1028 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
1029 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1030 a maximum grid-scale Reynolds number. Also, changes all length calculations
1031 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1032 Suggested values of viscosity parameters found in mom_calc_visc.
1033 Many new viscosity diagnostics available.
1034
1035 checkpoint57s_post
1036 o Add clearing-house for viscosity calculations, mom_calc_visc and
1037 correct numerous bugs in LeithD and Smagorinsky discretizations.
1038 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1039 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1040 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1041 and with Strain-Tension viscous term calculation (mom_hdissip.F).
1042 The Strain-Tension form is now called with useStrainTensonVisc=.true.
1043 ViscAhStrain and viscAhTension are now retired.
1044 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1045 o In response to JMC's bug report, genmake2 now ignores any soft-links
1046 that it finds in the *current* directory when searching for files.
1047 Soft-links found in any other source directories will still work as
1048 they did before.
1049 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1050 a C routine to unlimit the stack size
1051 o mnc-ify pkg/aim snapshot vars
1052 o mnc-ify pkg/land as requested by Daniel
1053 o various changes to mnc including:
1054 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1055 - output can now be grouped so that all files within a group
1056 change the ITER portion of their names in lock-step together
1057 - can now read ("global") PER-FACE (in addition to PER-TILE) files
1058 and works with both EXCH1 and EXCH2 (but needs more testing)
1059 - writing works for all verification test cases w/ g77 on Linux
1060
1061 checkpoint57r_post
1062 o make MNC variable initialization happen earlier
1063 o add diagnostics for (almost) each term of the momentum Eq.
1064 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1065 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1066 o remove MINIMAL_TAVE_OUTPUT option ;
1067 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1068 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1069 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1070 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1071 o add time-dependent SST, SSS control
1072 o cost terms in ecco/ modularized (new cost_generic.F)
1073 o cost_averages routines are modularized (new cost_averagesgeneric.F)
1074 o new infrastructure for seaice model vs. obs misfits in seaice/
1075 * driver from the_main_loop.F is seaice_cost_driver.F
1076 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1077 * gradient check in Exp. 6a of natl_box_adjoint/
1078 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1079 (see README file)
1080
1081 checkpoint57q_post
1082 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1083 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1084 - bug was reported by Jean-Michel and Ian Fenty
1085 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1086 update exp. cpl_aim+ocn output.
1087 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1088 Needed for high-res. runs with large global files
1089 to be able to limit tapelev size
1090 o Changed some tests for adjoint:
1091 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1092 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1093 * global_ocean.90x40x15/ back to default 3-level checkpointing
1094 o Modifications to enable scripted COMMON to MODULE conversion
1095 * verification/OpenAD/code/ has necessary scripts and description;
1096 * converts, compiles and runs successfully;
1097
1098 checkpoint57p_post
1099 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1100 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1101 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1102 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1103 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1104 (was already the case for dissipation with mom_vecinv,
1105 and also the case for grad.PhiHyd when staggered-timeStep)
1106 This will allow to put dissipation out-off the AB time-stepping.
1107 Unfortunately, affects truncation error. Update output of exp. that "fails"
1108 (cg2d matching number) and leave the others for later: front_relax(10),
1109 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1110 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1111
1112 checkpoint57o_post
1113 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1114 (2) its ready to be documented during the 20050801 DocFest
1115 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1116 for ideal_2D_oce and lab_sea on linux_ia32_g77
1117 o set to #undef CTRL_SET_OLD_MAXCVARS_30
1118 in global1x1_tot/code_seaice_adj to access indices 32, 33
1119 (worth another tag)
1120
1121 checkpoint57n_post
1122 o adding precip control xx_precip 32
1123 o adding swflux control xx_swflux 33
1124 o Replacing 10 forcing penalty cost routines by 1 generic.
1125 o Implementing partitioning in time-mean and variable adjustment
1126 for atmos. state.
1127 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1128 o in natl_box_adjoint:
1129 * updated exp 1 to 10
1130 (but does not have time-mean vs. variable split results yet)
1131 o updated global1x1/*_seaice_adj/
1132 to incorporate latest changes
1133 o enable useSingleCpuIO for mdsio vector routines
1134 (applies in particular to tapelev I/O)
1135 o removed inefficient K-loop in all active_file*control*.F
1136
1137 checkpoint57m_post
1138 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
1139 and advect_cs (use EXCH-2 and standard cs-32 grid files).
1140 o pkg/exch2: filling of face-corner halo regions is optional
1141 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
1142
1143 checkpoint57l_post
1144 tag before updating tutorials (pre-release-2)
1145 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
1146 for output and interpolation of input fields onto model grid)
1147 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
1148 Affects results of exp. rotating_tank ; update output.txt.
1149 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
1150 and taking the square quantity and/or using a fraction-weight field.
1151 o fix aim_diagnostics_init.F mate numbers.
1152 o add mnc output capability to diagnostics/diagstat and update
1153 our cvsignore files for the ACSII output generated
1154
1155 checkpoint57k_post
1156 o lab_sea now uses diagnostics package and provides a suite of
1157 new EXF diagnostics output.
1158
1159 checkpoint57j_post
1160 o exf
1161 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
1162 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
1163 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
1164 * extended diagnostics output
1165 - now includes all EXF variables
1166 - hs, hl moved to common block
1167 - separate S/R for diagnostics, called after ctrl vector is added
1168 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
1169 - EXFqnet contains true Qnet (i.e. includes qsw)
1170 * updated verif. lab_sea, global_with_exf
1171 * Rearranging hflux (exf_mapfields -> exf_getforcing)
1172 to ensure that diagnostics sees a true EXFqnet
1173 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
1174 o diagnostics pkg: change pointers so that 1 diagnostic can be used
1175 several times with different frequencies.
1176 o mnc-ify the thsice package as requested by Daniel Enderton
1177 - the monitor--MNC output needs work
1178 - many attributes need to be added (most are currently blank)
1179 o mnc-ify theaim_v23 package as requested by Daniel Enderton
1180 - many attributes need to be added (most are currently blank)
1181 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
1182 o add Sadourny like discretization to the 4th.O vorticity advection scheme
1183 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
1184 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
1185 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
1186 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
1187 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
1188
1189 checkpoint57i_post
1190 o Diagnostics package was changed: diagnostic allocation is now deactivated
1191 by setting an empty file name in the namelist (used to be by setting 0 frequency)
1192 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
1193 add 1rst Order upwind vertical Shear.
1194 o add a quick fix for A/B checkpointing in OFFLINE mode
1195 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
1196 end-run around the C/Fortran linking horror in eesup/src/timers.F
1197 o added pkg/runclock: allows user to terminate run based on wall clock
1198 o added non-hydrostatic scaling parameter: nh_am2
1199 o pkg/my82: futile attempt to make results compiler-independent by adding
1200 some "_d 0", etc. no effect.
1201 o for mnc output, fill the 'T' coordinate var with myTime and create a
1202 separate 'iter' variable for iteration count
1203 o pkg/diagnostics:
1204 add new capability: output of Global/Regional & per-level statistics ;
1205 tested against monitor output (including land & thSIce) on various exp.
1206 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
1207
1208 checkpoint57h_done
1209 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
1210 data.diagnostics, data.gchem, data.ptracers) is done.
1211
1212 o pkg/diagnostics: prepare for Global/Regional statistics.
1213 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
1214 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
1215 and rename it: DIFFERENT_MULTIPLE
1216
1217 checkpoint57h_post
1218 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
1219 o pkg/diagnostics: change output frequency, now in seconds (instead
1220 of Nb of iterations). This requires to change data.diagnostics.
1221 checkpoint57h_pre
1222
1223 o in mnc, let the user create the output dir if both mnc_outdir_date
1224 and mnc_outdir_num are false
1225 o add fflags() to pkg/diagnostics which allows one to specify, on a
1226 per-file basis, the file precision [default behavior is unchanged]
1227 o added diagnostics to pkg/kpp, including computation of mixed layer
1228 depth based on a temperature/density criterion
1229 o updated verification/natl_box to test the new pkg/kpp diagnostics
1230 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
1231 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
1232 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
1233 not mnc -- this mistake was found by JMC and is now corrected
1234
1235 checkpoint57g_post
1236 o add Adams-Bashforth 3rd Order time stepping:
1237 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
1238 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
1239 checkpoint57g_pre
1240
1241 o make lambda[Theta,Salt]ClimRelax spatially varying
1242 (default remains spatially uniform constant based on tau)
1243 o added new control variables
1244 * init. uVel, vVel, etanN
1245 * lambda[Theta,Salt]ClimRelax
1246 o separate masks used for ctrl_pack/unpack 'from write_grid' output
1247 (suggested by G. Forget)
1248
1249 checkpoint57f_post
1250 o add parameter "baseTime" = model base time = time at iteration zero
1251 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
1252 account for baseTime shift
1253 o move Coriolis arrays from PARAMS.h to GRID.h
1254 checkpoint57f_pre
1255
1256 o mnc-ifying the seaice package
1257 o introduced an alternative length scale calculation for use in the limiting
1258 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
1259 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
1260 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
1261 as well as grad(vort3). Made it compatible with both approximate form
1262 for the cubed sphere and full form of these gradients. Added flag
1263 useFullLeith to select between approximate and full form.
1264 o add "d0" in getcon.F to reduce differences between compilers/platforms
1265 update output.txt of exp. fizhi-gridalt-hs
1266 o change port_rand funtion to allow to set the seed.
1267 o fix obscure MNC bug involving conversion between reals and integers
1268 - it caused no problems with certain (eg. gcc, ifc) compilers but the
1269 new version is now more standards-compliant
1270 o adjoint-related modifications
1271 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
1272 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
1273 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
1274
1275 checkpoint57e_post
1276 o Adding eddy stress controls a la Ferreira et al.
1277 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
1278
1279 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
1280 update output.txt of exp. fizhi-gridalt-hs
1281 o add more "Z" dimensions and associated coordinate vars to MNC
1282 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
1283 o parameter calendarDumps: when set, approximate months (30-31 days) and years
1284 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
1285 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
1286 months and years. Requires pkg/cal.
1287 o diagnostics: add pickup functionality
1288 - off by default for backwards compatibility
1289 - current version only uses MDSIO -- MNC will be added
1290 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
1291 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
1292
1293 checkpoint57d_post
1294 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
1295 o modify verification/ideal_2D_oce so that it tests the creation of mnc
1296 output from the diagnostics package
1297 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
1298 o make genmake2 more portable by using ".$FS" instead of ".f" for more
1299 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
1300 o add coordinate variables to the MNC output from the diagnostics package
1301 o change MNC-flags default value: true when useMNC=TRUE
1302 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
1303 the ability (off by default) to read the grid information using MNC
1304 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
1305 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
1306 o do snap-shot diagnostics at the middle of the time-interval (instead of
1307 at the end).
1308 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
1309 new test for AIM with thSIce + slab-ocean
1310 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
1311 o move state variable diagnostics to the beginning of the time step ;
1312 (note: still needs some work specially for snap-shot diagnostics)
1313 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
1314
1315 checkpoint57c_post
1316 o Change testing option (-ieee) to get closer agreement between g77 & ifort
1317 o generate new output.txt files on faulks with g77 & the new -ieee option
1318 checkpoint57c_pre
1319
1320 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
1321 update output.txt of exp. global_ocean.90x40x15
1322 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
1323 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
1324 o add saltFlux(+File) forcing capability with periodicExternalForcing
1325 o allow to use pkg diagnostics for GM-Redi & ThSIce output
1326 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
1327 o improvements for the MNC output from DIAGNOSTICS:
1328 - correct handling of the unlimitied dimension
1329 - all dims now have associated coordinate variables
1330 - variables located at U, V, and Corner ("Z") points are now written
1331 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
1332 *all* data points are output
1333 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
1334 o added pkg/seaice/seaice_monitor.F
1335 o mdsio_readfield.F can now read files visible only to master MPI process.
1336 o pkg/seaice: some test code for ice-modified ocean stress
1337 o exf_getffields interpolation defaults to bilinear for all scalar forcing
1338 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
1339 spurious negative numbers for precipitation and humidity. Will cause
1340 some small numerical differences for integrations using pkg/exf/exf_interp.F.
1341 o pkg/ctrl/
1342 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
1343 May be enabled via doPackDiag
1344 * introduce z-scaling of
1345 + gradient (doZscalePack) and
1346 + control (doZscaleUnpack)
1347 o pkg/mdsio/
1348 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
1349 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
1350
1351 checkpoint57b_post
1352 o simplify options in diagnostics_fill arguments (remove weird combinations)
1353 o fix MNC coordinate variables so that they now contain per-face index
1354 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
1355 general, EXCH2 grids are only aligned to a "local" coordinate system
1356 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
1357 o Implement instantaneous output within pkg diagnostics:
1358 setting a negative frequency in data.diagnostics produces
1359 "snap-shot" output (as opposed to time-average if freq > 0)
1360 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
1361 NOTE: change ptracer diagnostics name: use 2 characters to work with
1362 more than 9 tracers. Add also diagnostics of advect & diffus flux.
1363 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
1364 becomes the coordinate variable for the 'T' dimension
1365 o add CF-style coordinate variables to MNC
1366 - just a first cut: numbers are meaningless on the cubesphere and
1367 missing along the T axis but otherwise it works!
1368 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
1369 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
1370 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
1371 this is based directly on what the model compute, so that the content of
1372 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
1373 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
1374 o clean up build options files for SunOS, in particular
1375 - remove -traditional from xmakedepend
1376 - change -xarch=v9 to -xarch=native for f77
1377 - restore use of make (not gmake)
1378 - add CC=gcc if using g77
1379 o changes per discussion of AM, JMC, & EH3 today:
1380 - move redundant "grid" variables out of "state" -- in preparation of
1381 creating proper CF-style coordinate variables and in recognition
1382 that any/all grid variables can be easily copied (eg. w/NCO) from
1383 the grid files into any of the other NetCDF files
1384 - *always* output grid variables with MDSIO (this will eventually be
1385 changed)
1386 - output MNC grid file if useMNC is true
1387 o every instance of _END_MASTER() has been found and replaced with
1388 _END_MASTER( myThid ) in order to satisfy certain picky Sun
1389 preprocessors
1390 o re-arrange diagnostics pkg initialisation:
1391 - allow each package to extend the available diagnostics list
1392 - add some checking and fix small problems (multi-threaded, ...)
1393 - new S/R diagnostics_fill (replace fill_diagnostics):
1394 look through the short list of active diag. (instead of the long list)
1395 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
1396
1397 checkpoint57a_post
1398 o this set of changes restores TAMC compatibility
1399 tested for global_ocean.90x40x15 adjoint on trough
1400 (what a pain)
1401
1402 checkpoint57a_pre
1403 o some modifs in tools/build_options for sunos
1404 o call ctrl_pack for ctrl at end for optimcycle=0
1405
1406 checkpoint57
1407 o add horizontal bi-harmonic viscosity for vertical velocity
1408 - new parameter viscA4W (defaults to viscA4)
1409 - affects only non-hydrostatic code
1410 - to be done: no-slip lateral boundary conditions
1411 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
1412 o implement Implicit Vertical advection for pTracers
1413 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
1414 (implemented also for implicit vertical diffusion & advection)
1415 o OBCS: extend application of tracer open boundary conditions
1416 to a strip beyond the boundary of width Olx/Oly
1417 o add call monitor to TAF set of required calls (flow directives)
1418 and include in natl_box_adjoint
1419 o untangle a few ifdefs related to cost, ctrl, autodiff
1420 untangel a few ALLOW_ECCO_OPTIMIZATION
1421 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
1422 (theta2, salt2 in ecco_cost_weights)
1423
1424 checkpoint56c_post
1425 o OBCS as control variables
1426 - update ctrl_ad_diff.list, obcs_ad_diff.list
1427 - remove balance of obcs controls from default
1428 - fix index bug nobcs in ctrl_init
1429 - fix dummy fields filen in ctrl_pack
1430 - add dummy weights for obcs
1431 o lsopt: comment out fort.94 output
1432 o optim:
1433 - remove unnecessary header files
1434 - adjusted namelists
1435 - add xerbla.F to Makefile
1436 o exf:
1437 - multiple modifications of exf_check_range
1438 - unit change in exf_init_runoff from [m/year] to [m/s]
1439 o mdsio:
1440 - i/o-vector change debugLevel from debLevA to debLevB
1441
1442 checkpoint56b_post
1443 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
1444 is called from DO_THE_MODEL_IO
1445 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
1446 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
1447 - clean up PTRACERS_WRITE_TIMEAVE a little
1448 o add another verification experiment that tests both the cfc-pkg and
1449 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
1450 reactive tendencies treated inline with regular timestepping
1451 o testreport previously did a lousy job of comparing small numbers, so
1452 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
1453 implemented in the little c-progam tmp_cmpnum.c which is embedded in
1454 testreport.
1455 o ptracers_monitor: bug fix for MPI
1456
1457 checkpoint56a_post
1458 o GCHEM: finish reorganizating the package
1459 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
1460 (introduces another 3D-array for each passive tracer, but only if
1461 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
1462 gchemTendency is not needed because the timestep is done separately)
1463 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
1464 - GCHEM is now---more or less cleanly---separate from PTRACERS
1465 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
1466 so clear to me how that should be done in a general way.
1467 o CFC: improve formatting of output in CFC_ATMOS
1468 o PTRACERS:
1469 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
1470 that ALL experiments with ptracers enable can be checked. This makes
1471 GCHEM_MONITOR obsolete.
1472 - include a runtime parameter PTRACERS_monitorFreq that defaults to
1473 monitorFreq
1474 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
1475 o add PTRACERS (PTR0[1-5]) to testreport output
1476 o exf_check_range:
1477 * default changed to .TRUE.
1478 * will check values for niter0 if debLevA, every timestep if debLevB
1479 * STOP in exf_check_range if 'out of range'
1480 * range chosen generous to allow for potential extema
1481 TBD: a version with stricter range
1482 permitted range would be runtime parameters
1483 o GMredi:
1484 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
1485 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
1486 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
1487 o GCHEM:
1488 - move call to GCHEM_FORCING_SEP, so that it is now called before
1489 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
1490 - introduced a useGCHEM runtime flag and applied it everywhere.
1491 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
1492 this flag is now only visible within GCHEM-pkg routines.
1493 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
1494 be replaced by a 3D array that is computed before thermodynamics; for
1495 this, the tracer ID iTracer had to be included into the parameter list
1496 of ptracers_forcing
1497 - set up forward_step to call gchem_forcing, that will replace
1498 gchem_forcing_int in ptracers_forcing
1499 - cleaning up
1500 o small cleaning of exch2: remove files that are also in eesupp/src
1501
1502 checkpoint56
1503 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
1504 o mnc: cleanup "full" files--fixes out-of-memory problem
1505 o ECCO-GODAE
1506 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
1507 * fully merged and updated from SIO code
1508 windstress sign change affects
1509 - exf_inscal_[u/v]stress
1510 - sign of xx_tau[u/v] adjustments
1511 - signs in cost_scat
1512 * ctrl_get_gen: avoid update of tau[u/v] for first few days
1513 * natl_box_adjoint updated and compressed
1514 * 2-level checkpoint switch added
1515 (tested in EXP. 1 of natl_box_adjoint)
1516 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
1517 o SVD
1518 * first complete, non-hacked version for SVD calculations
1519 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
1520 performed via direct access files admtlm_vector.it????
1521 (via ctrl_[un]pack)
1522 * optimcycle is used for ARPACK iteration counter
1523 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
1524 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
1525 and add linear transforms where necessary
1526 * controls are initial/final SST, SSS (can be extended; need to check
1527 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
1528 o mdsio: filename info to both stderr, stdout
1529 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
1530 from sign change
1531
1532 checkpoint55j_post
1533 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
1534 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1535 o add consistent build directories and .cvsignore files to verification
1536 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
1537 o make all subroutines 30 or less characters in length for certain older
1538 compilers to work (a thorough search only turns up two routines in
1539 pkg/ptracers)
1540 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
1541 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1542
1543 checkpoint55i_post
1544 o change arrays for total vertical diffusivity (2.D if explicit,
1545 3.D if implicit) ; each ptracer uses its own background value.
1546 o added mnc/NetCDF output capability to ocn_compon_interf
1547 - added bits to verification/cpl_aim+ocn so that it can run on
1548 ITRDA and other clusters without the mpirun "-wd" option
1549 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
1550 configuration
1551 o give MNC the ability to create additional files rather than
1552 exceeding a specified file size limit "MNC_MAX_FILESIZE"
1553 - the default is just less than 2GB which is a practical limit
1554 on many systems
1555 o Compute the non-local term using either KPP vertical diffusivity (=default)
1556 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
1557
1558 checkpoint55h_post
1559 o add verification test "vermix"
1560 o remove all the *_ioinc flags and replace with the single global
1561 outputTypesInclusive flag
1562 o allow to set a vertical profile of vertical diffusivity for T & S
1563 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
1564 o useMNC moved from data.mnc to data.pkg
1565
1566 checkpoint55g_post
1567 o Renaming carbon AD experiments to comply with testreport conventions
1568 o Updating adjoint of Held-Suarez hs94.1x64x5
1569 o Fixing directives for non-ECCO forward_step, after ECCO directives
1570 have been fixed to avoid recomp. of do_oceanic_phys
1571 Works well for global_ocean.90x40x15,
1572 but recomp. issue remains for carbon
1573 o Updating adjoint output for natl_box_adjoint after
1574 pkg/ecco has been modified (see taga c55d_post)
1575
1576 checkpoint55f_post
1577 o rename to timeave_init_fixed
1578
1579 checkpoint55e_post
1580 o some delicate re-shuffle of store directives to avoid one
1581 extra call of do_oceanic_physics
1582 affects ecco_the_main_loop.F, do_oceanic_physics.F
1583 checkpoint_lev1_directives.h
1584 o NB: this may break global_ocean adjoint temporarily,
1585 but it is clear how to fix it. Will do later, need this now.
1586
1587 checkpoint55d_post
1588 o ECCO specific cost function terms (up-to-date with 1x1 runs)
1589 o ecco_cost_weights is modified to 1x1 runs
1590 o modifs to allow observations to be read in as
1591 single file or yearly files
1592 o enable to read exf forcing fields as either
1593 single file or yearly files (flag useExfYearlyFields)
1594 checkpoint55d_pre
1595
1596 o switch between 2-level and 3-level checkpointing
1597 o add ability of MNC to write local and "partial" (eg. 2D slices where
1598 the full 3D field is never actually stored) arrays to NetCDF files
1599 with the correct (that is, the complete multi-dimensional) set of
1600 array indicies
1601 - used in mom_vecinv() to write the diagFreq output
1602 - tested (demonstrated) in verification/aim.5l_cs
1603 o further mnc-ification
1604 - add verification/lab_sea to the list with mnc setups
1605 - fix undefined mnc v-names in cd_code
1606 - add kpp to mnc output (both snapshot and timeave)
1607 o non-hydrostatic code
1608 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
1609 in calc_gw.F
1610 - defaults to viscAh
1611 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
1612 friction or Leith) in non-hydrostatic mode, as long as there is
1613 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
1614 o pkg/cost
1615 extend simple cost functions to treat time mean quantities
1616 (T,U,V) via cost_accumulate_state from cost_tile
1617 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
1618 be 2 times larger than the minimum size the advection scheme requires.
1619 now get a perfect conservation of salt in advect_cs test-exp (updated)
1620 o GGL90 (Gaspar's TKE mixed layer)
1621 - add horizontal diffusion of TKE, requires exchanges in
1622 do_fields_blocking_exchanges, horizontal diffusivity is zero by
1623 default. In OPA there is no horizontal diffusion of TKE but the
1624 mixing coefficients are computed from a horizontal average of TKE of
1625 6 points or so. I think that diffusion has a little more physical
1626 justification.
1627 - clean up ggl90_calc in the hope of reducing memory usage (this hope
1628 was in vain)
1629 - mask tke-variable in ggl90_init
1630 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
1631 o fix biharmonic diffusion on CS-grid.
1632 o more obcs stuff
1633 - added obcs_external_fields_load as an alternative to the EXF-pkg option
1634 for reading boundary values. This routine is called from
1635 obcs_prescribe_read
1636 - updated obcs_check
1637 - changed sponge layer relaxation parameter units for days to seconds
1638 - turned off sponge layer by default
1639 - changed argument list of OBCS_CALC to myTime+deltaTclock
1640 - fixed about 35 bugs in obcs_external_fields_load
1641
1642 checkpoint55c_post
1643 o obcs stuff
1644 - new runtime flags useOBCSprescribe, useOBCSbalance
1645 - re-arranged obcs_calc
1646 - moved exf_getobcs to obcs_prescibe_read
1647 obcs_prescibe_read is called after ORLANSKI stuff
1648 and independent of it (executable can contain all).
1649 - updated obcs_check
1650 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
1651 These may be necessary only if tangential velocities are
1652 prescribed at OB, not sure, needs testing.
1653 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
1654 which simplifies the calls and passes the ifc check-bounds test
1655
1656 checkpoint55b_post
1657 o add a 2D scalar, Z location, exchange_2 routine.
1658 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
1659 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
1660 affects advect_cs results (for the wrong reason): update output.txt
1661 o use a more standard discretization for biharmonic viscosity ;
1662 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
1663 affects results of dome set-up: update output.txt
1664 o fix gad_advection.F (CubedSphere part), back to version 1.23
1665 o fix bug in mom_vi_del2uv.F (CubedSphere part).
1666
1667 checkpoint55a_post
1668 o merged code to
1669 * prescribe/read time-dependent open boundaries
1670 (works in conjunction with exf, cal)
1671 * sponge layer code for open boundaries
1672 * each boundary N/S/E/W now has its own CPP option
1673 (healthy for the adjoint)
1674
1675 checkpoint55
1676 o up-to-date adjoint of previous breaks
1677 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
1678 - global_ocean_ebm: adjoint still needs fix (TLM ok)
1679 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
1680 - carbon: * remove tr1-related adjoint verification
1681 * add ptracer as control variable
1682 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
1683 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
1684
1685 checkpoint54f_post
1686 o in verification/carbin/ remove experiment related to
1687 ALLOW_PASSIVE_TRACER (array tr1 etc)
1688 code_ad/ input_ad/ results_ad
1689
1690 o add two new packages
1691 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
1692 + subject to optimization (memory)
1693 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
1694 + subject to reordering (many GOTOs in the original code)
1695 + so far opps is called for every (i,j) point, and then operates in
1696 the vertical; one may want to reorder the scheme in order operate in
1697 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
1698 fields)
1699 o overhaul of IO so that we now have flags for MDSIO and/or MNC
1700 - all verification tests compile and run with linux_ia32_g77
1701 - defaults are compatible with current input files--nothing
1702 should change if you were not previously using MNC
1703 - MNC output has been added in numerous places (eg. timeave)
1704 but there are still a few writes not yet do-able with MNC
1705 (this is in progress)
1706 - flags now allow for either/or/both use of MDSIO and MNC and
1707 documentation will soon follow
1708 - numerous small formatting cleanups for ProTeX
1709 o add version info (via BUILD_INFO.h) to MNC and stdout
1710
1711 checkpoint54e_post
1712 o add two new packages
1713 - pp81 (Packanowski and Philander, 1981), Richardson number and
1714 stratification dependent mixing
1715 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
1716 - these scheme operate in a similar manner as KPP (without ghat, of
1717 course), however there is only one diffusivity that is used for both
1718 temperature and salinity (and passive tracers)รง
1719 o add offline package
1720 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
1721 provided by Stephanie Dutkiewicz
1722 o genmake2: add ability to search for C compilers and cleanup test output
1723 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
1724
1725 checkpoint54d_post
1726 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
1727 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
1728 leading to additional shift by 5 days each year of integration
1729 (i.e. leading to considerable offset over the years)
1730 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
1731 o start with no AB and no initial filtering (staggerTimeStep):
1732 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
1733 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
1734 (external loading & cpl import/export stay in forward_step.F)
1735 o update coupling interface to work with new staggerTimeStep
1736 o change MDSIO ptracers_pickup.
1737 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
1738 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
1739 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
1740
1741 checkpoint54c_post
1742 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
1743 this affects (truncation error) output.txt of test-exp:
1744 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
1745 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
1746 o change Qnet to always be the net heat flux, (+upward).
1747 affects (truncation error) output of natl_box exp.: updated
1748 o define the max number of passive tracers in PTRACERS_SIZE.h
1749 o start to test mnc routinely in exp0
1750 o add sea-ice loading (sIceLoad) as a new forcing field.
1751
1752 checkpoint54b_post
1753 o add testreport "-j JOBS" option for parallel builds (tested and pretty
1754 impressive on Altix and Opteron systems)
1755 o diagnostics can now write NetCDF files through the mnc package
1756 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
1757 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
1758 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
1759 affects (truncation error) output of lab_sea & natl_box exp.: updated
1760 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
1761
1762 checkpoint54a_post
1763 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
1764 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
1765 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
1766 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
1767 + internal_wave (shift in writing cg2d_ini_res)
1768 checkpoint54a_pre
1769
1770 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
1771 - modified verification/lab_sea and natl_box_adjoint accordingly
1772
1773 checkpoint54
1774 checkpoint53g_post
1775 o prepare splitting of thermodynamics: store convect.counter in common block
1776 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
1777 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
1778 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
1779 o new parameter "nShapS": allow to treat differently S from T (nShapT)
1780 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
1781 o restore adjointability
1782
1783 checkpoint53f_post
1784 o modifications that affect AIM experiment results (update output.txt):
1785 - no advection of S at top interface Nr (pkg/generic_advdiff)
1786 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
1787 o AIM pkg:
1788 - include stability function into surf.Flux derivative relative to Tsurf
1789 - calculate clear-sky radiation & surface temp. change (for diagnostics)
1790
1791 checkpoint53e_post
1792 o merged cylindrical coord configuration
1793 o added rotating_tank experiment
1794 checkpoint53e_pre
1795
1796 checkpoint53d_post
1797 o faulks upgraded: re-generate output.txt that have changed:
1798 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
1799 o Added Bryan and Lewis, 1979, vertical diffusivity profile
1800 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
1801 o added Sadourny discretization of Coriolis
1802 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
1803 - re-enabled use of omega3 (useAbsVorticity)
1804 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
1805 vector-invariant equations
1806 - note: does *NOT* yet use same variable visc. for no-slip BC's.
1807 o recoded the lateral boundary conditions for non-hydrostatic w, this time
1808 hopefully without new bugs
1809 - still to do: biharmonic friction for non-hydrostatic w
1810 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
1811 o regenerated output for global_ocean_ebm (using -ieee)
1812 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
1813 of mom_common/
1814 - simple re-arrangement of instructions within computing loop
1815 checkpoint53d_pre
1816
1817 checkpoint53c_post
1818 o new version of coupler for AIM+thSIce and Ocean models
1819 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
1820 - land: change Evaporation of snow
1821 - aim with thSIce: fix bug in snow-precip.
1822 o changes to calc_gw.F
1823 - bug fix for w^2 term near the bottom boundary
1824 - (hopefully) improve the lateral slip boundary condtions for use with
1825 partial/looped cells
1826 - because the bug fix changes two verification experiments anyway (exp5
1827 and plume on slope), change the lateral boundary condition from half slip
1828 to the value of no_slip_sides
1829 o ebm package wasnt quite up to the parallel task. Fixed that.
1830 o Adjoint of EBM package + verification
1831 * TLM OK
1832 * ADM not sufficient accuracy yet (needs further testing)
1833
1834 checkpoint53b_post
1835 o Commiting new energy balance model to repository
1836 * package is pkg/ebm
1837 * verif. is verification/global_ocean_ebm
1838 * references are in ebm_driver.F
1839 C * X. Wang, P. Stone and J. Marotzke, 1999:
1840 C Global thermohaline circulation. Part I:
1841 C Sensitivity to atmospheric moisture transport.
1842 C J. Climate 12(1), 71-82
1843 C * X. Wang, P. Stone and J. Marotzke, 1999:
1844 C Global thermohaline circulation. Part II:
1845 C Sensitivity with interactive transport.
1846 C J. Climate 12(1), 83-91
1847 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
1848 C Destabilization of the thermohaline circulation
1849 C by atmospheric eddy transports.
1850 C J. Climate 7(12), 1870-1882
1851 o Will need long integration testing.
1852 checkpoint53b_pre
1853
1854 o created pkg/mom_common in preparation for variable viscosity code
1855 o renamed and split ini_mnc_io
1856 o pkg/land: only liquid water can diffuse or run-off
1857 o AIM using land: soil wetness availability account for snow
1858 o added printMapIncludesZeros to EEPARMS namelist
1859
1860 checkpoint53a_post
1861 o restore TAMC compatiility for exf_constants.h
1862 (no usage of _d in .h)
1863 o Additional storing in KPP in an attempt to fix
1864 TAMC problem with adjoint of KPP code.
1865 (no success...)
1866 Identical code works fine with TAF.
1867 o Fixed verification/natl_box_adjoint experiments.
1868 Initial conditions for Experiments 4 and 5 are now
1869 set to "SEAICE_initialHEFF=0", which is more reasonable,
1870 and hence gives results closer to that of Experiment 2.
1871 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
1872
1873 checkpoint53
1874 o stable checkpoint with up to date adjoint
1875 TLM tests only run for 1st grdchk at the moment. Its unclear if
1876 this is a code problem or a problem with resetting code for g_
1877 variables that is being autogenerated wrong.
1878 Otherwise:
1879 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
1880 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
1881 are both still in chaos following their security messes.
1882
1883 checkpoint52n_post
1884 o various build (mostly genmake2) changes including:
1885 - ability to build/run more easily within Cygwin and MacOS X
1886 - more complicated Makefiles with a stronger dependence on Gnu Make
1887 o pkg/seaice modifications
1888 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
1889 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
1890 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
1891 - changed proxy for geostrophic velocity and updated
1892 verification/lab_sea/results/* accordingly
1893 - removed ADI dynamic solver from pkg/seaice
1894 - replaced all occurrences of 1/CSTICE or 1/CSUICE
1895 they caused a segmentation fault under certain circumstances
1896 - removed unused field WATR
1897 o bug fix in exf-package:
1898 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
1899 now reflect that.
1900 o small fixes in the cal-package:
1901 - set reference date to first of January for the 'model'-calendar
1902 - failing of cal_CheckDate in cal_FullDate now actually results in a
1903 warning
1904 o small modifications in exf-package to increase flexibility:
1905 - change climtempfreeze from a constant to a runtime parameter that
1906 is specified in data.exf_clim (default = -1.9)
1907 - introduce runtime parameter windstressmax (default = 2.0) that is
1908 specified in data.exf
1909 o fix in pkg/thsice:
1910 - update Evap (Tsf changes) to be consistent with Latent heat flux
1911 - maintain snow precipitation unchanged (even if Tsf >=0).
1912 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
1913
1914 checkpoint52m_post
1915 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
1916 this does not change any of the results, because myIter=0 in swfrac always
1917 lead to jwtype=2 (the default anyway), but the call makes little sense
1918 as a default
1919 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
1920 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
1921 atmospheric model (AIM) to use it ; add a "slab ocean" component.
1922 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
1923 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
1924 o extending useSingleCpuIO option to work with new exch2 I/O format
1925 - old-style, missing-tile I/O is still accessible by defining CPP
1926 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
1927 o monitor package can write to NetCDF files and/or STDOUT
1928 o fix re-definition bug in MNC_GRID_INIT_ALL()
1929 o doc/api_reference added
1930 - a framework for building an API Reference Manual using all
1931 the "protex" comments embedded in the code
1932 - see pkg/generic_advdiff, pkg/mnc for examples
1933 o MNC:
1934 - make myThid the last argument for all subroutines
1935 - new default for the grid files: NO halos
1936 - add useMNC and other run-time flags
1937 - separate per-file-group handling of the unlimited dimension
1938 - early initialization of MNC w/ flags read at the eeboot stage
1939 and lookup tables set in initialize_fixed
1940 - write all MNC output to a freshly-created directory
1941 o thermodynamics sea-ice (thsice) is now tested with testreport.
1942 o test exp. advect_cs: use the standard cs32 grid ; update output.
1943 o Added functionality to grdchk:
1944 pick global i,j,k position (or nearest wet) where to perform check.
1945
1946 checkpoint52l_post
1947 o new land formulation:
1948 a) use ground enthalpy as prognostic variable to ensure exact
1949 energy conservation.
1950 b) account for water temperature and for latent heat of freezing
1951 in all processes (rain, run-off, ground storage)
1952 c) compute surface and ground temperature implicitly.
1953 o aim_v23 modification for new land model:
1954 a) Treat separately land / ocean / sea-ice surface fluxes
1955 to allow implicit computation of land & sea-ice surface temp.
1956 b) add snow precipitation.
1957 checkpoint52l_pre
1958
1959 o fix problem (when 1 tile is empty) in min/max monitor.
1960 o fix bug in timeAve (u,vZetatave in common block)
1961 o no restoring terms under ice for pkg/seaice
1962 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
1963 o bug fix for pkg/seaice pickups
1964 o change MNC call locations and add coordinate attributes
1965 o mask vorticity at the corner ; affects global_ocean.cs output
1966 o fix ini_curvilinear_grid ; test CS experiments with mpi
1967 o aim.5l_cs: modify sea-ice fraction input file ; update output
1968 o exf: Adding simple range check routine for exf fields after read
1969
1970 checkpoint52k_post
1971 o removed top-level directory "diags"
1972 - we migrated these functions to pkg/timeave a long time ago
1973 o fixed bug introduced in pkg/monitor
1974 o accuracy ctrlprec = 32 insuffient for gradient checks using
1975 averaged fields (I/O via cost_averages)
1976 -> use ctrl.h in active_file*.F to control I/O precision.
1977 o paramter list of CALL ADTHE_MAIN_LOOP
1978 o added initial do_the_model_io to ecco
1979 o set all ...Freq to zero after cost_final
1980 taveFreq, dumpFreq, pChkptFreq
1981 o MAIN and ECCO differentiability restored
1982
1983 checkpoint52j_post
1984 o fix nchklev in tamc.h for global_ocean...
1985 o Bringing flow and store directives up-to-date
1986 o Really weird thing!
1987 call do_the_model_io from the_main_loop with parameters
1988 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
1989 TAF places a faulty re-call of initialise_varia
1990 after cost_final call which should not be there!
1991 checkpoint52j_pre
1992
1993 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
1994 error messages
1995 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
1996 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
1997 debug output
1998 o modfied mdsio_writefield.F to handle non-global files under exch2
1999 o update AIM Cubed-Sphere exp (aim.5l_cs):
2000 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
2001 o update AIM Equatorial Channel exp:
2002 use standard aim_v23 pkg and change the SST fields to be more realistic.
2003 o globalFile now works with exch2
2004 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
2005 mon_vort3.F to make exch2 friendly with >1 tile per cube face
2006 o limit timeave output for hi-res integrations
2007
2008 checkpoint52i_post
2009 o removed CPP_EEOPTIONS.h from verification/*/code
2010 o updated the tiling for global_ocean_pressure
2011 checkpoint52i_pre
2012
2013 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
2014 the old pkg/aim).
2015
2016 checkpoint52h_pre
2017 o shortened offending lines in exch2_send_rx?.template
2018 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
2019 o genmake2: add build & execute test for NetCDF code
2020 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
2021 old grid files, moved CPP_EEMACROS.h to pkg/exch2
2022 o added useSingleCPUIO flag to monitor.F and mon_out.F
2023 o added temporary hack for sea-ice dynamics on the cube:
2024 metric terms are ignored and it is assumed that
2025 there is no sea-ice on cube faces 1, 2, 4, and 5.
2026
2027 checkpoint52f_post
2028 o added exch2 cube routines to pkg/exch2
2029 o modified hs94.cs-32x32x5 to use it
2030 o added new grid files to hs94.cs-32x32x5
2031 checkpoint52f_pre
2032
2033 checkpoint52e_post
2034 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
2035 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
2036 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
2037 to work with implicit vertical advection and AB ;
2038 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
2039 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
2040 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
2041 checkpoint52e_pre
2042
2043 o fix bug in impldiff when Nr=1 or Nr=2.
2044 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
2045 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
2046 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
2047 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
2048 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
2049 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
2050 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
2051
2052 checkpoint52d_post
2053 o re-tiled many expts to allow comparison in multi-processor mode
2054 - updated output accordingly
2055 - changed hs94.128x64x5 to use intial T from file rather than use the
2056 random number generator
2057 o add infrastructure in model routines for fizhi and gridalt packages
2058 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
2059 o changes to permit hi-res, cubed-sphere, configuration
2060 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
2061 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
2062 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
2063 of surface winds for the cube
2064 (A verification experiment, based on global_ocean.cs32x15, but with
2065 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
2066 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
2067 complete with example surface forcing files and matlab scripts to look
2068 at the output and compare it with that of global_ocean.cs32x15.)
2069 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
2070 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
2071 to conform to the common rule.
2072 o check-in the first version of the coupler + interfaces for multi-components
2073 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
2074 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
2075 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
2076 - ocean and atmos. share the same horizontal grid (no interpolation).
2077 - exchanges between component and coupler is done in forward_step
2078 o new verification experiment, cpl_aim+ocn:
2079 coupled ocean - AIM atmosphere on cs32 grid.
2080
2081 checkpoint52d_pre
2082 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
2083 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
2084
2085 checkpoint52c_post
2086 o Fixing OPTIONS files for use of exf:
2087 - ALLOW_ECCO not needed
2088 - ECCO_CPPOPTIONS.h should not be included from
2089 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
2090 as has been the case in the past
2091 - All cal/exf related options are currently set in
2092 single header file. Should remain so until we
2093 agree on a consistent new policy.
2094 o Removed all CPP options for cal package.
2095 cal has no more CPP options.
2096 o modified STOREs in GAD_ADVECTION
2097 o corrected key comp. for passkey
2098
2099 checkpoint52b_post
2100 o new version: "thsice" of thermodynamic sea-ice pkg:
2101 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
2102 - modify fluxes but do not change theta directly;
2103 - light cleaning of bulk_force pkg (still needed with thsice).
2104 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
2105 + output_thsice.txt to test thsice & bulk_force pkgs.
2106 o put back grid & coriolis monitor output.
2107 checkpoint52b_pre
2108
2109 o call "do_the_model_io" at the beginning (=> dump initial state)
2110 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
2111 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
2112 (need info on NUMBER_OF_PTRACERS)
2113 o missing PTRACERS headers in some routines
2114 o default tamc.h in pkg/autodiff supposed to crash
2115 to ensure proper customization
2116
2117 checkpoint52a_post
2118 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
2119 - moved surfaceTendencyTice from pkg/seaice to main code
2120 - subroutine FREEZE_SURFACE now limits only surface temperature
2121 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
2122 => new output.txt for global_ocean.cs32x15 & global_with_exf
2123 - keep the old version of FREEZE for backward compatibility;
2124 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
2125 - corresponding modifs for TAF directives
2126 o added surface flux output variables to TIMEAVE_STATVARS
2127 o time-averaged output for pkg/ptracers
2128 o fix problem with ECCO-related divided adjoint
2129 snapshot file was missing some ad-variables,
2130 but no warning issued by TAF
2131
2132 checkpoint52a_pre
2133 o some bug fixes for #undef REAL4_IS_SLOW
2134
2135 checkpoint52 = ecco_c52_e35
2136 o after testing adjoints of checkpoint51u_post
2137
2138 checkpoint51u_post
2139 o this is the post-merge tag of the ecco-branch
2140 (needs another clean checkout and re-testing)
2141 o various natl_box_adjoint configs and results
2142 but no input fields
2143 o obcs adjoint not yet merged!
2144 o adding ECCO global 1x1 and 2x2 degree configs
2145 o updated/extended some store directives for seaice
2146 o pkg/ecco now containes ecco-specific part of cost function
2147 o top level routines the_main_loop, forward_step
2148 supersede those in model/src/
2149 previous input data.cost now in data.ecco
2150 (new namelist ecco_cost_nml)
2151 o in ctrl/ cleaned some cross-dependencies and updated CPP options
2152
2153 checkpoint51t_post
2154 o this is the pre-merge tag of the ecco-branch
2155
2156 checkpoint51s_post
2157 o cleanup: removed various obsolete #define-s
2158 o pkg/grdchk
2159 - renamed 'ph-grd 3' to 'grad-res'
2160 - merged from ecco-branch
2161 (remaining bug fixes for obcs gradient checks)
2162 - additional high-precision output for testreport
2163 (grep for 'precision_grdchk_result')
2164
2165 checkpoint51r_post
2166 o cleaned up or removed CPP_OPTIONS.h files
2167 o updated results for some of the tests to reflect the new
2168 optfiles (-ieee: -O0 instead of -O3)
2169
2170 checkpoint51q_post
2171 o cd_code:
2172 - moved cd_scheme.F -> cd_code_scheme.F
2173 - separate read_checkpoint from cd_code_ini_vars.F
2174 - separated cd_code part from write_checkpoint
2175 - updated AD_SOURCE, generated .flow
2176 - added CD_CODE_VARS.h to the_main_loop
2177 - Moving cd_code specific store dir.s to pkg/cd_code
2178 o ctrl package totally restructured
2179 - pack/unpack now optional and decoupled from
2180 xx_/adxx_ I/O
2181 - ctrl_pack/unpack cleaned
2182 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
2183 - confined inclusion of AD_CONFIG.h to where necessary.
2184 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
2185
2186 checkpoint51p_post
2187 o create initial cd_code package
2188 - WARNING: the initialization of fields within packages
2189 is broken because INI_FIELDS (where READ_CHECKPOINT is
2190 called) is called *before* PACKAGES_INIT_VARIABLES.
2191 This seems to be backwards since
2192 1) its important to initially zero the entire field including
2193 the "halo" region
2194 2) zeroing needs to be done *before* reading pickup info
2195 and the pickup call might or might not happen in any
2196 particular run
2197 - this needs an overhaul for R2
2198 o cleanup verification/*/code/GMREDI_OPTIONS.h
2199 o cleanup testreport
2200
2201 checkpoint51o_post
2202 o bringing AD-related verif's up to date with genmake2
2203 - carbon/
2204 - global_ocean.90x40x15/
2205 - hs.94.1x64x5/
2206 - (front_relax/ )
2207 o (more) consistent directory structure for AD-related verif.'s
2208 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
2209 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
2210 o bug fix in find_alpha.F for MDJWF:
2211 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
2212 change rho -> rho-rhoConst
2213 - replace call find_rho to find_rhonum
2214 o initialisation of rFlx extended to full array (required by TAF)
2215 and shifted to thermodynamics
2216 o removed PTRACERS.h in ptracers routine
2217 o added surfacetendencyPtr to S/R parameter list pracers_forcing
2218 o Correcting initialisations for fVerU, fVerV.
2219 o helping TAF to recognize dependency on kUp for
2220 fVerU, fVerV
2221 o Replacing delZ by delR in pkg/ctrl/
2222 checkpoint51o_pre
2223
2224 o undid all of cp51 pending some cleanups and discussion
2225 o added the [#include "AD_CONFIG.h"] statement to all files that need
2226 it for adjoint/tl #defines
2227 o re-worked the build logic in genmake2 to support AD_CONFIG.h
2228 o removed tools/genmake since it no longer works
2229
2230 checkpoint51n_post
2231 o modifications to make FREEZE flux visible to pkg/kpp
2232 - moved surfaceTendencyTice from pkg/seaice to main code
2233 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
2234 - subroutine FREEZE now limits only surface temperature
2235 (this means new output.txt for global_ocean.90x40x15,
2236 global_ocean.cs32x15, and global_with_exf)
2237 o added surface flux output variables to TIMEAVE_STATVARS
2238
2239 checkpoint51n_pre
2240 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
2241 o added [#include "AD_CONFIG.h"] to all files that use the following
2242 defines:
2243 - ALLOW_ADJOINT_RUN
2244 - ALLOW_TANGENTLINEAR_RUN
2245 - ALLOW_ECCO_OPTIMIZATION
2246
2247 checkpoint51m_post
2248 o incorporating changes to get TAMC/TAF working in genmake2
2249 - added new TAMC/TAF targets to the Makefile
2250 - various cleanups related to package handling
2251 - these changes should have no impact on the forward model
2252
2253 checkpoint51l_post
2254 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
2255 - faster algorithm for cal_addtime.F
2256 - higher precision arithmetic, where needed
2257 - pkg/exf *startdate variables changed from calendar date to
2258 model integration time
2259
2260 checkpoint51l_pre
2261 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
2262 o enable to apply restoring on S & T only in a latitude band.
2263 o update output (external_forcing_surf modif. change truncation errors)
2264 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
2265
2266 checkpoint51k_post
2267 o change default to: useNHMTerms=.FALSE.
2268 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
2269 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
2270 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
2271 exp1, ideal_2D_oce
2272 - change data file of oceanic exp (leave the results unchanged for now)
2273 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
2274 o set gravitySign automatically according to the vertical coordinate used
2275 (and change sign: back to "logical" value: +1 when R increases downward)
2276 o added an include barrier to the default CPP_OPTIONS.h and
2277 removed the #include "PACKAGES_CONFIG.h" from it
2278 o fix a bug in mom_fluxform (from chk51j_post)
2279
2280 checkpoint51j_post
2281 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
2282 o adjusted some flow directives (dynamics, thermodynamics)
2283 o added cubed-sphere case to test cost function
2284 o heckpoint_lev?_directives.h now include
2285 pkg-specific directives, whenever those are enabled.
2286 o Moving pkg-specific flow directives to corresponding pkg
2287 Moving pkg-specific differentiation list to corresponding pkg
2288 Moving pkg-specific checkpoint-lev storing to corresponding pkg
2289 ---> conventions are
2290 - pkg_ad.flow
2291 - pkg_ad_diff.list
2292 - pkg_ad_check_lev?_dir.h
2293
2294 checkpoint51i_post
2295 o merge of the branch-genmake2
2296 - knowingly breaks the older genmake
2297 - automatic generation of all ALLOW_${PKG_NAME} defines
2298 - new testreport supersedes older testscript
2299 o large number of package inclusion and header cleanups
2300 checkpoint51i_pre
2301
2302 o new output for adjoin of global ocean vector invariant
2303 o fix for checkpoint of thermodynamic seaice and bulk_force
2304 o Steph gchem various cleanups
2305
2306 checkpoint 51h_pre
2307 o fixed some single quotes
2308 o modify gchem pkg to be more versatile
2309 o modifications to clean up dic pkg
2310 o add pkg/cfc
2311
2312 checkpoint51g_post
2313 o provide links for ARPACK and ADM*TLM
2314 o start removing verification/vero/
2315 o update AD-related stuff
2316 (in particular some IF-statements in model/src/ routines)
2317 o adding to verification/global_ocean.90x40x15/ adjoint of
2318 vector invariant setup
2319
2320 checkpoint51f_post
2321 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
2322 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
2323 of tracer Green's fucntions for ocean inversion project.
2324
2325 checkpoint51f_pre
2326 o Added on-the-fly spatial interpolation capability
2327 "USE_EXF_INTERPOLATION" to pkg/exf.
2328 - This is a temporary Cartesian-grid hack until
2329 the super-duper ESMF coupler becomes available.
2330 - See verification/global_with_exf/README for usage example.
2331 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
2332 flags and modified pkg/seaice accordingly.
2333 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
2334 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
2335 non-local transport term.
2336
2337 checkpoint51e_post
2338 o pkg/mom_vecinv:
2339 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
2340 - add time-ave diagnostic of vorticity advection.
2341 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
2342 o atmospheric geopotential: - include water vapor effect;
2343 - use p^kappa in p* scaling.
2344 o land pkg: read initial state from files.
2345 o AIM : add stratospheric drag in the upper level
2346
2347 checkpoint51d_post
2348 o change function ILNBLNK (=> last non-blank char.) to return zero
2349 (instead of the string length) when the string. char is empty
2350 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
2351 o modif's to restore TAMC compatibility
2352 - avoid "_d" constructs in PARAMETER declarations
2353 - avoid interrupting lines by comment lines
2354 o Use cluster local disks for purely local I/O
2355 vs. globally visible disks needed for ctrl stuff
2356 (merged from ecco-branch)
2357 - new active_file_loc... and mdsio_..._loc routines
2358 - affected packages: autodiff, ctrl, grdchk, mdsio
2359
2360 checkpoint51c_post
2361 o introducing integer flag debugLevel
2362 - debLevZero: suppress all output
2363 - debLevA: standard
2364 - debLevB: equivalent to current debugMode=.TRUE.
2365 o introducing pathname variable mdsioLocalDir for mdsio
2366 that can be specified at runtime
2367 (relevant for cluster I/O to local disk)
2368 `
2369 >>>checkpoint51b_post
2370 adjoint of ptracers
2371 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
2372 o extended state in checkpoint_lev?, etc.
2373 o alternative ctrl/cost with tr1 or ptracer
2374 o new comlev1_bibj_ptracers
2375 o new ptracers.flow
2376 o made ptracers_forcing same as external_forcing_s
2377 o added verification for adjoint with ptracers
2378 - adm. grdchk fail so far
2379 - tlm. grdchk OK
2380 - checked tapelev/comlev recomputations: OK
2381 <<<checkpoint51b_pre
2382
2383 checkpoint51a_post
2384 o added code for biogeochemistry package
2385 - new pkgs: dic, gchem
2386 - new subroutine in ptracers
2387 o modify code for biogeo packages
2388 - in model/src and pkg/ptracers
2389
2390 checkpoint51
2391 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
2392 - autodiff, ctrl, exf, grdchk, seaice
2393 kept separate packages
2394 - cost, ecco, obcs
2395 o updating verification/internal_wave, verification/lab_sea
2396 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
2397
2398 checkpoint50i_post
2399 o Preparing next differentiable checkpoint and sync
2400 of MAIN vs. ecco-branch
2401 - 1st step: this one is differentiable
2402 - 2nd step: next(! not this) checkpoint will have updated packages
2403 from ecco-branch)
2404
2405 checkpoint50h_post
2406 o new package "land": provide surface BC for AIM.
2407 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
2408 o AIM: use true log-P extrapolation for near surface temp (= as in
2409 F.Molteni paper) ; update aim.5l_cs output.
2410 o New variable in PARM03 for more flexible pickups
2411 o somewhat cleaned package initialisation sequence for
2412 ctrl/ cost/ ecco/ in packages_... routines
2413
2414 checkpoint50g_post
2415 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
2416 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
2417 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
2418 made the default because of faster convergence than ADI
2419
2420 checkpoint50f_post
2421 o exf totally restructured
2422 - replaced all exf_set_ routines by one generic exf_set_gen.F
2423 and made sure it's still differentiable
2424 - split exf_getffields.F into new exf_bulkformulae.F
2425 - exf_inscal_/exf_outscal_ suffixes consistent with field names
2426 - updated adjoint/makefile and relevant verif. accordingly
2427
2428 checkpoint50f_pre
2429 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
2430 + change Evap over land. (update aim.5l_cs output)
2431 o added missing .cvsignores and made uniform across expts
2432 o changed configuration of tidal_basin_2d expt
2433 o added pkg/debug functions for tracing code in fatal crashes
2434 o tidied pkg/monitor to use MONITOR_OPTIONS.h
2435 o new fn in pkg/monitor to stop model if solution grows too big
2436 o removed lots of single quotes from comments
2437
2438 checkpoint50e_post
2439 o make KPP work with PTRACERS
2440 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
2441 nearly a copy of kpp_transport_s
2442 - there is no analogue to SurfaceTendencyS, so I have to use
2443 gPtr(of the surface layer) instead
2444 o add a new platform SunFire+mpi (SunFire 15000) to genmake
2445 checkpoint50e_pre
2446
2447 checkpoint50d_post
2448 o change kpp output from multiple-record state files to single-record state
2449 files analogous to write_state.F
2450 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
2451 analogous to the cg2d-related output.
2452 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
2453 so that writing to internal file fn (with length 512) fails.
2454 checkpoint50d_pre
2455
2456 checkpoint50c_post
2457 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
2458 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
2459 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
2460 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
2461 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
2462
2463 checkpoint50c_pre
2464 Merging from release1_p13:
2465 o bug fix for pkg/seaice dynamic solver
2466 o Added SEAICE_initialHEFF to pkg/seaice
2467
2468 checkpoint50b_post
2469 o store u*,v* in gU,V instead of in guNm1,gvNm1
2470 o in order to put the momForcing out of the Adams-Bashforth:
2471 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
2472 to timestep.F
2473 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
2474 o re-generate output for highly sensitive test-exp:
2475 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
2476
2477 checkpoint50b_pre
2478 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
2479 o corrected CPP option mismatch in exf_Bulk... functions for case
2480 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
2481
2482 checkpoint50a_post
2483 o Bug fix for merging between c50 and KPP.
2484 ikey was passed from thermodynamics to kpp_calc via
2485 common block rather than being recomputed in kpp_calc,
2486 in contradiction with new key itdkey.
2487 New key ikppkey created, and tamc.h headers updated.
2488
2489 checkpoint50
2490 - 2nd step of merge with ecco-branch:
2491 merge changes in ecco-branch back into main trunk
2492 - bug fix in find_alpha
2493 - more storing in gmredi_calc_tensor.F, kpp_routines.F
2494 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
2495 - merged some sliced AD support routines
2496
2497 checkpoint49
2498 merged from ecco-branch:
2499 o exf:
2500 - Enable initialisation of forcing fields to constant
2501 (runtime) values.
2502 - in exf_getffields.F
2503 Reduce i-/j-loop to interior domain, discarding overlaps.
2504 That also fixes wrong TAF-key computations for key_1, key_2
2505 with bulf formulae.
2506 - exf_init.F modify #ifdef for exf_init_evap
2507 - exf_getffieldrec.F, ctrl_getrec.F
2508 The following INT-usages are not safe:
2509 fldsecs = int(fldsecs/fldperiod)*fldperiod
2510 fldcount = int(fldsecs/fldperiod) + 1
2511 and were modified.
2512 o autodiff: checkpoint_lev...
2513 - updated storing for bulk formulae (some arrays were missing)
2514 - added state for seaice package
2515 - synchronized with main branch
2516 o DIVA:
2517 Modif.s in
2518 - the_main_loop.F
2519 - the_model_main.F
2520 and added cost_final_restore.F cost_final_store.F
2521 o With these changes, it is possible to fully separate
2522 the first forward run to compute the cost function (mdthe_main_loop)
2523 and adjoint runs over individual DIVA intervals (adthe_main_loop)
2524 into separate model executions.
2525 This enables better tuning of DIVA to given queue sizes.
2526 o Loss of cost function value in consecutive DIVA runs is
2527 fixed by storing to 'costfinal' file.
2528 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
2529 beginning/end of adjoint integration is accounted for.
2530 The current changes apply to TAF-1.4.26.
2531 TAF has one remaining bug, requiring one manual change
2532 (see MITgcm manual).
2533 o cal: synchronized between MAIN and ecco-branch
2534
2535 checkpoint48i_post
2536 o Changes to restore differentiability of code w.r.t. previous tag
2537 (mostly adding new routines to make list and replacing
2538 pressure by totPhiHyd).
2539 o Updated and merged grdchk package
2540 - has both ADM and TLM checks
2541 - works for single- and multi-proc.
2542 - output cleaned
2543 - worked successfully for parallel DIVA
2544 o genmake:
2545 - Adding -platform=SP4
2546 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
2547 o Modif. for DIVA:
2548 ctrl_unpack should not be called in intermediate DIVA interval.
2549 (similar thing would apply for active files such as
2550 tbar, sbar, psbar, which should not be reinitialised;
2551 only relevant for ecco-branch)
2552
2553 checkpoint48h_post
2554 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
2555 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
2556 o Added SEAICE_initialHEFF to pkg/seaice
2557 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
2558
2559 checkpoint48g_post
2560 --- EOS:
2561 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
2562 store total Potential in totPhyHyd for diagnostics & EOS.
2563 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
2564 --- Pressure/geopotential gradient:
2565 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
2566 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
2567 ( changes results of global_ocean_pressure )
2568 o NLFS + z-coord.: add eta*Rho' contribution.
2569 o accurate phiHyd when using interface-W at the middle between 2 centers
2570 ( changes results of ideal_2D_oce )
2571 o includes r* 2nd term in potential gradient.
2572
2573 checkpoint48f_post
2574 Merging from release1_p12:
2575 o Modifications for using pkg/exf with pkg/seaice
2576 - improved description of the various forcing configurations
2577 - added basic radiation bulk formulae to pkg/exf
2578 - units/sign fix for evap computation in exf_getffields.F
2579 - updated verification/global_with_exf/results/output.txt
2580 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
2581 (SBO) core products, including oceanic mass, center-of-mass,
2582 angular, and bottom pressure (see pkg/sbo/README.sbo).
2583 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
2584 to avoid negative values in shallow regions.
2585 - updated verification/natl_box/results/output.txt
2586 - updated verification/lab_sea/results/output.txt
2587 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
2588 o Added useSingleCpuIO option (see PARAMS.h).
2589 o Updated useSingleCpuIO option in mdsio_writefield.F to
2590 work with multi-field files, e.g., for single-file pickup.
2591 o pkg/seaice:
2592 - bug fix in growth.F: QNET for no shortwave case
2593 - added HeffFile for specifying initial sea-ice thickness
2594 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
2595 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
2596 kpp_transport_t.F, forward_step.F, and the_main_loop.F
2597 o pkg/seaice:
2598 - adjoint-friendly modifications
2599 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
2600
2601 checkpoint48e_post
2602 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
2603 o dynamics: change definition of computational domain & adapt mom_fluxform
2604 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
2605 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
2606 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
2607 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
2608 global_ocean.90x40x15 global_with_exf global_ocean_pressure
2609 inverted_barometer solid-body.cs-32x32x1
2610 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
2611
2612 checkpoint48d_post
2613 o in preparation for r*:
2614 a) use pre-computed gradient of hydrostatic potential:
2615 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
2616 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
2617 => affects results of glob_oce_pressure (different truncation error)
2618 update output.txt of ideal_2D_oce & global_ocean_pressure
2619
2620 checkpoint48d_pre
2621 o in preparation for r*:
2622 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
2623 pass the 2 comp. of the grad. as arguments to momentum S/R.
2624 but for the moment, only used if it does not change the results.
2625 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
2626
2627 checkpoint48c_post
2628 Modifications in treatment of initial flux forcing controls
2629 to avoid extra storing of flux fields.
2630
2631 checkpoint48c_pre
2632 o Added tidal_basin_2d experiment (currently 1D!)
2633 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
2634
2635 checkpoint48b_post
2636 o r* coordinate added in #ifdef NONLIN_FRSURF block.
2637 (modification to pressure gradient not yet implemented)
2638 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
2639 (for U & V) that are used for vertical advection of momentum.
2640
2641 checkpoint48a_post
2642 o In preparation for r*, use temp. array to compute vertical transport
2643 in flux-form momentum pkg. => change results of few test-exp.
2644 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
2645 lab_sea, natl_box & plume_on_slope
2646
2647 checkpoint48
2648 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
2649
2650 checkpoint47j_post
2651 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
2652 o moved adexch from forward_step to addummy_in_stepping
2653 o added exch in ctrl_map_...
2654 o aveFreq.=0. at end of cost_final to avoid overwrite in
2655 reverse checkpointing loop
2656 o Yet more changes in gmredi:
2657 * adgmredi_calc_tensor
2658 avoiding all recomputation of gmredi_slope_limit
2659 * adgmredi_x/y/rtransport
2660 added flag for excessive storing to avoid recomp. of
2661 u/v/rtans, dTdx/y/z
2662 -> this is not really necessary and very memory-consuming
2663 * adgmredi_slope_psi:
2664 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
2665 * gmredi_slope_limit
2666 re-activated full calculation of taperfct for case 'ac02'
2667 o updating verification/ adjoints of carbon, global_ocean.90x40x15
2668
2669 checkpoint47i_post
2670 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
2671 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
2672 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
2673 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
2674 o gmredi: fix few bugs.
2675
2676 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
2677 This will be a good checkpoint to plug into the ecco-branch.
2678 o few modif.'s to get latest version adjointed
2679 (mainly kick out code in ini_linear_phisurf)
2680 o modif's to run adjoint with exactConserv
2681 o case GM_BOLUS_ADVEC should be cleaned
2682 S/R gmredi_slope_psi should be cleaned
2683 o verification/carbon now has exactConserv=.TRUE.
2684
2685 checkpoint47g_post
2686 o time-average AIM output: becomes independent from statvars time-average
2687 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
2688 o After TAF bug fix:
2689 Tested adjoint of gmredi package.
2690 Tests were done with checkpoint47 rather than with latest
2691 checkpoint47f_post since the latter is broken for the adjoint
2692 verification/carbon/ contains both ADM and TLM gradient checks.
2693 Here they are, before they get changed/lost/stolen.
2694 Mostly modif.'s to fix numerical sensitivities.
2695 Gradient checks OK for
2696 - GM_taper_scheme:
2697 * clipping
2698 * ac02
2699 * linear
2700 * glw91
2701 * dm95
2702 * ldd97
2703 - GMREDI_OPTIONS:
2704 * GM_VISBECK_VARIABLE_K
2705 * GM_NON_UNITY_DIAGONAL
2706 * GM_EXTRA_DIAGONAL
2707 * GM_BOLUS_ADVEC
2708 in conjunction with data.gmredi parameters to be checked in
2709 in a few minutes under verification/carbon/code/
2710
2711 checkpoint47f_post
2712 Merging from release1_p10:
2713 o modifications for using pkg/exf with pkg/seaice
2714 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
2715 and SEAICE_EXTERNAL_FLUXES
2716 - pkg/exf CPP options EXF_READ_EVAP and
2717 EXF_NO_BULK_COMPUTATIONS
2718 - usage examples are Experiments 8 and 9 in
2719 verification/lab_sea/README
2720 - verification/lab_sea default experiment now uses
2721 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
2722
2723 checkpoint47e_post
2724 o created a tag prior to creating a branch
2725
2726 checkpoint47d_post
2727 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
2728 at the bottom boundary had an erroneous half slip boundary condition
2729 o added bottom drag and no slip boundary condition capabilities to
2730 oceanic pressure coordinates code
2731 o added new verification experiment global_ocean_pressure, this experiment is
2732 also described in the tutorial section of the manual
2733 checkpoint47d_pre
2734
2735 checkpoint47c_post
2736 o Added a verification experiment for a global cubed-sphere ocean run
2737 - verification/global_ocean.cubed32x32x30
2738 - uses pkg/therm_seaice and pkg/bulk_forcing
2739
2740 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
2741 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
2742 when using P-coordinate; only implemented for atmospheric config.
2743 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
2744 NOTES: requires option NONLIN_FRSURF to be "#define".
2745 o update advect_xz/results/output.txt (left from checkpoint44g_post)
2746
2747 checkpoint47b_post
2748 Merging from release1_p9:
2749 o pkg/seaice
2750 - removed GOTO's and added taf directives
2751 - double precision constants to reduce the g77 (Linux)
2752 to F77 (SGI) differences reported in release1_p8
2753 o tools/genmake
2754 - added SGI options
2755 o verification/testscript
2756 - updated to that of checkpoint47a_post
2757 o verification/global_ocean.90x40x15/input/eedata
2758 - modified for SGI f77 compatibility
2759 o verification/lab_sea
2760 - added description of sea-ice model
2761 - added missing matlab routines
2762 - added test of thermodynamics parallelization
2763
2764 checkpoint47a_post
2765 o new pkg: aim_v23
2766 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
2767 for now, keep the same surface forcing as before.
2768 - Part-Cell implemented into AIM; check that Heat & Water are conserved
2769 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
2770 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
2771 o add diagnostic of surface correction term in monitor output
2772
2773 o bulk_force and therm_seaice
2774 - Two packages: bulk_force (Bulk forcing)
2775 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
2776 - Earlier integration from Stephaine Dutkiewicz
2777 and Patrick Heimbach.
2778 - Two ifdef statements for compile time,
2779 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
2780
2781 checkpoint47
2782 differentiable version of checkpoint46n_post
2783 o bug fix in quasihydrostaticterms
2784 o * "clean" adjoint code (in terms of extensive recomputations)
2785 can now be obtained for all GMREDI options (i.e. for
2786 - GM_VISBECK_VARIABLE_K
2787 - GM_NON_UNITY_DIAGONAL
2788 - GM_EXTRA_DIAGONAL
2789 - GM_BOLUS_ADVEC )
2790 * However, wrong gradient check problem remains unsolved.
2791 * New CPP options have been introduced for different
2792 tapering schemes
2793 o external_fields_load now part of differentiation list
2794 o pressure needs multiple storing;
2795 would be nice to have store_pressure at beginning or
2796 end of forward_step, e.g. by having phiHyd global (5-dim.)
2797 (NB: pressure is needed for certain cases in find_rho,
2798 which is also invoked through convective_adjustment).
2799 o recomputations in find_rho for cases
2800 'JMD95'/'UNESCO' or 'MDJWF' are OK.
2801 o #define ATMOSPHERIC_LOADING should be differentiable
2802 o ini_forcing shifted to begining of initialise_varia
2803 o Incorporating QNVS line search routines into MITgcm
2804 (this is separate code, and therefore not under pkg)
2805 lsopt/, optim/
2806 o Updated verification/carbon/
2807 - #define GM_VISBECK_VARIABLE_K
2808 - GM_taper_scheme = 'ldd97'
2809
2810 checkpoint46n_post
2811 Merging from release1_p8:
2812 o verification/natl_box:
2813 updating new external_fields_load routine
2814 o New package: pkg/seaice
2815 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
2816 The sea-ice code is based on Hibler (1979-1980).
2817 Two sea-ice dynamic solvers, ADI and LSR, are included.
2818 In addition to computing prognostic sea-ice variables and diagnosing
2819 the forcing/external data fields that drive the ocean model,
2820 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
2821 The implied surface heat flux is then stored in variable
2822 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
2823 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
2824 non-local transport term. Because this call precedes model
2825 thermodynamics, temperature under sea-ice may not be "exactly" at
2826 the freezing point by the time theta is dumped or time-averaged.
2827 N.B.: fairly large differences in accuracy occur across
2828 different platforms/compilers; comparison between
2829 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
2830 generated output gives:
2831 T S U V
2832 C D M c m s m s m s m s
2833 n p a R g m m e . m m e . m m e . m m e .
2834 f n k u 2 i a a d i a a d i a a d i a a d
2835 g d e n d n x n . n x n . n x n . n x n .
2836
2837 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
2838 o GAD:
2839 - generated new common blocks to account for call of
2840 same gad routines with differing traceridentities
2841 (needed to modify tracerIdentity indices in GAD.h)
2842 - generated separate common blocks for case useCubedSphereExchange
2843 (Department of Futurology)
2844 - parameter lists to gmredi_?transport: added tracerIdentity
2845 - added new key indices to tamc.h
2846 o external_fields_load:
2847 - added this routine to TAF list
2848 - needed to make some common blocks global and additional storing
2849 along the same lines as exf package (checkpoint_lev?_directives.h)
2850 o exf:
2851 updated external forcing package
2852 - bug fixes carried over from ecco-branch
2853 (missing OBCS_OPTIONS.h in two routines)
2854 - enable easy to use "no forcing".
2855 - added exf I/O for atmospheric loading
2856 - added exf I/O for runoff data
2857 - transfered scaling between exf <-> MITgcm to exf namelist
2858 o Adding new verification experiment global_with_exf.
2859 This verification experiment is almost identical to the
2860 global_ocean.90x40x15 experiment, except that it uses
2861 the exf (and cal) package instead of the
2862 external_fields_load routine (cf README file).
2863
2864 checkpoint46m_post
2865 o modified testscript to return -- when there are no lines of "%MON" output
2866 o added new flag "quasiHydrostatic" for QH mode
2867 and new routine quasihydrostaticterms()
2868 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
2869 New routine: mom_u_coriolis_nh()
2870 o fixed sign of non-hydrostatic metric terms in u and v equations.
2871 Depend on correct sign of gravitySign.
2872 o added work.pc* to .cvsignore in aim directories using ifc
2873 o introduced flag for controllin non-hydrostatic metric terms
2874 o removed gravitySign from PARM04
2875 o switched to g77/ifc from pgf77 in aim experiments
2876
2877 checkpoint46l_post
2878 o made convective adjustment work with pressure coordinates:
2879 - changed the direction of k-loop in convective_adjustment.F for the
2880 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
2881 - adjusted the reference pressure k-index in convective_adjustment.F
2882 - adjusted the convection condition in convect.F (in analogy to
2883 calc_ivdc.F)
2884 - convective_adjustment no longer computes anything on the halos
2885 - removed the warnings about negative salinity from find_rho.F and
2886 find_alpha.F; instead the new routine look_for_neg_salinity, called
2887 at the beginning of find_rho, find_alpha, and find_beta, does a
2888 check of the entire slice, if CPP-option
2889 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
2890 checkpoint46l_pre
2891
2892 checkpoint46k_post
2893 o fixed the verification/global_ocean.90x40x15 experiment:
2894 - new bathymetry (the world according to A., JMC, and M.)
2895 - new initial fields and forcing fields (*.bin files)
2896 - new POLY3.COEFFS (for the next release one should switch to a full
2897 equation of state: JMD95P or MDJWF)
2898 - fixed several errors and redundancies in the data file
2899 - experiment uses looped cells
2900 - added matlab directory with diagnostic scripts for plotting of output
2901
2902 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
2903 - read AIM physics parameters from a file (data.aimphys)
2904 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
2905
2906 checkpoint46j_post
2907 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
2908 o move wVel computation at the end of the time step, in S/R integr_continuity
2909 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
2910 o update timeave pkg for wVel diagnostic.
2911 checkpoint46j_pre
2912
2913 checkpoint46i_post
2914 o Clean up AIM package (and keep the results unchanged):
2915 include CPP_OPTION and use IMPLICT NONE in all routines ;
2916 declare all the variables _RL ; use _d 0 for all numerical constants.
2917 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
2918
2919 checkpoint46h_post
2920 o cleaned up the use of rhoNil and rhoConst.
2921 - rhoNil should only appear in the LINEAR equation of state, everywhere
2922 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
2923 and the dynamical equations are all divided by rhoConst
2924 o introduced new parameter rhoConstFresh, a reference density of fresh
2925 water, to remove the fresh water flux's dependence on rhoNil. The default
2926 value is 999.8 kg/m^3
2927 o cleanup up external_forcing.F and external_forcing_surf.F
2928 - can now be used by both OCEANIC and OCEANICP
2929 checkpoint46h_pre
2930
2931 Added code to convert surface volume flux (fresh water) into
2932 a mass flux when using P coordinates in the ocean (OCEANICP).
2933 Note: It assumes you have set rho0=rhoConst=density of fresh water.
2934
2935 checkpoint46g_post
2936 o Include a new diagnostic variable phiHydLow for the ocean model
2937 - in z-coordinates, it is the bottom pressure anomaly
2938 - in p-coordinates, it is the sea surface elevation
2939 - in both cases, these variable have global drift, reflecting the mass
2940 drift in z-coordinates and the volume drift in p-coordinates
2941 - included time averaging for phiHydLow, be aware of the drift!
2942 o depth-dependent computation of Bo_surf for pressure coordinates
2943 in the ocean (buoyancyRelation='OCEANICP')
2944 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
2945 Theta, Salinity, and Pressure in the parameter list. This routine is
2946 presently contained in find_rho.F. This routine does not give the
2947 correct density for 'POLY3', which would be a z-dependent reference
2948 density.
2949 o cleaned up find_rho
2950 - removed obsolete 'eqn' from the parameter list.
2951 o added two new verification experiments: gop and goz
2952 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
2953 checkpoint46g_pre
2954
2955 checkpoint46f_post
2956 o Enable tangent linear (forward mode) gradient checks:
2957 - extended active file handling to g_... files
2958 - added TANGENT_SIMULATION to theSimulationMode
2959 - extended grdchk package accordingly
2960 o added tangent linear setup in verification/carbon/code_ftl
2961 o added adjoint setup in verification/front_relax/code_ad
2962
2963 checkpoint46e_post
2964 o Added new equation of state -> MDJWF
2965 - EOS of McDougall et al., 2002, JAOT, submitted
2966 - caveat: the equation of state is only valid for a smaller (more
2967 realistic?) range of values than JMD95P/Z and UNESCO
2968 - added masks to the calculation of pressure in store_pressure
2969 - added more check values for density in check_eos (ini_eos.F), some of
2970 the old check values are out of the range of the MDJWF-eos, so don't
2971 expect perfect matches for those
2972 checkpoint46e_pre
2973
2974 checkpoint46d_post
2975 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
2976 'OCEANICP', also initialised field pressure correctly in ini_eos in the
2977 case of pressure coordinates. eosType='JMD95Z' in
2978 combination with buoyancyRelation='OCEANICP' now causes an error.
2979 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
2980 in find_alpha/beta.
2981 checkpoint46d_pre
2982
2983 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
2984 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
2985
2986 checkpoint46c_post
2987 o Changes necessary for ocean in p-coordinates
2988 - Added new buoyancy relation = 'OCEANICP'
2989 - Added new parameters = gravitySign (this used to be contained inside
2990 the factor dRdZ which I added when we first switched to R coordinates).
2991 X GM/Redi is not compatible (yet)
2992 X bottom drag and no-slip need to be debugged.
2993 checkpoint46c_pre
2994
2995 checkpoint46b_post
2996 o Added new equation of state -> JMD95Z and JMD95P
2997 - EOS of Jackett and McDougall, 1995, JAOT
2998 - moved all EOS parameters into EOS.h
2999 - new routines ini_eos.F, store_pressure.F
3000 o Added UNESCO EOS, but not recommended because it requires
3001 in-situ temperature (see JMD95)
3002 o Modified formatting for knudsen2.f in utils/knudsen2 and added
3003 unesco.f to be used with POLY3
3004 checkpoint46b_pre
3005
3006 checkpoint46a_post
3007 o Added (atmospheric) pressure loading
3008 - new field in FFIELDS.h, etc...
3009 - new cpp flag ATMOSPHERIC_LOADING
3010 o Changed hFacC to _hFacC in calc_phi_hyd.F
3011 o Added SHORTWAVE_HEATING to some files for consistency
3012 checkpoint46a_pre
3013
3014 checkpoint46
3015 further merges from release1_p5
3016 o new ctrl package
3017 - adopted from ECCO environment to enable optimization
3018 - added Eliassen Palm fluxes to controls
3019 o added Eliassen Palm flux controls to gradient check package
3020 o cost package
3021 - Compatible with new ctrl package
3022 - added Eliassen Palm cost hooks
3023 - modif's of existing cost functions
3024 o Adjoint-related bug fixes in kpp:
3025 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
3026 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
3027 o autodiff package
3028 - flow directives:
3029 + new for S/R do_the_model_io
3030 + enhanced for S/R checkpoint
3031 + new gmredi.flow
3032 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
3033 disable adcommon.h/g_common.h by default.
3034 - fixed problem for adjoint of global_max
3035 o modified verification/carbon/
3036 o New setup for adjoint of global_ocean
3037 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
3038 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
3039 o incorporated hooks for sponge layer code (external_forcing.F)
3040
3041 checkpoint45d_post
3042 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
3043 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
3044 (affects plume_on_slope "cg2d" output)
3045 o add new parameter deltaTfreesurf for free-surface time stepping
3046 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
3047 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
3048 o change phiMin in exp1 (to agree with documentation)
3049 o add new flags:
3050 - T,S forcing inside/outside Adams-Bashforth
3051 - turn off temp,salt advection and/or forcing
3052 - for each tracer, define internal flag for multiDimAdvection & A-B
3053 o monitor: change definition of KE to check conservation of Energy
3054
3055 checkpoint45c_post
3056 o Removed f90 comments ("!")
3057 o Modified initialisations to enable exf package for MITgcm
3058 (without invoking ECCO_PACKAGE).
3059 o modifications to gradient check package (Martin Losch)
3060 - enable centered differences
3061 - modified format of standard output
3062
3063 checkpoint45b_post
3064 o cleaned exchange calls in cg2d
3065 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
3066 o included CPP option SINGLE_LAYER_MODE in thermodynamics
3067 to configure barotropic setup (Martin Losch)
3068 o moved some initialisations within bi,bj loop in dynamics
3069 (TAF flow dependency)
3070 o in initialise_varia, moved call packages_init_variables
3071 before convective_adjustment_init
3072 (corresponding adjustment of TAF tape initialisation).
3073 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
3074
3075 checkpoint45a_post
3076 o compute Rho over the whole domain (extend iMin,jMin indices)
3077 o specific exchange for X-slice domain (case Ny=1)
3078 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
3079 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
3080
3081 checkpoint44h_post = checkpoint45
3082 o Fix to restore differentiability:
3083 place at which packages_init_variables is called in
3084 initialise_varia is crucial for reverse control flow.
3085 o modifications in GMRedi to enable stable adjoint
3086 (corresponding modif's in thermodynamics, dynamics)
3087 o added missing hook for sponge layer code in external_forcing
3088 o modified test cost functions
3089 o storing in gad_advection (plus removal of write(0,*)!
3090 o missing headers TR1.h added in convective_adjustment routines
3091 o errorMessageUnit set non-equal zero in eeboot
3092 (conflict on some platforms, e.g. IBM SP3)
3093 o modified carbon verif.
3094
3095 checkpoint44h_pre
3096 o vertical grid option: allow to put the Interface at the middle between
3097 2 cell-centers ; replace delZ in pkg/kpp by drF.
3098 o GM Advective form: Tracers are advected using the residual transport (=
3099 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
3100
3101 checkpoint44g_post
3102 o fix surface correction term in multiDimAdvection (affects plume_on_slope
3103 results) ; ifdef missing in thermodynamics.F
3104
3105 checkpoint44f_pre,checkpoint44f_post
3106 o added PTRACERS package
3107 This allows an arbitrary number of passive tracers to be integrated
3108 forward simultaneously with the dynamicaly model.
3109 + Implemented so far:
3110 - basic forward algorithm (time-stepping, advection, diffusion, convection)
3111 - I/O and checkpointing
3112 - GM/Redi *but* using the GM/Redi coefficient of Salt
3113 + Not implemented so far:
3114 - KPP
3115 - OBCS
3116 + No specific example supplied (yet) but global_ocean.90x40x15 has the
3117 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
3118 line in data.pkg.
3119 + This package is disabled by default since it increases storage.
3120
3121
3122 o testscript: added -cleanup option
3123 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
3124 b) enable to filter 2D fields.
3125
3126 checkpoint44e_pre,post
3127 o re-wrote convective adjustment to use pre-calculated weights
3128 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
3129 Adds: model/src/convective_weights.F, convectively_mixtracer.F
3130 Original calls to convect() still in place.
3131
3132 chkpt44d_pre,post
3133 o added missing EXCLUDE_MONITOR flags
3134 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
3135 (incompatible typ in MIN/MAX expressions caused problems
3136 on IBM SP3)
3137 o in genmake added variable MAKEDEPEND
3138 plus resetting for case SunOS
3139 o added timer_stats.c routine for IBM SP3
3140 o removed variables in dynamics
3141 !!! I forgot to create tag chkpt44d_pre !!!
3142 !!! But chkpt44d_pre = chkpt44c_post !!!
3143
3144 o real fresh water flux implemented with non-linear free-surface.
3145
3146 chkpt44c_pre,post
3147 o few fix (mask in shap_s2, EmPmR in external_field_load,
3148 USE_NATURAL_BCS in solve_for_P);
3149 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
3150
3151 checkpoint44b_pre/_post
3152 o merge of relevant stuff from the ecco-branch:
3153 - genmake: removed $S64 overwrite for case SunOS
3154 - pkg/exf: update and corrections for field swapping and obcs
3155 - pkg/ecco: parameter lists for the_model_main, the_main_loop
3156 harmonized between ECCO and MITgcm
3157 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
3158 updated checkpointing_lev... lists for obcs
3159 - model/src: minor changes in forward_step, plot_field
3160 added directive for divided adjoint in the_main_loop
3161 - pkg/mdsio: added mdsio_gl_slice
3162
3163 o check parameters & config (chkpt44a_pre,post)
3164 o OBC and NonLin_FrSurf.
3165
3166 checkpoint44
3167 o fix bug in mom_vi_del2uv
3168 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
3169 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
3170 o update AIM experiments (NCEP input files)
3171 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
3172 o added some stuff for AD
3173
3174 checkpoint43
3175 o added two new advection tests
3176 o added global 4x4 degree ocean test
3177 o added test of H&S94 with free surface on cube
3178 o some final mods for gradient check, adjoint,...
3179
3180 checkpoint42
3181 Fixed AD-related problems:
3182 o Store directives up-to-date with re-arranged Adams-Bashforth
3183 (mainly thermodynamics.F)
3184 o New store directives for multi-dim. advection schemes
3185 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
3186 * new common block and key passkey
3187 (mainly gad_advection.F)
3188 o Modified store directives for split of dynamics/thermodynamics
3189 for the case ALLOW_KPP
3190 o Cleaned argument list for timestep_tracer.F
3191
3192 checkpoint41
3193 o re-formatted/added comments in prologues of key subroutines
3194 to work with protex
3195
3196 checkpoint40
3197 o moved calc_gs, calc_gt and calc_tr1 back to model/src
3198 o added FLT (floats) package from Arne along with demo. experiment
3199 o re-arranged Adams-Bashforth scheme for tracers to allow easier
3200 implementation of forward-in-time forcing terms
3201 o more mods for non-linear free-surface including new variable
3202 o modified multi-dim method to work on cube
3203 o bug fix in KPP (from DM)
3204
3205 checkpoint40pre9
3206 o added DST advection schemes
3207 o fix MPI bug on SGI's
3208 o modifications for non-linear free-surface
3209 o fixed conditionals for fixed flow/passive tracer only mode
3210 o added tension/strain form of stress tensor
3211 o changes to commenting of arguments for TAF/TAMC
3212 o added/updated many matlab scripts
3213 o added multi-dimensional advection method for tracers
3214
3215 checkpoint40pre8
3216 o new package rw/
3217 Added method for dumping intermediate local arrays:
3218 mdsio_writetile - same as mdsio_writefield except works from inside
3219 bi,bj loop
3220 mdsio_writelocal - same as mdsio_writetile except works for local
3221 arrays
3222 write_local_r? - higher-level wrapper for mdsio_writelocal
3223 Controlled by diagFreq. Defaults to zero (ie. no dumps)
3224 Example given at end of mom_vecinv.F that dumps some local arrays.
3225 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
3226 control flux-form versus vector invariant code.
3227 Switch is runtime flag vectorInvariantMomentum (defaults to false)
3228 or genmake -DISABLE ...
3229 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
3230 (additional storing is now needed for case vecinv;
3231 currently nothing implemented to switch this storing off
3232 in case fluxform is used since no CPP flag available).
3233
3234 checkpoint40pre7
3235 o bug fix in dynamics.F
3236 calc_viscosity called before k=1,Nr loop.
3237 o added some #ifdef's ALLOW_PASSIVE_TRACER
3238 o cleaned initialisations in ctrl_map_ini
3239 related to TAF
3240
3241 checkpoint40pre6
3242 o split dynamics into thermodynamics & dynamics
3243 o corresponding split of calc_diffusivity into
3244 calc_diffusivity, calc_viscosity
3245 (kpp_calc_diff, kpp_calc_visc).
3246 o Added diffkr, kapgm to control variables
3247 o bug fix in gmredi_slope_limit for ldd97
3248
3249 checkpoint40pre5
3250 o proper initialization of Adams-Bashforth time stepping
3251 + uses forward step for very first step of model (iter=0)
3252 o re-generated *all* output since almost all output is modified by this
3253 change (sorry but we've been putting this one off for about 2 years)
3254 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
3255 *not* regenerated since they are already out of date and I don't
3256 want to create the impression that they are suddenly working.
3257 o removed KAP stuff for DEC's
3258 o modified/added many .cvsignore files in */code and */input
3259 o added new expt "solid-body.cs-32x32x1"
3260 + this uses an alternative form of ini_curvilinear_grid.F which
3261 is not necessarily any better than the current one...
3262
3263 checkpoint40pre4
3264 o added re-initialisations of utrans,vtrans,rtrans in
3265 calc_common_factors which are crucial for TAF.
3266 o extended iMin,jMin range for calc_common_factors,
3267 calc_diffusivity
3268 o added option ALLOW_PASSIVE_TRACER
3269 o a few minor updates and fixes
3270
3271 checkpoint40pre3
3272 o created calc_gtr1.F for gad package
3273 o split the_main_loop and re-introduced forward_step
3274 o some recomputations of nIter0 for TAMC
3275
3276 checkpoint40pre2
3277 o Updated to latest branch of AJA, JMC
3278 o Added gradient check package
3279 o Added routines for passive tracer handling
3280 o Added carbon sequestration sensitivity experiment
3281
3282 checkpoint39
3283 o Modifications and fixes to support TAMC
3284 (mainly missing or wrong directives)
3285 o Corrected common blocks when fooling TAMC to produce adjoint I/O
3286 in addummy_in_stepping
3287 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
3288 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
3289 o Included following packages:
3290 cal: calendar
3291 exf: external forcing
3292 ecco: essential routines to control use of cal, exf
3293 (NB: this is not the full ECCO environment)
3294 o disabled some packages by default in genmake
3295
3296 checkpoint38
3297 o see notes_c37_adj.txt
3298 o corrected wrong layer index in external_forcing_t
3299 o replaced the_main_loop/forward_step by the_main_loop
3300 o removed forceoutput from write_state
3301 (replaced criteria for initial/final state)
3302 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
3303
3304 checkpoint37
3305 o mdsio.F routine split and packaged in pkg/mdsio
3306 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
3307 used unless genmake -disable=mdsio)
3308 o allow a more precise surface-geopotential gradient for the atmosphere
3309 taking into account the change in space of Alpha (=1/rho) at the surface.
3310 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
3311 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
3312 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
3313 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
3314 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
3315 o Time-Average diagnostics defined as a pseudo package "timeave".
3316 o pickup files : old pickup (before c35) did not work with new code (c35
3317 and after) unless activating 2 commented lines in initialise-varia.
3318 o Non-Hydrostatic pickup file Pb fixed.
3319 o bug with Rigid-lid version (since c35) fixed.
3320
3321 checkpoint36
3322 o implement Crank-Nickelson barotropic time-stepping
3323 o recover Time-Average diagnostics
3324 o fix Pb in checkpoint (PR#19)
3325 o AIM become a standard package ; clean unused CPP_kees
3326
3327 checkpoint35
3328 o subtantial rewrite of dynamics.f
3329 o allows staggered time-stepping
3330 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
3331 o added bottom drag (linear + quadratic)
3332
3333 checkpoint34
3334 o Modified exchange routines for correct reverse simulation.
3335 o Added verification output to comply with bug fix in impldiff.F
3336 as of c33 (exp2, natl_box).
3337 o Corrected store directives in dynamics.F
3338 o Corrected array boundaries in impldiff.F
3339 o Corrected array dimensions in gmredi.
3340 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
3341 o Added routine GLOBAL_SUM_INT to global_sum.F
3342 o Added mdsio_gl.F for ECCO purposes.
3343
3344 checkpoint33
3345 o Fixed bug in lower BC in impldiff.F
3346 o Fixed confusion about units of forcing arrays in FFIELDS.h
3347 namely Fu,Fv,Qnet,Qsw,EmPmR:
3348 - Removed verification/natl_box/code/external_fields_scale.F
3349 (did not differ from that in model/src)
3350 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
3351 (see FFIELDS.h for description)
3352 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
3353 kpp_calc.F and kpp_transport_t.F
3354 - Removed model/src/external_fields_scale.F and calls to it
3355 - verification/natl_box uses flux data with "atmospheric" sign so
3356 a special version of external_fields_load.F is used to
3357 change the data as it's read in. This way, the arrays
3358 have the right units and signs at all times tha a user could
3359 possibly use them.
3360 o Corrected genmake to delete a temporary file during configuration
3361
3362 checkpoint32
3363 o Scaling of forcing fields moved from external_forcing.F to
3364 external_fields_scale.F, called directly after loading fields.
3365 o Surface relaxation terms added to surface tendency fields in
3366 extra subroutine.
3367 o impldiff.F changed to avoid storing by TAMC of huge intermediate
3368 fields.
3369 o Changes in GMRedi to comply with packaging structure.
3370 o Modifications and bug fixes in KPP package.
3371 o Verification experiment for KPP added (verification/nat_box/)
3372
3373 checkpoint31
3374 o Packages interface brought in line with defined standard
3375 -> new routines packages_...F
3376 -> changes in initialise_fixed.F, initialise_varia.F
3377 -> enables initialisation interface for ECCO package
3378 o Rescaling of external forcing fields immediately after read
3379 (removed from external_forcing.F)
3380 -> new: surface_fields_scale.F
3381 -> affects ini_foorcing.F, external_fields_load.F
3382 o Computation of surface tendencies before tendency updates.
3383 -> new: external_forcing_surf.F
3384 o Change of variable names useGMRedi, useKPP, useECCO
3385 o Further changes in dynamics.F, impldiff.F for TAMC
3386 o Tested for experiments 0, 2, 4.
3387 - not yet tested for GMRedi.
3388 - not yet tested for KPP.
3389
3390 checkpoint30
3391 o Updates for OBCs
3392 o New experiment for test OBCs (internal_wave)
3393 o New output.txt in verification/exp4/results/
3394 o Updates for KPP: calculation of viscosity corrected, new variables
3395 kpp_dumpFreq and kpp_taveFreq
3396 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
3397 and entry for T90 in genmake
3398
3399 checkpoint29
3400 o packaged KPP and GM/Redi
3401
3402 checkpoint28
3403 o Corrected initialization of hFacMin for difference vertical coordinates
3404 o Modified calculation of partial cell thickness to more robust algorithm
3405 o config_summary.F: replaced write_1D_... by write_0D_...
3406 read_write.F: added subroutines write_0D_...
3407 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
3408 included some initialisations required for TAMC.
3409 o routine calc_isoslopes: modified sqrt computation to make it
3410 differentiable for zero argument.
3411 o routines dynamics, impldiff:
3412 included store directives and tape key computations required for TAMC.
3413 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
3414
3415 checkpoint27
3416 o fixed calc_isoslopes() to so that cancellation of terms in tensor
3417 formulation works properly with variable resolution.
3418 o restructured the calling tree between the_model_main() and dynamics()
3419 o split initialise() into initialise_fixed() and initialise_varia()
3420 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
3421 in new routine ini_psurf()
3422
3423 checkpoint26
3424 o moved some #ifdef in optional routines to encompass everything
3425 except the argument declarations. This was using up some memory.
3426 o fixed macros like _ADT to work with both versions of Linux cpp
3427 o cleaned up some unused and uninitialized variables
3428 (helps when debugging with strict compile options)
3429 o split up CPP_EEOPTIONS.h into options and macros
3430 (macros are now in eesupp/inc/CPP_EEMACROS.h)
3431 o patch for 2 processor JAM mode
3432
3433 checkpoint25
3434 o updates for OBCs and NH
3435 o dramatically reduced memory usage
3436 o added "JAM" routines for use on Artic network
3437 o parameterization of convection by implicit vertical diffusion
3438 o added a diagnostic of convective index
3439 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
3440 (this is was partly for OBCs and NH but also in anticipation of
3441 an explicit free-surface option)
3442 o initial state input files for U and V
3443
3444 checkpoint24
3445 o Removed some spurious "REAL"s
3446 o Updated KPP to latest version from JPL
3447 o Added a COS(latitude) in horizontal viscosity
3448
3449 checkpoint23
3450 o Added del^4 diffusion for salt and temperature
3451 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
3452
3453 checkpoint22
3454 o Made many small changes: implicit none, format(i5), etc...
3455 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
3456
3457 checkpoint21
3458 o Introduced new I/O package that supports direct-access records (mdsio.F)
3459 o Split-up mid-level I/O routines
3460 o Updated input data for experiments 0,1,2,4 and 5
3461 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
3462
3463 checkpoint20
3464 o Tidied up open-boundaries some more
3465 o Added non-hydrostatic code
3466 o Fixed some input data
3467 o Modified MPI start-up to work in "coupled" context.
3468
3469 checkpoint19
3470 o Tidied up directory structure for verification experiments.
3471 o Added new code for open boundaries.
3472 o Corrected advective terms near boundaries.
3473 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
3474 o Implemented free-slip/no-slip BCs and del^4 dissipation.
3475 o Split default parameters out of ini_parms.F into set_defaults.F.
3476
3477 checkpoint18
3478 o Further changes for optional code generation with
3479 CPP - ugh!
3480
3481 checkpoint17
3482 o Beginning to incorporating modularity
3483 for supporting atmos. and ocean configs.
3484 o Small changes for TAMC complinace
3485 o New ultra simple test case. Barotropic box
3486 configuration "exp0".
3487
3488 checkpoint16
3489 o Minor changes to exchange routines to support
3490 accumulation in reverse mode. Adjoint of an
3491 assignment is an addition.
3492 o Changes to support compilation by TAMC (LR(1)
3493 syntax) and by g77 under Linux ( 72 character
3494 limit ).
3495
3496 checkpoint15
3497 Rewrote exchange routines to allow
3498 o General tile <-> tile connectivity.
3499 o TAMC reverse mode flag ( is this really needed? )
3500 o Variable width overlap and exchange region widths.
3501 o Hooks for sharing data via DMA, Arctic, Memory Channel,
3502 shmput/shmget, VIA, SYSV shmem and every other cool
3503 communication method.
3504
3505 checkpoint14
3506 Consistent isomorphism chages made. These allow dynamical core
3507 to support both pressure and meters as a vertical coordinate.
3508
3509 checkpoint13
3510 Release which corrects global_max problem and a couple
3511 of KGM time-averaging diagnostic errors. Also contains
3512 a double-gyre experiment setup as well as the baseline
3513 4 degree global template. The double gyre template is
3514 organised to allow it to be applied automatically to
3515 the baseline configuration.
3516
3517 branch-point-rdot
3518 A few tidy-ups have been made bt the real point of this
3519 check-point (excuse the pun) is to allow a branch to be
3520 made for the purposes of adding the rDot alterations.
3521 I don't want to commit the rDot to the main-trunk until
3522 we've actually tested it...
3523
3524 checkpoint12
3525 Tidy up and added generic genmake script (formerly
3526 configure script).
3527 Released to testers.
3528
3529 checkpoint11
3530 Re-arranged initialise() and introduced ini_vertical_grid()
3531 and ini_masks_etc().
3532
3533 checkpoint10
3534 Introduced the configure script.
3535 Separated out the diags package.
3536 Added template for writing time-averages of tile/intermediate quantities.
3537 Updated SIZE.h in exp2 and made the data big-endian.
3538
3539 checkpoint9
3540 MPI fix. Filename changes (meta/data). salbin*y stuff.
3541 General tidy-up.
3542 SST.bin SSS.bin added to verification/exp2
3543
3544 checkpoint8
3545 Inludes time-dependant forcing and time-averaging.
3546 Works at 4x4 and 2.8125x2.8125 global
3547
3548 checkpoint7-4degree-ref
3549 Branch from checkpoint7. Released for application to
3550 global modeling and general modeling - process studies, regional
3551 model etc..
3552 Configured for verification/exp2 - 4 degree global, two process.
3553
3554 checkpoint7
3555 Created by cnh
3556 Simple 4 degree global simulation
3557 configuration.
3558 Includes climatological wind,
3559 hydrography, bathymetry etc
3560 Does not include Heat Flux and E-P
3561
3562 checkpoint6
3563 Created by cnh
3564 merged checkpoint5 with CD and
3565 spherical polar code.
3566 Still some problems with GM Redi
3567 abd full topography.
3568
3569 checkpoint5
3570 Created by AJA
3571 contains updates to GM Redi
3572 and reordered timestepping loop
3573 for Implicit Diffusion.
3574
3575 checkpoint4
3576 Created by cnh
3577 Contains memory saving macros ( _rdxc etc..) for when
3578 grid variations are limited.
3579 Contains polynomial coeffs for EOS and knudsen program
3580 for generation.
3581
3582 checkpoint3
3583 Created by cnh
3584 Added extra flags for runtime options
3585 Added this file
3586 Added implicit free-surface
3587 Added pre-conditioner
3588 Put compare01 into repository ( compare01/... )
3589 Put data and eedata into repository ( verification/exp1 )
3590
3591 checkpoint2
3592 Created by AJA
3593 Added GM/Redi
3594
3595 checkpoint1
3596 Created by AJA
3597 Restructured kloop in dynamics.F
3598 Added non-linear EOS
3599
3600 baseline
3601 Original checked in code

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