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Revision 1.973 - (show annotations) (download)
Thu Apr 10 13:56:08 2008 UTC (15 years, 7 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint59p
Changes since 1.972: +9 -3 lines
checkpoint59p

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.972 2008/04/06 03:37:44 jmc Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 checkpoint59p
8 o gchem / dic / cfc :
9 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
10 - add new parameter files: "data.dic" & "data.cfc" ;
11 - various re-arrangement in initialisation & header file ;
12 - fix tutorial_global_oce_biogeo for multi-threaded test.
13 o pkg/dic: test for "pickup_dic" file when restarting ;
14 if no pickup-file, can restart with a re-initialised pH (same as it did
15 before) providing pickupStrictlyMatch is set to False.
16 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
17 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
18 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
19 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
20 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
21 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
22 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
23 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
24 scheme to use for vorticty-term ;
25 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
26 (with default selectVortScheme, return to original discretisation)
27 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
28 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
29 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
30 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
31 also fix diagnostics VISCAHW & VISCA4W.
32
33 checkpoint59o
34 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
35 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
36 move a few statemens out the main loop into separate loops
37 o pkg/shelfice:
38 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
39 (kg/m^2/s), does not break tests, because in verification/isomip,
40 rhoConstFresh=rhoConst (by accident)
41 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
42 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
43 new file model/src/seawater.F, so that they are available for all pkgs.
44 - convert potential temperature into in-situ temperature. This changes the
45 isomip tests => update tests
46 o add a flag writePickupAtEnd (default=true) to be able to suppress
47 writing a pickup at the last timestep
48 o tools/mpack-1.6 :
49 - disable automake (not working) and autoconf (not needed).
50 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
51 also cleaner with much less compilation warnings.
52 o pkg/profiles:
53 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
54 (for "less than 32 characters name" compiler requirement)
55 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
56 conditions that have a different sampling frequency than S/T/U/V obcs
57 o pkg/diagnostics (stats-diags):
58 - fix global Min/Max in case 1 processor get only empty tiles
59 o genmake2: replace (4 times)
60 make genmake_tc_1.o >> genmake_warnings 2>&1
61 with
62 COMM="$CC $CFLAGS -c genmake_tc_1.c"
63 echo $COMM >> genmake_warnings
64 $COMM >> genmake_warnings 2>&1
65 to make genmake2 always see the value of CC as specified in the optfile.
66 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
67 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
68 - modify verification advect_cs test to test SOM-advection on CS-grid.
69 o pkg/ctrl:
70 - Rewrite of ctrl_map_ini_ecco.F,
71 introducing a generic routine (ctrl_map_ini_gen.F).
72 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
73
74 checkpoint59n
75 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
76 number in dedicate array "hdiag":
77 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
78 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
79 - many small changes (integer format) for large number of diagnostics
80 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
81 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
82 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
83 usingSphericalGrid, this allows to define the rotated grid coordinates
84 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
85 geographical coordinates according to the inverse of the rotation defined
86 by the Euler angles, so that Coriolis parameter and online-interpolation by
87 exf works with the geographical coordinates on XC/YC/XG/YG.
88 Naturally, this feature does not work with all packages, so some
89 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
90 profiles), because there the coordinates are assumed to be regular
91 spherical grid coordinates.
92 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
93 - introduce isopycnal diffusion coefficient control.
94 o tools/adjoint_options:
95 - additional control vector components.
96 o pkg/mnc: have mnc create marginally meaning full coordinate variables
97 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
98 o pkg/mypackage:
99 - add example of read/write pickup for state-var ;
100 - add entry points to the main code for state-vars diags & write-pickup.
101 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
102 transitions for useExfYearlyFields
103 - add new subroutine that determines the file to read from for
104 use*YearlyFields = .TRUE. and .FALSE.
105 - add a verification experiment to global_with_exf that tests
106 useExfYearlyFields with USE_EXF_INTERPOLATION defined
107 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
108 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
109 subroutines (which could be generated from a template, because they are
110 almost identical), for now they are included in obcs_prescribe_read.F for
111 simplicity
112 o pkg/exf:
113 - add a little more diagnostic to exf_interp_read (in analogy to
114 mds_read_field, can be turned off with debugLevel < debugLevA=1)
115 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
116 ugly but fast by unrolling short inner loops, inserting a unroll=8
117 directive in routine lagran, and splitting a loop and making do while the
118 outermost loop (the latter requires the intoduction of index arrays)
119 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
120 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
121 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
122 o verification/seaice_obcs: updated for restart test and latest options
123 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
124 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
125 for now this is only available for the C-grid code and also within
126 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
127
128 checkpoint59m
129 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
130 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
131 o gad_som : fix flux output (& diagnostics) to have same units as other
132 advection scheme fluxes (was previously multiplied by deltaT).
133 o added verification/seaice_obcs both to test seaice open boundaries
134 and to provide an example matlab scrpt for generating them
135 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
136 o pkg/salt_plume: clean up salt_plume_frac.F to
137 remove redundancy in PlumeMethod 1 and 4
138 o pkg/kpp: added saltplume diagnostics
139 o pkg/obcs and pkg/seaice:
140 - do not set uice and vice to zero when OB*icefile are unspecified
141 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
142 - moved seaice tracer obcs after call to seaice_growth
143 o pkg/salt_plume: added various options for salt plume depth
144 criterion and for vertical distribution of the salt
145
146 checkpoint59l
147 o pkg/ptracers: new version of ptracers pickup:
148 read meta file and write only fields which are needed to restart.
149 ( same logic as main pickup file ; also using pickupStrictlyMatch )
150 o pkg/seaice:
151 - add timescale for melting due to warm mixed layer as a means of
152 setting SEAICE_availHeatFrac more conveniently
153 - add a CPP-flag/runtime parameter check for flooding algorithm
154 - reformulated availHeat in seaice_growth.F to be independent of AREA
155 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
156 unit changes
157 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
158 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
159 SX vector computer.
160 o pkg/seaice:
161 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
162 seaice forcing fields can now be read only through pkg/exf
163 - removed some unused halos
164 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
165 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
166 or U/VICE from U/VWIND before computing U/VSTRESS
167
168 checkpoint59k
169 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
170 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
171 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
172 all experiments pass when compile with un-initialised var. checking option.
173 o added pkg/salt_plume
174 o script to test restart (for now, in MITgcm_contrib/jmc_script)
175 o pkg/seaice: new read/write pickup version.
176 read meta file and write only fields which are needed to restart.
177 ( same logic as main pickup file ; also using pickupStrictlyMatch )
178 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
179 o lab_sea.hb87: modify the domain & update output.hb87.txt :
180 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
181 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
182 process. Fixed here by closing the domain at the Northern boundary.
183 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
184 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
185 a set of consecutive levels in/from a 3-D array.
186 o pkg/ptracers:
187 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
188 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
189
190 checkpoint59j
191 o in pkgs: dic, obcs, offline, rbcs:
192 standard way to compute coeff. for time interpolation between 2 time reccords
193 which retains full precision (& make results less dependent on compiler).
194 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
195 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
196 packages instead of reading ice cover and wind speed separately
197 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
198 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
199 to allow to compile customized code before the update)
200 o cleaning-up:
201 - fix CPP instruction syntax in pkg/obcs
202 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
203 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
204 - fix some threads issue in IO parts.
205 o pkg/dic:
206 - add tons of "_d 0" (--> much better testreports !)
207 and then update outputs of tutorial_global_oce_biogeo
208 o pkg/mom_fluxform:
209 add a special version of momentum advection intended to conserve momentum
210 next to a bathymetry step or a coastline edge. (default = off = #undef)
211 o new read/write pickup version:
212 - for now, only implemented for main (mdsio) pickup file.
213 - write out only what is needed to restart; merge pickup_nh , pickup_ph
214 and main pickup together.
215 - read meta file; read only what is needed to restart; stop if a field
216 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
217 if it make sense (even if the restart is not perfect).
218 - if no meta file, assume that pickup to read corresponds exactly to
219 a pickup that would currently be written.
220 - read pickup written in the old format (until checkpoint59i) if it
221 recognizes an old meta file (no field-list).
222 - add a meta file in exp. which starts from a pickup: 2 cases:
223 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
224 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
225 b) a meta file describing the content of the associated pickup file
226 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
227 o pkg/mdsio & pkg/rw:
228 - new routine to read a meta file ; new set of routine to read
229 Multiple-fields file (with meta file).
230 o added open boundary conditions capability for seaice
231 HSNOW, HSALT, UICE, and VICE
232
233 checkpoint59i
234 o adjoint:
235 * fix multiDimAdvection adjoint
236 (partial recomputation problem by TAF for fVerT(:,:,kDown)
237 and comlev1 size definition (maxpass vs. max. number of tracers)
238 * verification/global_ocean.90x45x15 adjoint now tests
239 NLFS and multiDimAdvection using DST3 (=30)
240 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
241 o pkg/kpp: add "_d 0" to real constant (if missing);
242 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
243 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
244 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
245 for internal parameters related to restart process (formerly from PARAMS.h)
246 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
247 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
248 as argument. (only atm2d & obcs write_pickup have not yet been updated)
249 o pkg/monitor:
250 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
251 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
252 - account for deep Atmosphere factor and density factor (anelastic)
253 o added open boundary conditions capability for seaice HEFF and AREA
254 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
255 thermodynamics
256 - requires a little reorganization, which affects the testreport results
257 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
258 so that now the conservative form is tested
259 - add a few comments
260 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
261 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
262 o add new diagnostics to seaice: advective, diffusive fluxes (only for
263 multidim-advection, for scheme 2 they are not filled) and transports,
264 thermodynamic growth rates
265 o change units of EmPmR (inside the code, + within coupling interface)
266 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
267 Affects results @ truncation level (cg2d match) and update output of
268 experiments: lab_sea(6), global_ocean.90x40x15(10),
269 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
270 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
271 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
272 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
273
274 checkpoint59h
275 o pkg/exf:
276 - improve vectorization by moving if-statement out of loops in
277 exf_mapfields, exf_radiation
278 - exf_bulkformulae.F: introduce 2D fields and vectorize code
279 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
280 o testreport:
281 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
282 monitor & update offline_exf_seaice exp. output.
283 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
284 o pkg/seaice:
285 - bug fix in the evp solver: boundary conditions were affected be
286 masking of zMax/zMin (changes results)
287 - minor bug fix in boundary conditions in seaice_calc_strainrates
288 (changes results for no_slip)
289 - seaice_lsr.F: make interpolation of eta dependent on boundaries
290 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
291 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
292 stress formulation and no-slip boundary conditions
293 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
294 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
295 o pkg/seaice: a first HSALT time stepping equation has been checked in
296 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
297 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
298 without requiring DO-IF statements
299 o pkg/thsice:
300 use continuous power-law function for partition of energy between lateral
301 melting/freezing and thinning/thickening ; old code using step function
302 still available with #undef THSICE_FRACEN_POWERLAW
303 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
304 o testreport: change AD testing : check against results/output_adm.txt
305 using same scripts as for forward test.
306
307 checkpoint59g
308 o adjoint testing: in preparation for changing testreport:
309 - output format: cost and grad written on separated lines
310 - ad output results in directory "results" (instead of "results_ad")
311 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
312 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
313 o pkg/ecco: allow user defined cost function contributions
314 o testreport:
315 Allow to choose (per experiment) the list of tested output variables
316 and the main variable (used to issue a pass/FAIL ) ;
317 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
318 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
319 Also modify printing of summary:
320 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
321 b) echo the list of tested variables in the individual summary.txt of
322 each experiment.
323 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
324 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
325 (but still depend on the tile decompostion of the domain).
326 o pkg/seaice: change a discretization detail to make the B-grid code
327 "more symmetric". This change is likely to remove all "ridges/leads" that
328 where quasi-aligned with the grid in B-grid solutions. It may also be
329 the solution to the stress coupling issues with the B-grid.
330 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
331 remove .cvsignore from input dir. (since testreport no longer run here).
332 o pkg/thsice:
333 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
334 - fix reshaping of sea-ice just after advection:
335 melt all the ice only if ice-volume is too small.
336 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
337 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
338 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
339 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
340 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
341 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
342 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
343 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
344 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
345 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
346 -> update output.txt
347 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
348 this affects truncation error: -> update output.txt of exp:
349 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
350 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
351
352 checkpoint59f
353 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
354 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
355 a bounded range (in forward mode)
356 o pkg/ecco, ctrl, autodiff and mom_common:
357 internal parameter controls, completements of implementations
358 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
359 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
360 (not seem any difference in testing results).
361 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
362 at face corners.
363 o pkg/generic_advdiff:
364 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
365 loop range indices for computing vertical advection tendency
366 and do the calculation in the interior only (no overlap) ;
367 for now, only implemented for SOM advection (to save CPU time).
368 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
369 o exch2 adjoint
370 First set of changes:
371 - add exch2 hand-written adjoint templates
372 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
373 This will require cleanup in pkg/autodiff/*.F
374 (changed routines currently kept separate in verif. code/)
375 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
376 that used to hide exch2 or cubed-sphere specific code
377 (commented via 'cph-exch2')
378 o pkg/seaice
379 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
380 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
381 output of global_ocean.cs32x15.thsice .
382
383 checkpoint59e
384 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
385 for B-grid vector (not yet tested) and C-grid vector (<- only used
386 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
387 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
388 (#ifdef ALLOW_SALT_PLUME)
389 o gather_2d/scatter_2d: removed halo regions
390 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
391 scheme and the corresponding test case (under front_relax dir). For now,
392 only available with Skew-flux form and not yet tested in realistic set-up.
393 adjoint: store directives updated, but gradient checks deteriorated,
394 so maybe GM/Redi adjoint is now broken.
395 o seaice adjoint
396 * add AREA, HEFF, HSNOW as control variable
397 (should not change lab_sea results)
398 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
399 o pkg/seaice:
400 * added computation of saltFlux in seaice_growth;
401 For time being, sea ice salinity is assumed constant
402 contribution of snow flooding to freshening of sea ice is neglected.
403 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
404 defaults to 0.0 in order to maintain backward compatibility.
405 Typical values for SEAICE_salinity are 4 to 10 g/kg.
406 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
407 * added SEAICE_availHeatFrac, which specifies fraction of surface level
408 heat content used to melt or grow ice
409 * commented out cap of HICE: it helps keep ice thinner
410 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
411 * applied OBCS T/S mask to HEFFM sea ice mask
412
413 checkpoint59d
414 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
415 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
416 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
417 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
418 and change default value of parameter "GM_Small_Number";
419 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
420 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
421 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
422 o pkg/ecco: cost function when applying pkg/smooth to controls
423 o pkg/ctrl: add forcingPrecond run time parameter
424 o pkg/seaice:
425 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
426 - fix bug in metric terms of u-equation in LSR solver (implicit part),
427 changes verification/lab_sea
428 - rearrange implicit part of u-equation in LSR solver to make it easier to
429 read, understand, and debug. This causes changes at the truncation level.
430 - fix (serious) bug in the boundary conditions (sign error in the implicit
431 part) of the LSR solver. Changes all LSR results.
432 - fixed problem with HSNOW initialization to avoid thick snow when AREA
433 is initilized with small values - does not change lab_sea results.
434 - added HsnowFile initialization capability
435 o pkg/smooth: addition to model/src and pkg/ctrl so allow
436 initialization of pkg/smooth and application to control vector
437 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
438 o dependencies: pkg/profiles requires pkg/cal
439 o pkg/profiles:
440 - added option ALLOW_PROFILES_GENERICGRID
441 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
442 that interpolation information (grid points and coefficients) is provided
443 within the netcdf input files.
444 -> sample matlab scripts can be found in MITgcm_contrib/gael
445 that allow you to prepare netcdf input files.
446 - also modified: cleaner include statements, cleaner error print statements,
447 cleaner stops when error, and more tests of the netcdf input files consistency.
448 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
449 o pkg/seaice:
450 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
451 requires a new routine: seaice_diagnostics_fill.F
452 - make sure that seaice does not move if not forced (pressure replacement
453 method, Hibler and Ip, 1995), changes results
454 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
455 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
456 It is turned off by default (=-1.), because it changes the results.
457 - make it possible to read AREA from a file, too.
458
459 checkpoint59c
460 o add S/R and diagnostics for oceanic mixed-layer depth
461 o move GMRedi call after all vertical mixing schemes (including KPP)
462 o pkg/thsice:
463 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
464 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
465 o pkg/obcs:
466 - bug fix for balance code
467 o pkg/seaice:
468 - allow values of SEAICE_elasticParm > 1
469 - add new parameter SEAICE_evpTauRelax as an alternative
470 to SEAICE_elasticParm
471 - make lsr boundary conditions free slip (by default), changes result
472 - add code for no slip boundary conditions for lsr
473 - set minimum of zeta to zero (and not 4e8) (changes results)
474 - add a cap on AREA after advecting AREA if seaice_growth is not called
475 o change calculation of Visbeck K:
476 - no longer depend on tapering scheme; instead, compute slope (limited
477 by GM_maxSlope). this is equivalent to what was comuted before with
478 clipping or linear tappering.
479 - fix vertical averaging (wrong by 1/2 level)
480 - leave the old version (but will not be maintained) within
481 #ifdef OLD_VISBECK_CALC / #endif
482 - update output of exp. ideal_2D_oce
483 o change error catch in calc_r_star to improve vectorization
484 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
485 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
486 o adjoint:
487 Re-organized adjoint checkpointing according to Matt Mazloff
488 (but with modifs/completions/cleanups)
489 Storing is now bundled into large arrays to optimized I/O
490 (and second step in cleanup of the_main_loop)
491
492 checkpoint59b
493 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
494 - export/import (between ocean & coupler) fields needed for ocean DIC.
495 o pkg/seaice:
496 - get rid of three more exchanges seaice_calc_viscosities (required
497 different loop boundaries in seaice_lsr and seaice_ocean_stress)
498 - bug fix in seaice_ocean_stress (update of lab_sea required)
499 - reduce loop boundaries to necessary minimum also in seaice_evp
500 - go back to the old way of computing deltaC/Z as the adjoint likes that
501 better
502 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
503 passive tracer to an Age Tracer) + update output.txt
504 o pkg/exf:
505 - implement A-grid / C-grid selection for wind-stress input files.
506 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
507 for now, in exf_bulk_largeyeager04.F only :
508 - change implementation for case where windspeed + 2. components wind-stress
509 are read-in. AND use rhoConstFresh to convert evap.
510 o pkg/seaice:
511 - use correct EXCH_UV for wind-forcing (on A-grid).
512 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
513 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
514 o pkg/exf:
515 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
516 EXF_INTERPOLATION:
517 - merge global_with_exf/code version of exf_interp_read.F
518 to the main code ;
519 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
520 reading the file ; Important: This options needs to be defined to recover
521 previous code.
522 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
523 - no longer loose real*8 precision along the way when using exf_iprec=64.
524 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
525 - change discretisation of evp-solver in order to avoid another exchange
526 (changes lab_sea) and clean up a little
527 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
528 help the adjoint (this also changes the results slightly)
529 - add a few "_d 0" where they had been missing in seaice_evp.F
530 - cleaning up: remove unused seaice_calc_rhs.F
531 o pkg/exf: some cleaning-up:
532 - change various "constants" into runtime parameters
533 - cleaned-up Large&Yeager04 routine which should eventually
534 replace exf_bulkformulae.F (changed names of S/R and CPP)
535 and merged various ALLOW_ATM_WIND options
536 only used with thsice pkg (in thsice_get_exf.F):
537 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
538 which are used when useStabilityFct_overIce=TRUE (= the default)
539 - change default values of ice & snow emissivity and scale downward LW
540 by ice & snow emissivity.
541 o pkg/thsice:
542 fix few little problems, in thsice_calc_thickn.F:
543 - growth vertically (and not laterally) if iceFrac == iceMaskMax
544 - melt only laterally if hIce < hThinIce (as the comments say)
545 and in thsice_extend.F:
546 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
547 - start to form ice as soon as the minimum ice-volume is reachable.
548 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
549 and cpl_aim+ocn
550 o pkg/kpp
551 - move computation of surface related input fields to KPP into a new
552 subroutine kpp_forcing_surf.F
553 - remove wrong (within bi,bj loops) EXCH calls.
554 - little cleaning (add argument myThid in last position, cvs header ...)
555 - for now, fix conservation problem by exchanging KPPviscAz (may not
556 be the best fix)
557 o pkg/seaice
558 - check for inconsistent evp parameter/cpp-flag combination
559 - remove leftover errIO flat for obsolete name list error handling
560 o OpenAD
561 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
562
563 checkpoint59a
564 o pkg/seaice: some parameter clarifications and a little bit of clean up
565 o pkg/thsice: rename run-time parameters:
566 himin -> hIceMin
567 himin0 -> hThinIce
568 hihig -> hThickIce
569 i0 -> i0swFrac
570 transCoef -> bMeltCoef
571 frac_energy -> fracMelting
572 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
573 with default values (for now) that do not change the results.
574 remove old version of thsice vars advection in pkg/seaice.
575 o in FFIELDS.h:
576 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
577 - make pLoad & sIceLoad always available (but still only used if
578 ATMOSPHERIC_LOADING is #define).
579 o pkg/kpp: replaced _KPP_RL with _RL
580 o bug fixes for vertical diffusivity computations when both KPP and
581 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
582 are no longer updating the vertical diffusivity array
583 (passed as argument) but are (re-) setting those arrays.
584 o pkg/seaice: fix bug in evp solver, while doing that
585 - change (improve?) discretization of stress computations for both
586 cgrid-lsr and evp solver
587 - add a new routine to compute strain rates
588 - the above changes lab_sea results
589 - add no slip conditions for evp solver (off by default), lsr-version
590 may follow
591 - fix exchange for shear at Z-points (does not change lab_sea)
592 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
593 (to force the user to pick a time step since there is not "safe" way
594 of choosing it)
595 - add principal stress diagnostics
596 - rearrange fields for evp a little to avoid having to call a: too many
597 exchanges and b: exchanges for stress trensor components which we do
598 not have.
599 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
600 of evp, complete rewrite for lsr case (latter is does not yet work
601 in all cases)
602 o pkg/kpp: add code to have mixing in shelf ice caverns
603 - add myThid to all kpp routines (long overdue)
604
605 checkpoint59
606 o pkg/exf:
607 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
608 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
609 - move exf header files from lower_case.h to UPPER_CASE.h ;
610 add missing cvs Header & Name
611 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
612 - add namelist param. selectStressGridPosition, exf_monFreq
613 - retire many _CLIM routines, and remove data.exf_clim
614 + params moved to data.exf
615 + climsst, climsss now handled by exf_set_gen, i.e.
616 climss?period=0 refers to constant field,
617 climss?period=-12 to monthly forcing
618 - split up namelists in data.exf
619 o pkg/seaice:
620 - remove seaice_exch and seaice_exch_uv
621 - remove superfluous exchange of theta
622 - add myThid to seaice_budget_ocean/ice
623 - add new interface for atmospheric wind forcing (C-grid only)
624 + new routine
625 + two new field (taux, tauy for stress over ice)
626 + removed one global field (DAIRN) for C-grid case only
627 o pkg/thsise
628 - 2nd set of modifs for thsice adjoint in conjunction with exf
629 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
630
631 checkpoint58y_post
632 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
633 vertical diffusivity, similar to that in MOM4; turned on using
634 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
635 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
636 o Added capability for 3D specification of background vertical diffusion
637 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
638 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
639 "data" file that contains the 3D vertical diffusivity coefficients.
640 o ice dynamics (pkg/seaice) with thsice thermodynamics:
641 - add code within pkg thsice to advect & diffuse sea-ice fields
642 similar to (and will replace) what has been added in seaice_advdiff.F,
643 but: - conserving Mass, Heat & Salt.
644 - better when using non-linear advection scheme (not yet fully tested)
645 - can also be used in atmospheric set-up (for now, only the diffusion).
646
647 checkpoint58x_post
648 o IO option for global-file compact format:
649 - add options when generating topology (utils/exch2/matlab-topology-generator)
650 - add I/O capability (pkg/mdsio).
651 - adapt utils/matlab/rdmds.m to read this format.
652 for now long-line format not yet supported by pkg/mdsio (& exch2).
653 o shelfice: add a few diagnostics
654
655 checkpoint58w_post
656 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
657 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
658 (and replace horiVertRatio in NH code).
659 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
660 and tutorial_plume_on_slope (sensitive to truncation)
661 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
662 directly to drive seaice model (C-grid only)
663 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
664 - reintroduce computation of wind from stress,
665 - compute tau (in exf_bulkformulae.F) from windstress averaged to
666 mass points to avoid tau = 0
667 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
668 o rdmnc.m: make it work with "global" files created with gluemnc
669 o rdmnc.m : some improvements in dealing with singleton dimension
670 (tested on all testreport mnc output files).
671 o genmake2: disable pkg/profiles if netcdf test fails.
672 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
673 o move call to cal_readparms up to make calendar parameters/variable available
674 to all packages
675
676 checkpoint58v_post
677 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
678 useDynP_inEos_Zc tested.
679 o pkg/exf: changes to properly interpolate/mask/scale initial fields
680 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
681 and portions thereof. See read_cs.txt for description and examples.
682 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
683 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
684 following the great-circle arc between those 2 points.
685 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
686 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
687 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
688 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
689 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
690 - still needs work (not working with some options ; efficiency to improve)
691 and serious testing.
692 - use this scheme for temperature & salinity in 2 advection test exp.:
693 advect_xy & advect_xz, respectively.
694
695 checkpoint58u_post
696 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
697 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
698 o testreport: add option "-skipdir" to skip some test.
699 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
700 momentum calculation.
701 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
702 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
703 remove checkpoint.F and the_correction_step.F (no longer used);
704 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
705 o add option (linFSConserveTr) to correct for tracer source/sink due to
706 Linear Free surface
707 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
708 o pkg/thsice: fix reading mnc-pickups
709
710 checkpoint58t_post
711 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
712 o pkg/mdsio:
713 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
714 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
715 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
716 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
717 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
718 either MDS_READ_FIELD or MDS_WRITE_FIELD )
719 - new S/R (to replace MDSWRITEMETA), which allows to write more
720 informations (variable names, time ...) to meta files.
721 - modify rdmds.m to give back the meta file content.
722 o pkg/diagnostics: change vertical interpolation to be safer, and more
723 flexible (define p-levels to interpolate to in data.diagnostics);
724 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
725 diagnostic pointer.
726 o pkg/seaice: more cleaning up of seaice_growth, added many comments
727 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
728 o fix multi-category seaice:
729 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
730 SEAICE_MULTICATEGORY
731 - fix short wave heat flux
732 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
733 and allow to use EVP solver. Change forward lab_sea: test both EVP
734 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
735 o Initial check-in of lab_sea adjoint
736 (very similar to natl_box_adjoint/code_seaice)
737 * used C-grid and EVP solver
738 * used KPP, GM/Redi
739 * uses inAdExact=.TRUE.
740 * gradient checks fail for both ADM and TLM
741 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
742 f.d. gradients actually seem more problematic than ADM, TLM gradients;
743 issue is related to forward mismatch between g77 an ifort
744 o pkg/seaice: overhaul of thermodynamics
745 - growth.F and groatb.F are replaced by new routine seaice_growth.F
746 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
747 - move a few global fields out of SEAICE.h into seaice_growth.F and
748 make them 2D (FICE/QNETO/ ...)
749 - remove FO (it is the same as QNETO)
750 - introduce a few local fields to avoid modifying external fields such
751 as atemp, etc.
752
753 checkpoint58s_post
754 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
755 changed exf_set_gen.F so that
756 genperiod=0 means input file is one time-constant field and
757 genperiod=-12 means input file contains 12 monthly means
758 o CG2D: use pre-computed solver main-diagonal (stored in common block);
759 this affects truncation error ; generate new output file for exp. which
760 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
761 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
762 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
763 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
764 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
765 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
766 o start implementation of deep-atmosphere and anelastic formulation
767 o verification: remove 2nd copy of input files and use script "prepare_run"
768 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
769 o mom_common/vecinv/fluxform: fix a few initialisation isssues
770 o profiles: fix for multithreaded case
771
772 o diagnostics: rename few diags:
773 s/'PRESSURE'/'RCENTER '/g
774 s/'TICE '/'oceFreez'/g
775 s/'TAUX '/'oceTAUX '/g
776 s/'TAUY '/'oceTAUY '/g
777 s/'SWFLUX '/'oceQsw '/g
778 s/DIFx/DFxE/g
779 s/DIFy/DFyE/g
780 and add few ocean-forcing diagnostics:
781 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
782 o modifications to pkg/seaice/growth.F and budget.F, which change results of
783 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
784 as actual snow thickness. It now refers everywhere to effective snow
785 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
786
787 checkpoint58r_post
788 o modifications to pkg/seaice/growth.F, which change results of
789 lab_sea experiment: fixes pertain to melting snow over open water, to
790 masking EVAP under sea ice, and to using the correct AREA variable for
791 computations of EVAP, PRECIP, HSNOW, and GHEFF
792 o add ability to read bathy, salt, and theta using MNC (off by def)
793 o add flooding algorithm and advection of HSNOW for pkg/seaice;
794 both are turned off by default and do no change any results
795 o seaice advection with pkg/thsice: a step toward the use of non-linear
796 advection scheme, but #ifdef or commented out for now (requires more EXCH).
797 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
798 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
799 in natl_box (affects results @ truncation level: update output.txt)
800 o multi-threading and IO:
801 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
802 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
803 (needed to work with SingleCpuIO): tested in all verif. exp.
804 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
805 affects the results (but none of the verification test uses this scheme).
806 o Adding some pkg/diagnostics capability to pkg/seaice
807 (will certainly be subject to changes)
808 o ctrl: adding new control variables:
809 lwflux, lwdown, evap, snowprecip, apressure, runoff
810
811 checkpoint58q_post
812 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
813 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
814 high_res_cube configuration by 4% on Columbia.
815 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
816 add (in global_with_exf/code) a version of EXF_INTERP_READ without
817 dynamical allocation (seems to work in multi-threaded).
818 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
819 single CPU io) so that TAF does not have to see EESUPPORT.h
820 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
821
822 checkpoint58p_post
823 o obcs: stop if obcs is used with useCDscheme = .true.
824 o shelfice:
825 - fix a sign error so that no slip at shelfice interface works
826 - remove stop for combination non-hydrostatic code and shelfice. That does
827 not mean, that the results are correct, but at least they are numerically
828 stable
829 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
830 o added adjoint exch routined for all exch*3d* routines
831 and updated flow directives
832
833 checkpoint58o_post
834 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
835 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
836 o change controling S/R for writing pickup file (new S/R do_write_pickup)
837 and clean-up reading/writing of pickup files.
838 o fix local version of read/write pickup (NH part) in rotating_tank/code
839 o simplify EXCH interface:
840 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
841 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
842 o added the regrid package
843 o shelfice:
844 - add a simple boundary layer scheme to reduce noise
845 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
846
847 checkpoint58n_post
848 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
849 local variable (not in common block).
850 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
851 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
852 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
853 to work with SingleCpuIO.
854 o add "_d 0" to real constant of pkg/cfc subroutines ;
855 update exp. cfc_exemple & tutorial_cfc_offline output files.
856 o multi-threading and IO:
857 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
858 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
859 - barrier before and after reading.
860 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
861 - avoid using MDS_WRITELOCAL for LAND pkg output.
862 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
863 common-block variables ; Allows multi-threading with master-thread IO.
864 o change default MAX_NO_THREADS from 32 to 4 ;
865 and stop cleanly when MAX_NO_THREADS is too small.
866 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
867
868 checkpoint58m_post
869 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
870 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
871 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
872 keep global_ocean.90x40x15 (for AD testing) with former secondary test
873 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
874 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
875 add MITgcm_tutorials (= code + all the tutorials)
876 o ecco, option to compute cost for total ssh (mean+anom)
877 o consistent with addition of ptracer and ssh in pkg/profiles
878 o profiles: adding ptracer and ssh
879 o testreport: change multi-test output-file name
880 (from output.txt.{name} to output.{name}.txt)
881 o profiles: now ok for mutli-tiles case
882 o seaice: add 4 parameters for different advection schemes for area,
883 (effective) seaice thickness, enthalphy, and snow height. Their default
884 is the standard parameter SEAICEadvScheme
885 o calc_gw:
886 - add cosFacU in zonal viscous flux (harmonic.visc.).
887 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
888 of tutorial_plume_on_slope.
889 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
890 o calc_gw: true flux-form, account for horizontal grid spacing.
891 update rotating_tank results, but not plume_on_slope (affected at
892 truncation level, 11 digits).
893
894 checkpoint58l_post
895 o calc_gw:
896 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
897 - remove side-drag for now (need to fix it); update plume_on_slope results.
898 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
899 o commit code to make SST/SSS weights spatially variable
900 (based on either variable in-situ or variable initial T/S weights)
901 o pkg/ecco:
902 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
903 now based on horizontally varying weights wthetaLev, wsaltLev
904 * cost_averagesflags now returns year indices in addition to day, month
905 * sflux balance is performed on annual basis
906 (sflxumm, sfluxmm2, bal_sfluxmm)
907 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
908 including separate counting and multipliers
909 o pkg/rbcs
910 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
911
912 checkpoint58k_post
913 o testreport:
914 - always build in dir. "build" (if not there, mkdir build instead of building
915 & running in input)
916 - run in dir run (if it exists), in build otherwise.
917 - call prepare_run (if input/prepare_run exists)
918 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
919 o pkg/exf modifications to interpolation and rotation routines for more
920 reasonable treatment of North Pole singularity: for tracers North Pole
921 value is set to northernmost zonal-mean value, for zonal velocity it is
922 set to zero, and for meridional velocity it is set to northernmost value.
923 o pkg/exf/exf_check_range.F
924 - add tile index to diagnostics and move stop statement to the very
925 end of the routine.
926 o pkg/diagnostics: (diagnostics_main_init.F)
927 define title of isomorphic variables according to the current config.
928 o pkg/thsice with pkg/seaice dynamics:
929 - fix domain of computation (interior only, required for exf) and do exchanges
930 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
931 o towards a standard way of dealing with multi-threading in MONITOR
932 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
933 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
934 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
935 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
936 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
937 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
938 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
939 o tracer advection:
940 - clean-up and simplify calc_common_factors.F
941 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
942 advection subroutine (but still not used within DST advection S/R)
943 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
944
945 checkpoint58j_post
946 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
947 from file (collects calls previously in FORWARD_STEP)
948 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
949 o adjoint store dir. adjusted accordingly
950 o genmake2
951 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
952
953 checkpoint58i_post
954 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
955 on wind stress (SEAICEstressFactor defaults to 1.)
956 o Total number of Timers is finite (<=40): comment out 2 non-essential one
957 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
958 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
959 on CS-grid: no longer loosing mass.
960 o exf & curvilinear-grid: no longer modify longitude xC & xG.
961 o pkg/ggl90: fix sloppy output and fix a bug
962 o pkg/seaice: added SEAICEuseEVPpickup parameter
963 - Set to false in order to start EVP solver with
964 non-EVP pickup files when using SEAICEuseEVP
965 - fix sign error in diffusion in seaice_calc_rhs
966
967 checkpoint58h_post
968 * Modifications for bottom topography control
969 o replace hFacC by _hFacC at various places
970 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
971 o add non-self-adjoint cg2d_nsa
972 o update autodiff support routines
973 o re-initialise hfac after ctrl_depth_ini
974 o works for 5x5 box, doesnt work for global_ocean.90x40x15
975 * Adding verification for 5x5 box (4-layer) bottom topography control
976
977 checkpoint58g_post
978 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
979 used for mean seasonal cycle, mean diurnal cycle); add an example
980 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
981 o pkg/ggl90:
982 - add parameter (minimum surface kinetic energy)
983 - fix bug (avoiding division by zero)
984 o couple pkg/thsice to pkg/seaice:
985 - modify advection in seaice to accomodate new scalar fields to be advected
986 - only muliDimAdection scheme work with seaice/thsice
987 - mapping of thsice-variables to seaice-variables, back and forth
988 - does not break the verification experiments, but does not give the
989 desired results either
990 o pkg/seaice
991 - make (default) second order advection a bit less confusing?
992
993 checkpoint58f_post
994 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
995 to pkg/seaice):
996 - new routines thsice_map_exf and thsice_get_exf provide the interface
997 - add an additional formal parameter to thsice_solve4temp
998 o pkg/exf:
999 - add new fields wspeed, snowprecip (to be able to couple to thsice)
1000 - correct Stefan-Boltzmann constant
1001 - new parameter for longwave surface emittance
1002 - separate some stuff from exf_bulkformulae into new routines
1003 exf_radiation, exf_wind
1004 - add new parameters and constants: longwave emissivity for ocean, ice
1005 and snow, evaporation parameters over ice
1006 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
1007 either wind from stress or stress from wind
1008 o pkg/thSIce:
1009 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
1010 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
1011 and THSICE_CALC_THICKN
1012 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
1013 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
1014 to make debugging easier.
1015 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
1016 o pkg/bulk_force:
1017 - clean-up comments and parameters ;
1018 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
1019 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
1020 generate new output for test-experiment: aim.5l_cs.thSI
1021 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
1022 testreport accordingly
1023
1024 checkpoint58e_post
1025 o SEAICE_CGRID adjoint done
1026 o R_STAR adjoint implemented.
1027 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
1028 * need to sort out init. of h0facc, etc.
1029 o Make pkg/profile fully independent of ecco,cost, etc. stuff
1030 to be able to use it in pure forward.
1031
1032 checkpoint58d_post
1033 o upgrade simple test-experiment to tutorial example:
1034 step.1: duplicate the experiment and (step.2) will remove the old copy.
1035 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
1036 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
1037 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
1038 tutorial_global_oce_biogeo <- copy of dic_example
1039 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
1040 tutorial_plume_on_slope <- copy of plume_on_slope
1041 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
1042 tutorial_global_oce_optim <- empty for now (David ?)
1043 tutorial_global_oce_in_p <- copy of global_ocean_pressure
1044 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
1045 o correct a sign problem in cost_scat.F
1046 o obcs and ptracers: fix boundary conditions for advections schemes
1047 with larger stencil
1048 o thsice adjoint: start
1049 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
1050 completeness
1051 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
1052 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
1053 o ptracers adjoint:
1054 * avoid extensive recomputatations
1055 * fix missing re-init. of gptr (missed by TAF)
1056 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
1057 me to turn off the excessive output to STDOUT that this package produces
1058 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
1059 and add those terms in Vector-Invariant formulation.
1060 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
1061 if the control period (xx_hfluxperiod etc) is 0
1062 o in profiles pkg, clean routines and fix details
1063 o in ecco pkg, reading ssh data:
1064 fix problem in case the model does not start at iter0=0
1065 o fix mnc-pickup/restart for ptracers
1066 o new package prifiles:
1067 code to compute profile-based cost by Gael Forget
1068 (modifs in ecco, ctrl, autodiff)
1069 o Benign bug fix in initialization (spotted by M. Mazloff) of
1070 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
1071
1072 checkpoint58c_post
1073 o adjoint: finish NLFS adjoint and provide reference output in
1074 verification/global_ocean.90x40x15/results_ad_nlfs
1075 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
1076 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
1077 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
1078 with SEAICE_CGRID defined.
1079 o move calendarDumps from "data" to "data.cal" and clean-up the code
1080 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
1081 o add useEXF & useCAL flags (for now, set in hard-coded way)
1082 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
1083 (were missing in NH mode, and wrong in quasihydrostatic mode).
1084 waiting for Chris updated version of calc_gw to add those CALLs.
1085 o fix bug in quasihydrostatic S/R ;
1086 add a test for this option: global_ocean.90x40x15.qshyd
1087 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
1088 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
1089 o add on/off flag useOffLine for package OFFLINE
1090 o seaice:
1091 - modify advection so that it works also on the C-grid
1092 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
1093 problem in multi-tile runs with C-grid
1094 - add flags for clipping ice velocities and/or masking solver forcing
1095 - fix drag (ocean on ice) formulation and a bug that caused noise in the
1096 C-grid solver
1097 - added a few comments to seaice_diffusion.F
1098 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
1099 are now exclusive)
1100 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
1101 required re-ordering the code a little:
1102 + make DAIRN global variable (defined in SEAICE)
1103 + move computation of the viscosities eta and zeta into a new separate
1104 routine (because I need to recompute them in seaice_ocean_stress.F)
1105
1106 checkpoint58b_post
1107 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
1108 update output.txt of exp. aim.5l_cs.thSI
1109 o various mnc cleanups and improvements:
1110 + shrink lookup tables by factor of ~4
1111 + better error reporting when running out of lookup space
1112 + able to handle longer path/file names (up to 500 chars)
1113 o adjoint:
1114 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
1115 - TBD: "hidden" mom_vecinv recomp. in dynamics
1116 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
1117 (allow to differentiate between forcing components using new integer flags:
1118 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
1119 and add new flag to put Dissipation tendency out of Adams-Bashforth.
1120 o ecco
1121 - enable trend removal from SSH anomaly obs.
1122 o adjoint
1123 - a fix for PmEpR when #undef EXACT_CONSERV
1124 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
1125 - try to fix "hidden" recomp. in forward_step for NLFS
1126 (NLFS seems broken sometimes after I checked it in)
1127 o seaice:
1128 - add c-grid version of the dynamic solver:
1129 + three new routines that are the c-grid substitute lsr, dynsolver
1130 and ostres
1131 + put a few fields that were local to dynsolver into global common
1132 blocks, so that I can move the computation of stresses etc into
1133 seaice_lsr (saves coding but may break the adjoint).
1134 - replace more hardwired parameters by runtime parameters
1135 - add ice masks that mask the rhs of the implicit solvers where there
1136 is no ice (commented out in seaice_dynsolver, because i am not sure
1137 if this works properly), eventually this should replace the clipping
1138 of ice velocities in seaice_dynsolver to +/-40cm/s.
1139 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
1140 include it only where its needed
1141 o move balancing of fluxes before the call of external_forcing_surf
1142 o seaice:
1143 - correct units of turning angles (now they are really in degrees)
1144 - move computation of GWATX/Y out of main routine into dynsolver
1145 - initialize GWATX/Y in seaice_init
1146 o Apply mask on Fresh-Water flux (needed for SSH forcing).
1147 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
1148 o seaice: add runtime flags for turning angles (default to zero)
1149 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
1150 and trend from exf forcing and ctrl control adjustments
1151 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
1152 (since checkpoint57x_post)
1153 o change the default rotation period to 86164.s = the Earth rotation
1154 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
1155 and based on a reference stratification. Tested within hs94.cs-32x32x5.
1156 o seaice advection: add code for choosing between the default (2nd order
1157 central differences) and multiDim advection schemes provided by
1158 pkg/generic_advdiff
1159 o seaice:
1160 - removed all references to SEAICE_GRID.h fields from
1161 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
1162 (cubed-sphere configuration will change a little)
1163 - grid computations in seaice_init are obsolete now.
1164 - cleaned up code a little so that is easier to read (hopefully).
1165 - added new (better?) discretizations of default advection and diffusion
1166 (turn on with SEAICEuseFluxForm)
1167 - replace 1 in 3d global fields by kSurface in growth.F
1168
1169 checkpoint58a_post
1170 o seaice:
1171 - bug fix in advect.F
1172 o shelfice:
1173 - separate shelfice load anomaly from pload (breaks with time
1174 dependent forcing), => introduce constant field shelficeLoadAnomaly.
1175 Its default is 0., but it may be computed more cleverly from (unknown)
1176 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
1177 done offline. A good approximation of the pressure load anomaly is
1178 necessary to avoid large initial adjustment processes underneath
1179 deep-reaching shelfice.
1180 - small fix in ISOMIP shelfice_thermodynamics
1181 - add more sophisticated thermodynamics of Hellmer (1989), this is
1182 now the default
1183 - give a few constants more intuitive names
1184 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
1185 if bulk formulae are used in long integration (especially EmPmR). Turn
1186 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
1187 if balancePrintMean, the imbalance that is substracted is printed to
1188 STDOUT.
1189 o fix bug (typo) in obcs_apply_eta.F
1190 o add a new package shelfice which enables us to model the circulation
1191 underneath shelf-ice with draughts of hundreds of meters.
1192 - works
1193 - to do: + include improved thermodynamics
1194 + check whether kSurfC (from model/inc/SURFACE.h) can be used
1195 instead of new field kTopC
1196 + can we use topoFile, Ro_surf and existing code in ini_depth.F
1197 instead of new field R_shelfIce and new code in ini_depth.F
1198 and ini_mask_etc.F?
1199 + adjust vertical mixing schemes?
1200 o seaice pkg:
1201 - add a cpp-flag to include a simple formula for a salinity dependent
1202 freezing point of sea water at the surface
1203 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
1204 meridional stresses are now different (and hopefully correct)
1205 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
1206 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
1207 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
1208 o pkg/diagnostics: add options and parameters for regional-statistics
1209 diagnostics ; define regions by reading a region-mask from a file
1210 (might add other options later)
1211 o pkg/bulk_force:
1212 - add option and parameters to use AIM surface-flux formulae.
1213 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
1214 others forcing fields (defined in PARM05, parameter file "data") are loaded
1215 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
1216 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
1217 - use the right EXCH call for uwind,vwind (to work on CS-grid).
1218 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
1219 and parameters (note: calcWindStress replaces .NOT.readwindstress).
1220 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
1221
1222 checkpoint58
1223 o add "--embed-source" option to genmake2 which, when the supporting
1224 tools can be compiled (as determined by genmake2) will turn on the
1225 embed_files package which then embeds the entire MITgcm source code
1226 (*.[fFhc] + Makefile) used for the build within the executable
1227 - requested by CNH but off by default
1228 - adds a paltry <9MB to the mitgcmuv executable in most cases
1229 - only writes the output when useEMBEDSRC in eedata is true
1230 o clean up 3-dim. relaxation codes:
1231 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
1232 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
1233 * Thanks to Tom Haine for testing!
1234
1235 checkpoint57z_post
1236 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
1237 affects output (@ truncation level) of exp. plume_on_slope ; updated.
1238 o fix the pickup behavior for obcs in combination with ptracers
1239 o fix a bug in ptracers_external_fields_load
1240 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
1241 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
1242 o transfered surface NH pressure to eta field (if exactConserv).
1243 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
1244 and update lab_sea output.txt file.
1245 o completing 3-dim. relaxation code: additional term
1246 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
1247 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
1248 * At compile time, in "EXF_OPTIONS.h" set
1249 #define ALLOW_CLIMTEMP_RELAXATION
1250 #define ALLOW_CLIMSALT_RELAXATION
1251 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
1252 tauThetaClimRelax3Dim = 15552000.0,
1253 tauSaltClimRelax3Dim = 15552000.0,
1254 * 3 cases:
1255 1) Use a constant-in-time 3-dim. field
1256 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
1257 3) Real-time relax. to time-evolving prescribed field
1258 o Adding Laplacian-type smoothness constraint on
1259 initial and boundary (forcing) controls (ic, bc)
1260 * enable at compile-time via
1261 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
1262 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1263 * Absolute scale somewhat unclear so far
1264 * no area weighting was included since no other cost term does so far
1265
1266 checkpoint57y_post
1267 First step for a NLFS adjoint
1268 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
1269 o new init. routines for calc_r_star, calc_surf_dr
1270 o still need to deal with ini_masks_etc
1271 o testreport seemed happy
1272 checkpoint57y_pre
1273
1274 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1275 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1276 o add new offset feature to offline pkg (plus minor cleanup)
1277 o cfc fixes for final year of integration
1278 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1279 be in GCHEM_OPTIONS).
1280
1281 checkpoint57x_post
1282 o fix testreport Pb in multiple test experiment.
1283 o cleanup our namelist syntax in verification:
1284 - make it more F95 standards compliant (some work still needed)
1285 - allows the vast majority of our tests to work with gfortran
1286 o Non-Hydrostatic:
1287 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1288 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1289 o Allow to apply AB on T,S rather than on AB(gT,gS):
1290 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1291 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1292 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1293 - need a "clever" read_pickup to restart from the other AB formulation
1294 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1295 o remove some unused variables (reduces number of compiler warnings)
1296 o adjoint
1297 * Disable useVariableViscosity for adjoint for time being
1298 (there are a number of extensive recomputations)
1299 * Initialize certain variables needed for adjoint
1300
1301 checkpoint57w_post
1302 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1303 fix the singleCpuIO RS version of MDSWRITEFIELD
1304 and add a WARNING if using globalFiles=T with multi-processors.
1305 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1306 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1307 o tracer advection scheme:
1308 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1309 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1310 was not very convenient).
1311 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
1312 (further tests needed for the implicit DST & Flux-Limiter schemes).
1313 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1314 and sRef for convenience, handy, when you want to initialize
1315 ptracers in a large domain with a constant non-zero value. Also,
1316 untangle ptracers_init.F a little.
1317
1318 checkpoint57v_post
1319 o change dome exp. to use variable viscosity in side-drag terms.
1320 o remove all the files from the cfc_offline test since they are now
1321 incorporated into tutorial_cfc_offline which has been producing
1322 identical results for a few days of testing
1323 o add new parameter: sideDragFactor to enable half-slip-side BC
1324 and change side-drag S/R to use viscosity from mom_calc_visc
1325 (can switch back by setting sideDragFactor=0.); affects results at
1326 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1327 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1328 o vorticity & strain are now computed without masking, to account for
1329 no-slip-side BC in variable viscosity calculation ; mask is applied
1330 anyway later on, before computing advection/coriolis terms.
1331 o modify exp4 to test new obcs support for reading from external files
1332 and for passive tracers
1333 o fix behavior of ptracers_monitor when monitor output is written to a
1334 netcdf-file; still not independent of monitor.F (writes in the same
1335 file).
1336 o change default value of tRef (put a uniform, meaningful value for ocean
1337 & atmos) and initialize sRef (was missing, as Martin mentioned).
1338 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
1339 to be proportional to enstrophy dissipation length. Thus,
1340 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1341 This is now consistent with Smagorinsky and with the manual.
1342
1343 checkpoint57u_post
1344 o OBCS and PTRACERS: add open boundary support for passive tracers
1345 - either use homogenous (pseudo) v.Neumann conditions or prescribe
1346 OB-values from file; this is not different from the way theta and salinity
1347 are treated
1348 - however, Orlanski-radiation conditions are not supported, and the model
1349 will stop if you use pTracers and Orlanski at the same time.
1350 - beefed up the rountine obcs_external_fields_load: now only those open
1351 boundary values are overwritten with values from files for which there
1352 are really files, otherwise the OB-fields remain untouched. This makes
1353 it possible to use different OBs at different ends of the domain (as
1354 with EXF)
1355 o reduce number of exch calls in shap_filt (s2).
1356 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1357 truncation level) 4/5 MLAdjust test results (11&12 digits match).
1358
1359 checkpoint57t_post
1360 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1361 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1362 same truncation, independent of the face number: affects affects several
1363 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1364 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1365 note that biharmonic viscosity + no-slip was not tested in any experiment.
1366 o fix bug in non-linear free-surf side-drag ; generate new output for
1367 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1368 o make mnc honor the writeBinaryPrec flag for most kinds of output
1369 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1370 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1371 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1372 o add brackets in multi-terms sum to get same truncation, independent of
1373 the face number (manage to get exactly same value of gU,gV at the cs-edge)
1374 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1375 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
1376 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1377 a maximum grid-scale Reynolds number. Also, changes all length calculations
1378 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1379 Suggested values of viscosity parameters found in mom_calc_visc.
1380 Many new viscosity diagnostics available.
1381
1382 checkpoint57s_post
1383 o Add clearing-house for viscosity calculations, mom_calc_visc and
1384 correct numerous bugs in LeithD and Smagorinsky discretizations.
1385 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1386 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1387 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1388 and with Strain-Tension viscous term calculation (mom_hdissip.F).
1389 The Strain-Tension form is now called with useStrainTensonVisc=.true.
1390 ViscAhStrain and viscAhTension are now retired.
1391 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1392 o In response to JMC's bug report, genmake2 now ignores any soft-links
1393 that it finds in the *current* directory when searching for files.
1394 Soft-links found in any other source directories will still work as
1395 they did before.
1396 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1397 a C routine to unlimit the stack size
1398 o mnc-ify pkg/aim snapshot vars
1399 o mnc-ify pkg/land as requested by Daniel
1400 o various changes to mnc including:
1401 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1402 - output can now be grouped so that all files within a group
1403 change the ITER portion of their names in lock-step together
1404 - can now read ("global") PER-FACE (in addition to PER-TILE) files
1405 and works with both EXCH1 and EXCH2 (but needs more testing)
1406 - writing works for all verification test cases w/ g77 on Linux
1407
1408 checkpoint57r_post
1409 o make MNC variable initialization happen earlier
1410 o add diagnostics for (almost) each term of the momentum Eq.
1411 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1412 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1413 o remove MINIMAL_TAVE_OUTPUT option ;
1414 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1415 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1416 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1417 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1418 o add time-dependent SST, SSS control
1419 o cost terms in ecco/ modularized (new cost_generic.F)
1420 o cost_averages routines are modularized (new cost_averagesgeneric.F)
1421 o new infrastructure for seaice model vs. obs misfits in seaice/
1422 * driver from the_main_loop.F is seaice_cost_driver.F
1423 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1424 * gradient check in Exp. 6a of natl_box_adjoint/
1425 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1426 (see README file)
1427
1428 checkpoint57q_post
1429 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1430 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1431 - bug was reported by Jean-Michel and Ian Fenty
1432 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1433 update exp. cpl_aim+ocn output.
1434 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1435 Needed for high-res. runs with large global files
1436 to be able to limit tapelev size
1437 o Changed some tests for adjoint:
1438 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1439 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1440 * global_ocean.90x40x15/ back to default 3-level checkpointing
1441 o Modifications to enable scripted COMMON to MODULE conversion
1442 * verification/OpenAD/code/ has necessary scripts and description;
1443 * converts, compiles and runs successfully;
1444
1445 checkpoint57p_post
1446 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1447 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1448 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1449 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1450 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1451 (was already the case for dissipation with mom_vecinv,
1452 and also the case for grad.PhiHyd when staggered-timeStep)
1453 This will allow to put dissipation out-off the AB time-stepping.
1454 Unfortunately, affects truncation error. Update output of exp. that "fails"
1455 (cg2d matching number) and leave the others for later: front_relax(10),
1456 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1457 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1458
1459 checkpoint57o_post
1460 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1461 (2) its ready to be documented during the 20050801 DocFest
1462 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1463 for ideal_2D_oce and lab_sea on linux_ia32_g77
1464 o set to #undef CTRL_SET_OLD_MAXCVARS_30
1465 in global1x1_tot/code_seaice_adj to access indices 32, 33
1466 (worth another tag)
1467
1468 checkpoint57n_post
1469 o adding precip control xx_precip 32
1470 o adding swflux control xx_swflux 33
1471 o Replacing 10 forcing penalty cost routines by 1 generic.
1472 o Implementing partitioning in time-mean and variable adjustment
1473 for atmos. state.
1474 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1475 o in natl_box_adjoint:
1476 * updated exp 1 to 10
1477 (but does not have time-mean vs. variable split results yet)
1478 o updated global1x1/*_seaice_adj/
1479 to incorporate latest changes
1480 o enable useSingleCpuIO for mdsio vector routines
1481 (applies in particular to tapelev I/O)
1482 o removed inefficient K-loop in all active_file*control*.F
1483
1484 checkpoint57m_post
1485 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
1486 and advect_cs (use EXCH-2 and standard cs-32 grid files).
1487 o pkg/exch2: filling of face-corner halo regions is optional
1488 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
1489
1490 checkpoint57l_post
1491 tag before updating tutorials (pre-release-2)
1492 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
1493 for output and interpolation of input fields onto model grid)
1494 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
1495 Affects results of exp. rotating_tank ; update output.txt.
1496 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
1497 and taking the square quantity and/or using a fraction-weight field.
1498 o fix aim_diagnostics_init.F mate numbers.
1499 o add mnc output capability to diagnostics/diagstat and update
1500 our cvsignore files for the ACSII output generated
1501
1502 checkpoint57k_post
1503 o lab_sea now uses diagnostics package and provides a suite of
1504 new EXF diagnostics output.
1505
1506 checkpoint57j_post
1507 o exf
1508 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
1509 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
1510 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
1511 * extended diagnostics output
1512 - now includes all EXF variables
1513 - hs, hl moved to common block
1514 - separate S/R for diagnostics, called after ctrl vector is added
1515 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
1516 - EXFqnet contains true Qnet (i.e. includes qsw)
1517 * updated verif. lab_sea, global_with_exf
1518 * Rearranging hflux (exf_mapfields -> exf_getforcing)
1519 to ensure that diagnostics sees a true EXFqnet
1520 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
1521 o diagnostics pkg: change pointers so that 1 diagnostic can be used
1522 several times with different frequencies.
1523 o mnc-ify the thsice package as requested by Daniel Enderton
1524 - the monitor--MNC output needs work
1525 - many attributes need to be added (most are currently blank)
1526 o mnc-ify theaim_v23 package as requested by Daniel Enderton
1527 - many attributes need to be added (most are currently blank)
1528 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
1529 o add Sadourny like discretization to the 4th.O vorticity advection scheme
1530 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
1531 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
1532 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
1533 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
1534 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
1535
1536 checkpoint57i_post
1537 o Diagnostics package was changed: diagnostic allocation is now deactivated
1538 by setting an empty file name in the namelist (used to be by setting 0 frequency)
1539 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
1540 add 1rst Order upwind vertical Shear.
1541 o add a quick fix for A/B checkpointing in OFFLINE mode
1542 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
1543 end-run around the C/Fortran linking horror in eesup/src/timers.F
1544 o added pkg/runclock: allows user to terminate run based on wall clock
1545 o added non-hydrostatic scaling parameter: nh_am2
1546 o pkg/my82: futile attempt to make results compiler-independent by adding
1547 some "_d 0", etc. no effect.
1548 o for mnc output, fill the 'T' coordinate var with myTime and create a
1549 separate 'iter' variable for iteration count
1550 o pkg/diagnostics:
1551 add new capability: output of Global/Regional & per-level statistics ;
1552 tested against monitor output (including land & thSIce) on various exp.
1553 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
1554
1555 checkpoint57h_done
1556 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
1557 data.diagnostics, data.gchem, data.ptracers) is done.
1558
1559 o pkg/diagnostics: prepare for Global/Regional statistics.
1560 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
1561 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
1562 and rename it: DIFFERENT_MULTIPLE
1563
1564 checkpoint57h_post
1565 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
1566 o pkg/diagnostics: change output frequency, now in seconds (instead
1567 of Nb of iterations). This requires to change data.diagnostics.
1568 checkpoint57h_pre
1569
1570 o in mnc, let the user create the output dir if both mnc_outdir_date
1571 and mnc_outdir_num are false
1572 o add fflags() to pkg/diagnostics which allows one to specify, on a
1573 per-file basis, the file precision [default behavior is unchanged]
1574 o added diagnostics to pkg/kpp, including computation of mixed layer
1575 depth based on a temperature/density criterion
1576 o updated verification/natl_box to test the new pkg/kpp diagnostics
1577 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
1578 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
1579 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
1580 not mnc -- this mistake was found by JMC and is now corrected
1581
1582 checkpoint57g_post
1583 o add Adams-Bashforth 3rd Order time stepping:
1584 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
1585 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
1586 checkpoint57g_pre
1587
1588 o make lambda[Theta,Salt]ClimRelax spatially varying
1589 (default remains spatially uniform constant based on tau)
1590 o added new control variables
1591 * init. uVel, vVel, etanN
1592 * lambda[Theta,Salt]ClimRelax
1593 o separate masks used for ctrl_pack/unpack 'from write_grid' output
1594 (suggested by G. Forget)
1595
1596 checkpoint57f_post
1597 o add parameter "baseTime" = model base time = time at iteration zero
1598 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
1599 account for baseTime shift
1600 o move Coriolis arrays from PARAMS.h to GRID.h
1601 checkpoint57f_pre
1602
1603 o mnc-ifying the seaice package
1604 o introduced an alternative length scale calculation for use in the limiting
1605 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
1606 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
1607 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
1608 as well as grad(vort3). Made it compatible with both approximate form
1609 for the cubed sphere and full form of these gradients. Added flag
1610 useFullLeith to select between approximate and full form.
1611 o add "d0" in getcon.F to reduce differences between compilers/platforms
1612 update output.txt of exp. fizhi-gridalt-hs
1613 o change port_rand funtion to allow to set the seed.
1614 o fix obscure MNC bug involving conversion between reals and integers
1615 - it caused no problems with certain (eg. gcc, ifc) compilers but the
1616 new version is now more standards-compliant
1617 o adjoint-related modifications
1618 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
1619 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
1620 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
1621
1622 checkpoint57e_post
1623 o Adding eddy stress controls a la Ferreira et al.
1624 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
1625
1626 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
1627 update output.txt of exp. fizhi-gridalt-hs
1628 o add more "Z" dimensions and associated coordinate vars to MNC
1629 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
1630 o parameter calendarDumps: when set, approximate months (30-31 days) and years
1631 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
1632 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
1633 months and years. Requires pkg/cal.
1634 o diagnostics: add pickup functionality
1635 - off by default for backwards compatibility
1636 - current version only uses MDSIO -- MNC will be added
1637 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
1638 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
1639
1640 checkpoint57d_post
1641 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
1642 o modify verification/ideal_2D_oce so that it tests the creation of mnc
1643 output from the diagnostics package
1644 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
1645 o make genmake2 more portable by using ".$FS" instead of ".f" for more
1646 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
1647 o add coordinate variables to the MNC output from the diagnostics package
1648 o change MNC-flags default value: true when useMNC=TRUE
1649 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
1650 the ability (off by default) to read the grid information using MNC
1651 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
1652 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
1653 o do snap-shot diagnostics at the middle of the time-interval (instead of
1654 at the end).
1655 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
1656 new test for AIM with thSIce + slab-ocean
1657 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
1658 o move state variable diagnostics to the beginning of the time step ;
1659 (note: still needs some work specially for snap-shot diagnostics)
1660 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
1661
1662 checkpoint57c_post
1663 o Change testing option (-ieee) to get closer agreement between g77 & ifort
1664 o generate new output.txt files on faulks with g77 & the new -ieee option
1665 checkpoint57c_pre
1666
1667 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
1668 update output.txt of exp. global_ocean.90x40x15
1669 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
1670 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
1671 o add saltFlux(+File) forcing capability with periodicExternalForcing
1672 o allow to use pkg diagnostics for GM-Redi & ThSIce output
1673 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
1674 o improvements for the MNC output from DIAGNOSTICS:
1675 - correct handling of the unlimitied dimension
1676 - all dims now have associated coordinate variables
1677 - variables located at U, V, and Corner ("Z") points are now written
1678 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
1679 *all* data points are output
1680 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
1681 o added pkg/seaice/seaice_monitor.F
1682 o mdsio_readfield.F can now read files visible only to master MPI process.
1683 o pkg/seaice: some test code for ice-modified ocean stress
1684 o exf_getffields interpolation defaults to bilinear for all scalar forcing
1685 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
1686 spurious negative numbers for precipitation and humidity. Will cause
1687 some small numerical differences for integrations using pkg/exf/exf_interp.F.
1688 o pkg/ctrl/
1689 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
1690 May be enabled via doPackDiag
1691 * introduce z-scaling of
1692 + gradient (doZscalePack) and
1693 + control (doZscaleUnpack)
1694 o pkg/mdsio/
1695 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
1696 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
1697
1698 checkpoint57b_post
1699 o simplify options in diagnostics_fill arguments (remove weird combinations)
1700 o fix MNC coordinate variables so that they now contain per-face index
1701 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
1702 general, EXCH2 grids are only aligned to a "local" coordinate system
1703 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
1704 o Implement instantaneous output within pkg diagnostics:
1705 setting a negative frequency in data.diagnostics produces
1706 "snap-shot" output (as opposed to time-average if freq > 0)
1707 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
1708 NOTE: change ptracer diagnostics name: use 2 characters to work with
1709 more than 9 tracers. Add also diagnostics of advect & diffus flux.
1710 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
1711 becomes the coordinate variable for the 'T' dimension
1712 o add CF-style coordinate variables to MNC
1713 - just a first cut: numbers are meaningless on the cubesphere and
1714 missing along the T axis but otherwise it works!
1715 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
1716 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
1717 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
1718 this is based directly on what the model compute, so that the content of
1719 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
1720 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
1721 o clean up build options files for SunOS, in particular
1722 - remove -traditional from xmakedepend
1723 - change -xarch=v9 to -xarch=native for f77
1724 - restore use of make (not gmake)
1725 - add CC=gcc if using g77
1726 o changes per discussion of AM, JMC, & EH3 today:
1727 - move redundant "grid" variables out of "state" -- in preparation of
1728 creating proper CF-style coordinate variables and in recognition
1729 that any/all grid variables can be easily copied (eg. w/NCO) from
1730 the grid files into any of the other NetCDF files
1731 - *always* output grid variables with MDSIO (this will eventually be
1732 changed)
1733 - output MNC grid file if useMNC is true
1734 o every instance of _END_MASTER() has been found and replaced with
1735 _END_MASTER( myThid ) in order to satisfy certain picky Sun
1736 preprocessors
1737 o re-arrange diagnostics pkg initialisation:
1738 - allow each package to extend the available diagnostics list
1739 - add some checking and fix small problems (multi-threaded, ...)
1740 - new S/R diagnostics_fill (replace fill_diagnostics):
1741 look through the short list of active diag. (instead of the long list)
1742 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
1743
1744 checkpoint57a_post
1745 o this set of changes restores TAMC compatibility
1746 tested for global_ocean.90x40x15 adjoint on trough
1747 (what a pain)
1748
1749 checkpoint57a_pre
1750 o some modifs in tools/build_options for sunos
1751 o call ctrl_pack for ctrl at end for optimcycle=0
1752
1753 checkpoint57
1754 o add horizontal bi-harmonic viscosity for vertical velocity
1755 - new parameter viscA4W (defaults to viscA4)
1756 - affects only non-hydrostatic code
1757 - to be done: no-slip lateral boundary conditions
1758 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
1759 o implement Implicit Vertical advection for pTracers
1760 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
1761 (implemented also for implicit vertical diffusion & advection)
1762 o OBCS: extend application of tracer open boundary conditions
1763 to a strip beyond the boundary of width Olx/Oly
1764 o add call monitor to TAF set of required calls (flow directives)
1765 and include in natl_box_adjoint
1766 o untangle a few ifdefs related to cost, ctrl, autodiff
1767 untangel a few ALLOW_ECCO_OPTIMIZATION
1768 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
1769 (theta2, salt2 in ecco_cost_weights)
1770
1771 checkpoint56c_post
1772 o OBCS as control variables
1773 - update ctrl_ad_diff.list, obcs_ad_diff.list
1774 - remove balance of obcs controls from default
1775 - fix index bug nobcs in ctrl_init
1776 - fix dummy fields filen in ctrl_pack
1777 - add dummy weights for obcs
1778 o lsopt: comment out fort.94 output
1779 o optim:
1780 - remove unnecessary header files
1781 - adjusted namelists
1782 - add xerbla.F to Makefile
1783 o exf:
1784 - multiple modifications of exf_check_range
1785 - unit change in exf_init_runoff from [m/year] to [m/s]
1786 o mdsio:
1787 - i/o-vector change debugLevel from debLevA to debLevB
1788
1789 checkpoint56b_post
1790 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
1791 is called from DO_THE_MODEL_IO
1792 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
1793 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
1794 - clean up PTRACERS_WRITE_TIMEAVE a little
1795 o add another verification experiment that tests both the cfc-pkg and
1796 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
1797 reactive tendencies treated inline with regular timestepping
1798 o testreport previously did a lousy job of comparing small numbers, so
1799 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
1800 implemented in the little c-progam tmp_cmpnum.c which is embedded in
1801 testreport.
1802 o ptracers_monitor: bug fix for MPI
1803
1804 checkpoint56a_post
1805 o GCHEM: finish reorganizating the package
1806 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
1807 (introduces another 3D-array for each passive tracer, but only if
1808 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
1809 gchemTendency is not needed because the timestep is done separately)
1810 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
1811 - GCHEM is now---more or less cleanly---separate from PTRACERS
1812 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
1813 so clear to me how that should be done in a general way.
1814 o CFC: improve formatting of output in CFC_ATMOS
1815 o PTRACERS:
1816 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
1817 that ALL experiments with ptracers enable can be checked. This makes
1818 GCHEM_MONITOR obsolete.
1819 - include a runtime parameter PTRACERS_monitorFreq that defaults to
1820 monitorFreq
1821 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
1822 o add PTRACERS (PTR0[1-5]) to testreport output
1823 o exf_check_range:
1824 * default changed to .TRUE.
1825 * will check values for niter0 if debLevA, every timestep if debLevB
1826 * STOP in exf_check_range if 'out of range'
1827 * range chosen generous to allow for potential extema
1828 TBD: a version with stricter range
1829 permitted range would be runtime parameters
1830 o GMredi:
1831 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
1832 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
1833 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
1834 o GCHEM:
1835 - move call to GCHEM_FORCING_SEP, so that it is now called before
1836 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
1837 - introduced a useGCHEM runtime flag and applied it everywhere.
1838 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
1839 this flag is now only visible within GCHEM-pkg routines.
1840 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
1841 be replaced by a 3D array that is computed before thermodynamics; for
1842 this, the tracer ID iTracer had to be included into the parameter list
1843 of ptracers_forcing
1844 - set up forward_step to call gchem_forcing, that will replace
1845 gchem_forcing_int in ptracers_forcing
1846 - cleaning up
1847 o small cleaning of exch2: remove files that are also in eesupp/src
1848
1849 checkpoint56
1850 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
1851 o mnc: cleanup "full" files--fixes out-of-memory problem
1852 o ECCO-GODAE
1853 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
1854 * fully merged and updated from SIO code
1855 windstress sign change affects
1856 - exf_inscal_[u/v]stress
1857 - sign of xx_tau[u/v] adjustments
1858 - signs in cost_scat
1859 * ctrl_get_gen: avoid update of tau[u/v] for first few days
1860 * natl_box_adjoint updated and compressed
1861 * 2-level checkpoint switch added
1862 (tested in EXP. 1 of natl_box_adjoint)
1863 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
1864 o SVD
1865 * first complete, non-hacked version for SVD calculations
1866 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
1867 performed via direct access files admtlm_vector.it????
1868 (via ctrl_[un]pack)
1869 * optimcycle is used for ARPACK iteration counter
1870 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
1871 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
1872 and add linear transforms where necessary
1873 * controls are initial/final SST, SSS (can be extended; need to check
1874 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
1875 o mdsio: filename info to both stderr, stdout
1876 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
1877 from sign change
1878
1879 checkpoint55j_post
1880 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
1881 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1882 o add consistent build directories and .cvsignore files to verification
1883 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
1884 o make all subroutines 30 or less characters in length for certain older
1885 compilers to work (a thorough search only turns up two routines in
1886 pkg/ptracers)
1887 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
1888 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1889
1890 checkpoint55i_post
1891 o change arrays for total vertical diffusivity (2.D if explicit,
1892 3.D if implicit) ; each ptracer uses its own background value.
1893 o added mnc/NetCDF output capability to ocn_compon_interf
1894 - added bits to verification/cpl_aim+ocn so that it can run on
1895 ITRDA and other clusters without the mpirun "-wd" option
1896 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
1897 configuration
1898 o give MNC the ability to create additional files rather than
1899 exceeding a specified file size limit "MNC_MAX_FILESIZE"
1900 - the default is just less than 2GB which is a practical limit
1901 on many systems
1902 o Compute the non-local term using either KPP vertical diffusivity (=default)
1903 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
1904
1905 checkpoint55h_post
1906 o add verification test "vermix"
1907 o remove all the *_ioinc flags and replace with the single global
1908 outputTypesInclusive flag
1909 o allow to set a vertical profile of vertical diffusivity for T & S
1910 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
1911 o useMNC moved from data.mnc to data.pkg
1912
1913 checkpoint55g_post
1914 o Renaming carbon AD experiments to comply with testreport conventions
1915 o Updating adjoint of Held-Suarez hs94.1x64x5
1916 o Fixing directives for non-ECCO forward_step, after ECCO directives
1917 have been fixed to avoid recomp. of do_oceanic_phys
1918 Works well for global_ocean.90x40x15,
1919 but recomp. issue remains for carbon
1920 o Updating adjoint output for natl_box_adjoint after
1921 pkg/ecco has been modified (see taga c55d_post)
1922
1923 checkpoint55f_post
1924 o rename to timeave_init_fixed
1925
1926 checkpoint55e_post
1927 o some delicate re-shuffle of store directives to avoid one
1928 extra call of do_oceanic_physics
1929 affects ecco_the_main_loop.F, do_oceanic_physics.F
1930 checkpoint_lev1_directives.h
1931 o NB: this may break global_ocean adjoint temporarily,
1932 but it is clear how to fix it. Will do later, need this now.
1933
1934 checkpoint55d_post
1935 o ECCO specific cost function terms (up-to-date with 1x1 runs)
1936 o ecco_cost_weights is modified to 1x1 runs
1937 o modifs to allow observations to be read in as
1938 single file or yearly files
1939 o enable to read exf forcing fields as either
1940 single file or yearly files (flag useExfYearlyFields)
1941 checkpoint55d_pre
1942
1943 o switch between 2-level and 3-level checkpointing
1944 o add ability of MNC to write local and "partial" (eg. 2D slices where
1945 the full 3D field is never actually stored) arrays to NetCDF files
1946 with the correct (that is, the complete multi-dimensional) set of
1947 array indicies
1948 - used in mom_vecinv() to write the diagFreq output
1949 - tested (demonstrated) in verification/aim.5l_cs
1950 o further mnc-ification
1951 - add verification/lab_sea to the list with mnc setups
1952 - fix undefined mnc v-names in cd_code
1953 - add kpp to mnc output (both snapshot and timeave)
1954 o non-hydrostatic code
1955 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
1956 in calc_gw.F
1957 - defaults to viscAh
1958 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
1959 friction or Leith) in non-hydrostatic mode, as long as there is
1960 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
1961 o pkg/cost
1962 extend simple cost functions to treat time mean quantities
1963 (T,U,V) via cost_accumulate_state from cost_tile
1964 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
1965 be 2 times larger than the minimum size the advection scheme requires.
1966 now get a perfect conservation of salt in advect_cs test-exp (updated)
1967 o GGL90 (Gaspar's TKE mixed layer)
1968 - add horizontal diffusion of TKE, requires exchanges in
1969 do_fields_blocking_exchanges, horizontal diffusivity is zero by
1970 default. In OPA there is no horizontal diffusion of TKE but the
1971 mixing coefficients are computed from a horizontal average of TKE of
1972 6 points or so. I think that diffusion has a little more physical
1973 justification.
1974 - clean up ggl90_calc in the hope of reducing memory usage (this hope
1975 was in vain)
1976 - mask tke-variable in ggl90_init
1977 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
1978 o fix biharmonic diffusion on CS-grid.
1979 o more obcs stuff
1980 - added obcs_external_fields_load as an alternative to the EXF-pkg option
1981 for reading boundary values. This routine is called from
1982 obcs_prescribe_read
1983 - updated obcs_check
1984 - changed sponge layer relaxation parameter units for days to seconds
1985 - turned off sponge layer by default
1986 - changed argument list of OBCS_CALC to myTime+deltaTclock
1987 - fixed about 35 bugs in obcs_external_fields_load
1988
1989 checkpoint55c_post
1990 o obcs stuff
1991 - new runtime flags useOBCSprescribe, useOBCSbalance
1992 - re-arranged obcs_calc
1993 - moved exf_getobcs to obcs_prescibe_read
1994 obcs_prescibe_read is called after ORLANSKI stuff
1995 and independent of it (executable can contain all).
1996 - updated obcs_check
1997 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
1998 These may be necessary only if tangential velocities are
1999 prescribed at OB, not sure, needs testing.
2000 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
2001 which simplifies the calls and passes the ifc check-bounds test
2002
2003 checkpoint55b_post
2004 o add a 2D scalar, Z location, exchange_2 routine.
2005 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
2006 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
2007 affects advect_cs results (for the wrong reason): update output.txt
2008 o use a more standard discretization for biharmonic viscosity ;
2009 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
2010 affects results of dome set-up: update output.txt
2011 o fix gad_advection.F (CubedSphere part), back to version 1.23
2012 o fix bug in mom_vi_del2uv.F (CubedSphere part).
2013
2014 checkpoint55a_post
2015 o merged code to
2016 * prescribe/read time-dependent open boundaries
2017 (works in conjunction with exf, cal)
2018 * sponge layer code for open boundaries
2019 * each boundary N/S/E/W now has its own CPP option
2020 (healthy for the adjoint)
2021
2022 checkpoint55
2023 o up-to-date adjoint of previous breaks
2024 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
2025 - global_ocean_ebm: adjoint still needs fix (TLM ok)
2026 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
2027 - carbon: * remove tr1-related adjoint verification
2028 * add ptracer as control variable
2029 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
2030 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
2031
2032 checkpoint54f_post
2033 o in verification/carbin/ remove experiment related to
2034 ALLOW_PASSIVE_TRACER (array tr1 etc)
2035 code_ad/ input_ad/ results_ad
2036
2037 o add two new packages
2038 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
2039 + subject to optimization (memory)
2040 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
2041 + subject to reordering (many GOTOs in the original code)
2042 + so far opps is called for every (i,j) point, and then operates in
2043 the vertical; one may want to reorder the scheme in order operate in
2044 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
2045 fields)
2046 o overhaul of IO so that we now have flags for MDSIO and/or MNC
2047 - all verification tests compile and run with linux_ia32_g77
2048 - defaults are compatible with current input files--nothing
2049 should change if you were not previously using MNC
2050 - MNC output has been added in numerous places (eg. timeave)
2051 but there are still a few writes not yet do-able with MNC
2052 (this is in progress)
2053 - flags now allow for either/or/both use of MDSIO and MNC and
2054 documentation will soon follow
2055 - numerous small formatting cleanups for ProTeX
2056 o add version info (via BUILD_INFO.h) to MNC and stdout
2057
2058 checkpoint54e_post
2059 o add two new packages
2060 - pp81 (Packanowski and Philander, 1981), Richardson number and
2061 stratification dependent mixing
2062 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2063 - these scheme operate in a similar manner as KPP (without ghat, of
2064 course), however there is only one diffusivity that is used for both
2065 temperature and salinity (and passive tracers)รง
2066 o add offline package
2067 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2068 provided by Stephanie Dutkiewicz
2069 o genmake2: add ability to search for C compilers and cleanup test output
2070 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
2071
2072 checkpoint54d_post
2073 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
2074 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
2075 leading to additional shift by 5 days each year of integration
2076 (i.e. leading to considerable offset over the years)
2077 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
2078 o start with no AB and no initial filtering (staggerTimeStep):
2079 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
2080 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
2081 (external loading & cpl import/export stay in forward_step.F)
2082 o update coupling interface to work with new staggerTimeStep
2083 o change MDSIO ptracers_pickup.
2084 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
2085 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
2086 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
2087
2088 checkpoint54c_post
2089 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
2090 this affects (truncation error) output.txt of test-exp:
2091 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
2092 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
2093 o change Qnet to always be the net heat flux, (+upward).
2094 affects (truncation error) output of natl_box exp.: updated
2095 o define the max number of passive tracers in PTRACERS_SIZE.h
2096 o start to test mnc routinely in exp0
2097 o add sea-ice loading (sIceLoad) as a new forcing field.
2098
2099 checkpoint54b_post
2100 o add testreport "-j JOBS" option for parallel builds (tested and pretty
2101 impressive on Altix and Opteron systems)
2102 o diagnostics can now write NetCDF files through the mnc package
2103 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
2104 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
2105 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
2106 affects (truncation error) output of lab_sea & natl_box exp.: updated
2107 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
2108
2109 checkpoint54a_post
2110 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
2111 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
2112 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
2113 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
2114 + internal_wave (shift in writing cg2d_ini_res)
2115 checkpoint54a_pre
2116
2117 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
2118 - modified verification/lab_sea and natl_box_adjoint accordingly
2119
2120 checkpoint54
2121 checkpoint53g_post
2122 o prepare splitting of thermodynamics: store convect.counter in common block
2123 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
2124 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
2125 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
2126 o new parameter "nShapS": allow to treat differently S from T (nShapT)
2127 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
2128 o restore adjointability
2129
2130 checkpoint53f_post
2131 o modifications that affect AIM experiment results (update output.txt):
2132 - no advection of S at top interface Nr (pkg/generic_advdiff)
2133 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
2134 o AIM pkg:
2135 - include stability function into surf.Flux derivative relative to Tsurf
2136 - calculate clear-sky radiation & surface temp. change (for diagnostics)
2137
2138 checkpoint53e_post
2139 o merged cylindrical coord configuration
2140 o added rotating_tank experiment
2141 checkpoint53e_pre
2142
2143 checkpoint53d_post
2144 o faulks upgraded: re-generate output.txt that have changed:
2145 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
2146 o Added Bryan and Lewis, 1979, vertical diffusivity profile
2147 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
2148 o added Sadourny discretization of Coriolis
2149 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
2150 - re-enabled use of omega3 (useAbsVorticity)
2151 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
2152 vector-invariant equations
2153 - note: does *NOT* yet use same variable visc. for no-slip BC's.
2154 o recoded the lateral boundary conditions for non-hydrostatic w, this time
2155 hopefully without new bugs
2156 - still to do: biharmonic friction for non-hydrostatic w
2157 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
2158 o regenerated output for global_ocean_ebm (using -ieee)
2159 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
2160 of mom_common/
2161 - simple re-arrangement of instructions within computing loop
2162 checkpoint53d_pre
2163
2164 checkpoint53c_post
2165 o new version of coupler for AIM+thSIce and Ocean models
2166 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
2167 - land: change Evaporation of snow
2168 - aim with thSIce: fix bug in snow-precip.
2169 o changes to calc_gw.F
2170 - bug fix for w^2 term near the bottom boundary
2171 - (hopefully) improve the lateral slip boundary condtions for use with
2172 partial/looped cells
2173 - because the bug fix changes two verification experiments anyway (exp5
2174 and plume on slope), change the lateral boundary condition from half slip
2175 to the value of no_slip_sides
2176 o ebm package wasnt quite up to the parallel task. Fixed that.
2177 o Adjoint of EBM package + verification
2178 * TLM OK
2179 * ADM not sufficient accuracy yet (needs further testing)
2180
2181 checkpoint53b_post
2182 o Commiting new energy balance model to repository
2183 * package is pkg/ebm
2184 * verif. is verification/global_ocean_ebm
2185 * references are in ebm_driver.F
2186 C * X. Wang, P. Stone and J. Marotzke, 1999:
2187 C Global thermohaline circulation. Part I:
2188 C Sensitivity to atmospheric moisture transport.
2189 C J. Climate 12(1), 71-82
2190 C * X. Wang, P. Stone and J. Marotzke, 1999:
2191 C Global thermohaline circulation. Part II:
2192 C Sensitivity with interactive transport.
2193 C J. Climate 12(1), 83-91
2194 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
2195 C Destabilization of the thermohaline circulation
2196 C by atmospheric eddy transports.
2197 C J. Climate 7(12), 1870-1882
2198 o Will need long integration testing.
2199 checkpoint53b_pre
2200
2201 o created pkg/mom_common in preparation for variable viscosity code
2202 o renamed and split ini_mnc_io
2203 o pkg/land: only liquid water can diffuse or run-off
2204 o AIM using land: soil wetness availability account for snow
2205 o added printMapIncludesZeros to EEPARMS namelist
2206
2207 checkpoint53a_post
2208 o restore TAMC compatiility for exf_constants.h
2209 (no usage of _d in .h)
2210 o Additional storing in KPP in an attempt to fix
2211 TAMC problem with adjoint of KPP code.
2212 (no success...)
2213 Identical code works fine with TAF.
2214 o Fixed verification/natl_box_adjoint experiments.
2215 Initial conditions for Experiments 4 and 5 are now
2216 set to "SEAICE_initialHEFF=0", which is more reasonable,
2217 and hence gives results closer to that of Experiment 2.
2218 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
2219
2220 checkpoint53
2221 o stable checkpoint with up to date adjoint
2222 TLM tests only run for 1st grdchk at the moment. Its unclear if
2223 this is a code problem or a problem with resetting code for g_
2224 variables that is being autogenerated wrong.
2225 Otherwise:
2226 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
2227 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
2228 are both still in chaos following their security messes.
2229
2230 checkpoint52n_post
2231 o various build (mostly genmake2) changes including:
2232 - ability to build/run more easily within Cygwin and MacOS X
2233 - more complicated Makefiles with a stronger dependence on Gnu Make
2234 o pkg/seaice modifications
2235 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
2236 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
2237 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
2238 - changed proxy for geostrophic velocity and updated
2239 verification/lab_sea/results/* accordingly
2240 - removed ADI dynamic solver from pkg/seaice
2241 - replaced all occurrences of 1/CSTICE or 1/CSUICE
2242 they caused a segmentation fault under certain circumstances
2243 - removed unused field WATR
2244 o bug fix in exf-package:
2245 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
2246 now reflect that.
2247 o small fixes in the cal-package:
2248 - set reference date to first of January for the 'model'-calendar
2249 - failing of cal_CheckDate in cal_FullDate now actually results in a
2250 warning
2251 o small modifications in exf-package to increase flexibility:
2252 - change climtempfreeze from a constant to a runtime parameter that
2253 is specified in data.exf_clim (default = -1.9)
2254 - introduce runtime parameter windstressmax (default = 2.0) that is
2255 specified in data.exf
2256 o fix in pkg/thsice:
2257 - update Evap (Tsf changes) to be consistent with Latent heat flux
2258 - maintain snow precipitation unchanged (even if Tsf >=0).
2259 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
2260
2261 checkpoint52m_post
2262 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
2263 this does not change any of the results, because myIter=0 in swfrac always
2264 lead to jwtype=2 (the default anyway), but the call makes little sense
2265 as a default
2266 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
2267 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
2268 atmospheric model (AIM) to use it ; add a "slab ocean" component.
2269 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
2270 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
2271 o extending useSingleCpuIO option to work with new exch2 I/O format
2272 - old-style, missing-tile I/O is still accessible by defining CPP
2273 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
2274 o monitor package can write to NetCDF files and/or STDOUT
2275 o fix re-definition bug in MNC_GRID_INIT_ALL()
2276 o doc/api_reference added
2277 - a framework for building an API Reference Manual using all
2278 the "protex" comments embedded in the code
2279 - see pkg/generic_advdiff, pkg/mnc for examples
2280 o MNC:
2281 - make myThid the last argument for all subroutines
2282 - new default for the grid files: NO halos
2283 - add useMNC and other run-time flags
2284 - separate per-file-group handling of the unlimited dimension
2285 - early initialization of MNC w/ flags read at the eeboot stage
2286 and lookup tables set in initialize_fixed
2287 - write all MNC output to a freshly-created directory
2288 o thermodynamics sea-ice (thsice) is now tested with testreport.
2289 o test exp. advect_cs: use the standard cs32 grid ; update output.
2290 o Added functionality to grdchk:
2291 pick global i,j,k position (or nearest wet) where to perform check.
2292
2293 checkpoint52l_post
2294 o new land formulation:
2295 a) use ground enthalpy as prognostic variable to ensure exact
2296 energy conservation.
2297 b) account for water temperature and for latent heat of freezing
2298 in all processes (rain, run-off, ground storage)
2299 c) compute surface and ground temperature implicitly.
2300 o aim_v23 modification for new land model:
2301 a) Treat separately land / ocean / sea-ice surface fluxes
2302 to allow implicit computation of land & sea-ice surface temp.
2303 b) add snow precipitation.
2304 checkpoint52l_pre
2305
2306 o fix problem (when 1 tile is empty) in min/max monitor.
2307 o fix bug in timeAve (u,vZetatave in common block)
2308 o no restoring terms under ice for pkg/seaice
2309 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
2310 o bug fix for pkg/seaice pickups
2311 o change MNC call locations and add coordinate attributes
2312 o mask vorticity at the corner ; affects global_ocean.cs output
2313 o fix ini_curvilinear_grid ; test CS experiments with mpi
2314 o aim.5l_cs: modify sea-ice fraction input file ; update output
2315 o exf: Adding simple range check routine for exf fields after read
2316
2317 checkpoint52k_post
2318 o removed top-level directory "diags"
2319 - we migrated these functions to pkg/timeave a long time ago
2320 o fixed bug introduced in pkg/monitor
2321 o accuracy ctrlprec = 32 insuffient for gradient checks using
2322 averaged fields (I/O via cost_averages)
2323 -> use ctrl.h in active_file*.F to control I/O precision.
2324 o paramter list of CALL ADTHE_MAIN_LOOP
2325 o added initial do_the_model_io to ecco
2326 o set all ...Freq to zero after cost_final
2327 taveFreq, dumpFreq, pChkptFreq
2328 o MAIN and ECCO differentiability restored
2329
2330 checkpoint52j_post
2331 o fix nchklev in tamc.h for global_ocean...
2332 o Bringing flow and store directives up-to-date
2333 o Really weird thing!
2334 call do_the_model_io from the_main_loop with parameters
2335 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
2336 TAF places a faulty re-call of initialise_varia
2337 after cost_final call which should not be there!
2338 checkpoint52j_pre
2339
2340 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
2341 error messages
2342 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
2343 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
2344 debug output
2345 o modfied mdsio_writefield.F to handle non-global files under exch2
2346 o update AIM Cubed-Sphere exp (aim.5l_cs):
2347 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
2348 o update AIM Equatorial Channel exp:
2349 use standard aim_v23 pkg and change the SST fields to be more realistic.
2350 o globalFile now works with exch2
2351 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
2352 mon_vort3.F to make exch2 friendly with >1 tile per cube face
2353 o limit timeave output for hi-res integrations
2354
2355 checkpoint52i_post
2356 o removed CPP_EEOPTIONS.h from verification/*/code
2357 o updated the tiling for global_ocean_pressure
2358 checkpoint52i_pre
2359
2360 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
2361 the old pkg/aim).
2362
2363 checkpoint52h_pre
2364 o shortened offending lines in exch2_send_rx?.template
2365 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
2366 o genmake2: add build & execute test for NetCDF code
2367 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
2368 old grid files, moved CPP_EEMACROS.h to pkg/exch2
2369 o added useSingleCPUIO flag to monitor.F and mon_out.F
2370 o added temporary hack for sea-ice dynamics on the cube:
2371 metric terms are ignored and it is assumed that
2372 there is no sea-ice on cube faces 1, 2, 4, and 5.
2373
2374 checkpoint52f_post
2375 o added exch2 cube routines to pkg/exch2
2376 o modified hs94.cs-32x32x5 to use it
2377 o added new grid files to hs94.cs-32x32x5
2378 checkpoint52f_pre
2379
2380 checkpoint52e_post
2381 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
2382 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
2383 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
2384 to work with implicit vertical advection and AB ;
2385 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
2386 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
2387 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
2388 checkpoint52e_pre
2389
2390 o fix bug in impldiff when Nr=1 or Nr=2.
2391 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
2392 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
2393 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
2394 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
2395 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
2396 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
2397 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
2398
2399 checkpoint52d_post
2400 o re-tiled many expts to allow comparison in multi-processor mode
2401 - updated output accordingly
2402 - changed hs94.128x64x5 to use intial T from file rather than use the
2403 random number generator
2404 o add infrastructure in model routines for fizhi and gridalt packages
2405 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
2406 o changes to permit hi-res, cubed-sphere, configuration
2407 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
2408 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
2409 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
2410 of surface winds for the cube
2411 (A verification experiment, based on global_ocean.cs32x15, but with
2412 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
2413 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
2414 complete with example surface forcing files and matlab scripts to look
2415 at the output and compare it with that of global_ocean.cs32x15.)
2416 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
2417 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
2418 to conform to the common rule.
2419 o check-in the first version of the coupler + interfaces for multi-components
2420 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
2421 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
2422 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
2423 - ocean and atmos. share the same horizontal grid (no interpolation).
2424 - exchanges between component and coupler is done in forward_step
2425 o new verification experiment, cpl_aim+ocn:
2426 coupled ocean - AIM atmosphere on cs32 grid.
2427
2428 checkpoint52d_pre
2429 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
2430 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
2431
2432 checkpoint52c_post
2433 o Fixing OPTIONS files for use of exf:
2434 - ALLOW_ECCO not needed
2435 - ECCO_CPPOPTIONS.h should not be included from
2436 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
2437 as has been the case in the past
2438 - All cal/exf related options are currently set in
2439 single header file. Should remain so until we
2440 agree on a consistent new policy.
2441 o Removed all CPP options for cal package.
2442 cal has no more CPP options.
2443 o modified STOREs in GAD_ADVECTION
2444 o corrected key comp. for passkey
2445
2446 checkpoint52b_post
2447 o new version: "thsice" of thermodynamic sea-ice pkg:
2448 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
2449 - modify fluxes but do not change theta directly;
2450 - light cleaning of bulk_force pkg (still needed with thsice).
2451 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
2452 + output_thsice.txt to test thsice & bulk_force pkgs.
2453 o put back grid & coriolis monitor output.
2454 checkpoint52b_pre
2455
2456 o call "do_the_model_io" at the beginning (=> dump initial state)
2457 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
2458 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
2459 (need info on NUMBER_OF_PTRACERS)
2460 o missing PTRACERS headers in some routines
2461 o default tamc.h in pkg/autodiff supposed to crash
2462 to ensure proper customization
2463
2464 checkpoint52a_post
2465 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
2466 - moved surfaceTendencyTice from pkg/seaice to main code
2467 - subroutine FREEZE_SURFACE now limits only surface temperature
2468 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
2469 => new output.txt for global_ocean.cs32x15 & global_with_exf
2470 - keep the old version of FREEZE for backward compatibility;
2471 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
2472 - corresponding modifs for TAF directives
2473 o added surface flux output variables to TIMEAVE_STATVARS
2474 o time-averaged output for pkg/ptracers
2475 o fix problem with ECCO-related divided adjoint
2476 snapshot file was missing some ad-variables,
2477 but no warning issued by TAF
2478
2479 checkpoint52a_pre
2480 o some bug fixes for #undef REAL4_IS_SLOW
2481
2482 checkpoint52 = ecco_c52_e35
2483 o after testing adjoints of checkpoint51u_post
2484
2485 checkpoint51u_post
2486 o this is the post-merge tag of the ecco-branch
2487 (needs another clean checkout and re-testing)
2488 o various natl_box_adjoint configs and results
2489 but no input fields
2490 o obcs adjoint not yet merged!
2491 o adding ECCO global 1x1 and 2x2 degree configs
2492 o updated/extended some store directives for seaice
2493 o pkg/ecco now containes ecco-specific part of cost function
2494 o top level routines the_main_loop, forward_step
2495 supersede those in model/src/
2496 previous input data.cost now in data.ecco
2497 (new namelist ecco_cost_nml)
2498 o in ctrl/ cleaned some cross-dependencies and updated CPP options
2499
2500 checkpoint51t_post
2501 o this is the pre-merge tag of the ecco-branch
2502
2503 checkpoint51s_post
2504 o cleanup: removed various obsolete #define-s
2505 o pkg/grdchk
2506 - renamed 'ph-grd 3' to 'grad-res'
2507 - merged from ecco-branch
2508 (remaining bug fixes for obcs gradient checks)
2509 - additional high-precision output for testreport
2510 (grep for 'precision_grdchk_result')
2511
2512 checkpoint51r_post
2513 o cleaned up or removed CPP_OPTIONS.h files
2514 o updated results for some of the tests to reflect the new
2515 optfiles (-ieee: -O0 instead of -O3)
2516
2517 checkpoint51q_post
2518 o cd_code:
2519 - moved cd_scheme.F -> cd_code_scheme.F
2520 - separate read_checkpoint from cd_code_ini_vars.F
2521 - separated cd_code part from write_checkpoint
2522 - updated AD_SOURCE, generated .flow
2523 - added CD_CODE_VARS.h to the_main_loop
2524 - Moving cd_code specific store dir.s to pkg/cd_code
2525 o ctrl package totally restructured
2526 - pack/unpack now optional and decoupled from
2527 xx_/adxx_ I/O
2528 - ctrl_pack/unpack cleaned
2529 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
2530 - confined inclusion of AD_CONFIG.h to where necessary.
2531 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
2532
2533 checkpoint51p_post
2534 o create initial cd_code package
2535 - WARNING: the initialization of fields within packages
2536 is broken because INI_FIELDS (where READ_CHECKPOINT is
2537 called) is called *before* PACKAGES_INIT_VARIABLES.
2538 This seems to be backwards since
2539 1) its important to initially zero the entire field including
2540 the "halo" region
2541 2) zeroing needs to be done *before* reading pickup info
2542 and the pickup call might or might not happen in any
2543 particular run
2544 - this needs an overhaul for R2
2545 o cleanup verification/*/code/GMREDI_OPTIONS.h
2546 o cleanup testreport
2547
2548 checkpoint51o_post
2549 o bringing AD-related verif's up to date with genmake2
2550 - carbon/
2551 - global_ocean.90x40x15/
2552 - hs.94.1x64x5/
2553 - (front_relax/ )
2554 o (more) consistent directory structure for AD-related verif.'s
2555 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
2556 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
2557 o bug fix in find_alpha.F for MDJWF:
2558 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
2559 change rho -> rho-rhoConst
2560 - replace call find_rho to find_rhonum
2561 o initialisation of rFlx extended to full array (required by TAF)
2562 and shifted to thermodynamics
2563 o removed PTRACERS.h in ptracers routine
2564 o added surfacetendencyPtr to S/R parameter list pracers_forcing
2565 o Correcting initialisations for fVerU, fVerV.
2566 o helping TAF to recognize dependency on kUp for
2567 fVerU, fVerV
2568 o Replacing delZ by delR in pkg/ctrl/
2569 checkpoint51o_pre
2570
2571 o undid all of cp51 pending some cleanups and discussion
2572 o added the [#include "AD_CONFIG.h"] statement to all files that need
2573 it for adjoint/tl #defines
2574 o re-worked the build logic in genmake2 to support AD_CONFIG.h
2575 o removed tools/genmake since it no longer works
2576
2577 checkpoint51n_post
2578 o modifications to make FREEZE flux visible to pkg/kpp
2579 - moved surfaceTendencyTice from pkg/seaice to main code
2580 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
2581 - subroutine FREEZE now limits only surface temperature
2582 (this means new output.txt for global_ocean.90x40x15,
2583 global_ocean.cs32x15, and global_with_exf)
2584 o added surface flux output variables to TIMEAVE_STATVARS
2585
2586 checkpoint51n_pre
2587 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
2588 o added [#include "AD_CONFIG.h"] to all files that use the following
2589 defines:
2590 - ALLOW_ADJOINT_RUN
2591 - ALLOW_TANGENTLINEAR_RUN
2592 - ALLOW_ECCO_OPTIMIZATION
2593
2594 checkpoint51m_post
2595 o incorporating changes to get TAMC/TAF working in genmake2
2596 - added new TAMC/TAF targets to the Makefile
2597 - various cleanups related to package handling
2598 - these changes should have no impact on the forward model
2599
2600 checkpoint51l_post
2601 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
2602 - faster algorithm for cal_addtime.F
2603 - higher precision arithmetic, where needed
2604 - pkg/exf *startdate variables changed from calendar date to
2605 model integration time
2606
2607 checkpoint51l_pre
2608 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
2609 o enable to apply restoring on S & T only in a latitude band.
2610 o update output (external_forcing_surf modif. change truncation errors)
2611 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
2612
2613 checkpoint51k_post
2614 o change default to: useNHMTerms=.FALSE.
2615 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
2616 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
2617 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
2618 exp1, ideal_2D_oce
2619 - change data file of oceanic exp (leave the results unchanged for now)
2620 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
2621 o set gravitySign automatically according to the vertical coordinate used
2622 (and change sign: back to "logical" value: +1 when R increases downward)
2623 o added an include barrier to the default CPP_OPTIONS.h and
2624 removed the #include "PACKAGES_CONFIG.h" from it
2625 o fix a bug in mom_fluxform (from chk51j_post)
2626
2627 checkpoint51j_post
2628 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
2629 o adjusted some flow directives (dynamics, thermodynamics)
2630 o added cubed-sphere case to test cost function
2631 o heckpoint_lev?_directives.h now include
2632 pkg-specific directives, whenever those are enabled.
2633 o Moving pkg-specific flow directives to corresponding pkg
2634 Moving pkg-specific differentiation list to corresponding pkg
2635 Moving pkg-specific checkpoint-lev storing to corresponding pkg
2636 ---> conventions are
2637 - pkg_ad.flow
2638 - pkg_ad_diff.list
2639 - pkg_ad_check_lev?_dir.h
2640
2641 checkpoint51i_post
2642 o merge of the branch-genmake2
2643 - knowingly breaks the older genmake
2644 - automatic generation of all ALLOW_${PKG_NAME} defines
2645 - new testreport supersedes older testscript
2646 o large number of package inclusion and header cleanups
2647 checkpoint51i_pre
2648
2649 o new output for adjoin of global ocean vector invariant
2650 o fix for checkpoint of thermodynamic seaice and bulk_force
2651 o Steph gchem various cleanups
2652
2653 checkpoint 51h_pre
2654 o fixed some single quotes
2655 o modify gchem pkg to be more versatile
2656 o modifications to clean up dic pkg
2657 o add pkg/cfc
2658
2659 checkpoint51g_post
2660 o provide links for ARPACK and ADM*TLM
2661 o start removing verification/vero/
2662 o update AD-related stuff
2663 (in particular some IF-statements in model/src/ routines)
2664 o adding to verification/global_ocean.90x40x15/ adjoint of
2665 vector invariant setup
2666
2667 checkpoint51f_post
2668 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
2669 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
2670 of tracer Green's fucntions for ocean inversion project.
2671
2672 checkpoint51f_pre
2673 o Added on-the-fly spatial interpolation capability
2674 "USE_EXF_INTERPOLATION" to pkg/exf.
2675 - This is a temporary Cartesian-grid hack until
2676 the super-duper ESMF coupler becomes available.
2677 - See verification/global_with_exf/README for usage example.
2678 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
2679 flags and modified pkg/seaice accordingly.
2680 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
2681 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
2682 non-local transport term.
2683
2684 checkpoint51e_post
2685 o pkg/mom_vecinv:
2686 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
2687 - add time-ave diagnostic of vorticity advection.
2688 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
2689 o atmospheric geopotential: - include water vapor effect;
2690 - use p^kappa in p* scaling.
2691 o land pkg: read initial state from files.
2692 o AIM : add stratospheric drag in the upper level
2693
2694 checkpoint51d_post
2695 o change function ILNBLNK (=> last non-blank char.) to return zero
2696 (instead of the string length) when the string. char is empty
2697 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
2698 o modif's to restore TAMC compatibility
2699 - avoid "_d" constructs in PARAMETER declarations
2700 - avoid interrupting lines by comment lines
2701 o Use cluster local disks for purely local I/O
2702 vs. globally visible disks needed for ctrl stuff
2703 (merged from ecco-branch)
2704 - new active_file_loc... and mdsio_..._loc routines
2705 - affected packages: autodiff, ctrl, grdchk, mdsio
2706
2707 checkpoint51c_post
2708 o introducing integer flag debugLevel
2709 - debLevZero: suppress all output
2710 - debLevA: standard
2711 - debLevB: equivalent to current debugMode=.TRUE.
2712 o introducing pathname variable mdsioLocalDir for mdsio
2713 that can be specified at runtime
2714 (relevant for cluster I/O to local disk)
2715 `
2716 >>>checkpoint51b_post
2717 adjoint of ptracers
2718 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
2719 o extended state in checkpoint_lev?, etc.
2720 o alternative ctrl/cost with tr1 or ptracer
2721 o new comlev1_bibj_ptracers
2722 o new ptracers.flow
2723 o made ptracers_forcing same as external_forcing_s
2724 o added verification for adjoint with ptracers
2725 - adm. grdchk fail so far
2726 - tlm. grdchk OK
2727 - checked tapelev/comlev recomputations: OK
2728 <<<checkpoint51b_pre
2729
2730 checkpoint51a_post
2731 o added code for biogeochemistry package
2732 - new pkgs: dic, gchem
2733 - new subroutine in ptracers
2734 o modify code for biogeo packages
2735 - in model/src and pkg/ptracers
2736
2737 checkpoint51
2738 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
2739 - autodiff, ctrl, exf, grdchk, seaice
2740 kept separate packages
2741 - cost, ecco, obcs
2742 o updating verification/internal_wave, verification/lab_sea
2743 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
2744
2745 checkpoint50i_post
2746 o Preparing next differentiable checkpoint and sync
2747 of MAIN vs. ecco-branch
2748 - 1st step: this one is differentiable
2749 - 2nd step: next(! not this) checkpoint will have updated packages
2750 from ecco-branch)
2751
2752 checkpoint50h_post
2753 o new package "land": provide surface BC for AIM.
2754 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
2755 o AIM: use true log-P extrapolation for near surface temp (= as in
2756 F.Molteni paper) ; update aim.5l_cs output.
2757 o New variable in PARM03 for more flexible pickups
2758 o somewhat cleaned package initialisation sequence for
2759 ctrl/ cost/ ecco/ in packages_... routines
2760
2761 checkpoint50g_post
2762 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
2763 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
2764 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
2765 made the default because of faster convergence than ADI
2766
2767 checkpoint50f_post
2768 o exf totally restructured
2769 - replaced all exf_set_ routines by one generic exf_set_gen.F
2770 and made sure it's still differentiable
2771 - split exf_getffields.F into new exf_bulkformulae.F
2772 - exf_inscal_/exf_outscal_ suffixes consistent with field names
2773 - updated adjoint/makefile and relevant verif. accordingly
2774
2775 checkpoint50f_pre
2776 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
2777 + change Evap over land. (update aim.5l_cs output)
2778 o added missing .cvsignores and made uniform across expts
2779 o changed configuration of tidal_basin_2d expt
2780 o added pkg/debug functions for tracing code in fatal crashes
2781 o tidied pkg/monitor to use MONITOR_OPTIONS.h
2782 o new fn in pkg/monitor to stop model if solution grows too big
2783 o removed lots of single quotes from comments
2784
2785 checkpoint50e_post
2786 o make KPP work with PTRACERS
2787 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
2788 nearly a copy of kpp_transport_s
2789 - there is no analogue to SurfaceTendencyS, so I have to use
2790 gPtr(of the surface layer) instead
2791 o add a new platform SunFire+mpi (SunFire 15000) to genmake
2792 checkpoint50e_pre
2793
2794 checkpoint50d_post
2795 o change kpp output from multiple-record state files to single-record state
2796 files analogous to write_state.F
2797 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
2798 analogous to the cg2d-related output.
2799 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
2800 so that writing to internal file fn (with length 512) fails.
2801 checkpoint50d_pre
2802
2803 checkpoint50c_post
2804 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
2805 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
2806 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
2807 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
2808 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
2809
2810 checkpoint50c_pre
2811 Merging from release1_p13:
2812 o bug fix for pkg/seaice dynamic solver
2813 o Added SEAICE_initialHEFF to pkg/seaice
2814
2815 checkpoint50b_post
2816 o store u*,v* in gU,V instead of in guNm1,gvNm1
2817 o in order to put the momForcing out of the Adams-Bashforth:
2818 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
2819 to timestep.F
2820 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
2821 o re-generate output for highly sensitive test-exp:
2822 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
2823
2824 checkpoint50b_pre
2825 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
2826 o corrected CPP option mismatch in exf_Bulk... functions for case
2827 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
2828
2829 checkpoint50a_post
2830 o Bug fix for merging between c50 and KPP.
2831 ikey was passed from thermodynamics to kpp_calc via
2832 common block rather than being recomputed in kpp_calc,
2833 in contradiction with new key itdkey.
2834 New key ikppkey created, and tamc.h headers updated.
2835
2836 checkpoint50
2837 - 2nd step of merge with ecco-branch:
2838 merge changes in ecco-branch back into main trunk
2839 - bug fix in find_alpha
2840 - more storing in gmredi_calc_tensor.F, kpp_routines.F
2841 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
2842 - merged some sliced AD support routines
2843
2844 checkpoint49
2845 merged from ecco-branch:
2846 o exf:
2847 - Enable initialisation of forcing fields to constant
2848 (runtime) values.
2849 - in exf_getffields.F
2850 Reduce i-/j-loop to interior domain, discarding overlaps.
2851 That also fixes wrong TAF-key computations for key_1, key_2
2852 with bulf formulae.
2853 - exf_init.F modify #ifdef for exf_init_evap
2854 - exf_getffieldrec.F, ctrl_getrec.F
2855 The following INT-usages are not safe:
2856 fldsecs = int(fldsecs/fldperiod)*fldperiod
2857 fldcount = int(fldsecs/fldperiod) + 1
2858 and were modified.
2859 o autodiff: checkpoint_lev...
2860 - updated storing for bulk formulae (some arrays were missing)
2861 - added state for seaice package
2862 - synchronized with main branch
2863 o DIVA:
2864 Modif.s in
2865 - the_main_loop.F
2866 - the_model_main.F
2867 and added cost_final_restore.F cost_final_store.F
2868 o With these changes, it is possible to fully separate
2869 the first forward run to compute the cost function (mdthe_main_loop)
2870 and adjoint runs over individual DIVA intervals (adthe_main_loop)
2871 into separate model executions.
2872 This enables better tuning of DIVA to given queue sizes.
2873 o Loss of cost function value in consecutive DIVA runs is
2874 fixed by storing to 'costfinal' file.
2875 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
2876 beginning/end of adjoint integration is accounted for.
2877 The current changes apply to TAF-1.4.26.
2878 TAF has one remaining bug, requiring one manual change
2879 (see MITgcm manual).
2880 o cal: synchronized between MAIN and ecco-branch
2881
2882 checkpoint48i_post
2883 o Changes to restore differentiability of code w.r.t. previous tag
2884 (mostly adding new routines to make list and replacing
2885 pressure by totPhiHyd).
2886 o Updated and merged grdchk package
2887 - has both ADM and TLM checks
2888 - works for single- and multi-proc.
2889 - output cleaned
2890 - worked successfully for parallel DIVA
2891 o genmake:
2892 - Adding -platform=SP4
2893 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
2894 o Modif. for DIVA:
2895 ctrl_unpack should not be called in intermediate DIVA interval.
2896 (similar thing would apply for active files such as
2897 tbar, sbar, psbar, which should not be reinitialised;
2898 only relevant for ecco-branch)
2899
2900 checkpoint48h_post
2901 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
2902 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
2903 o Added SEAICE_initialHEFF to pkg/seaice
2904 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
2905
2906 checkpoint48g_post
2907 --- EOS:
2908 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
2909 store total Potential in totPhyHyd for diagnostics & EOS.
2910 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
2911 --- Pressure/geopotential gradient:
2912 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
2913 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
2914 ( changes results of global_ocean_pressure )
2915 o NLFS + z-coord.: add eta*Rho' contribution.
2916 o accurate phiHyd when using interface-W at the middle between 2 centers
2917 ( changes results of ideal_2D_oce )
2918 o includes r* 2nd term in potential gradient.
2919
2920 checkpoint48f_post
2921 Merging from release1_p12:
2922 o Modifications for using pkg/exf with pkg/seaice
2923 - improved description of the various forcing configurations
2924 - added basic radiation bulk formulae to pkg/exf
2925 - units/sign fix for evap computation in exf_getffields.F
2926 - updated verification/global_with_exf/results/output.txt
2927 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
2928 (SBO) core products, including oceanic mass, center-of-mass,
2929 angular, and bottom pressure (see pkg/sbo/README.sbo).
2930 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
2931 to avoid negative values in shallow regions.
2932 - updated verification/natl_box/results/output.txt
2933 - updated verification/lab_sea/results/output.txt
2934 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
2935 o Added useSingleCpuIO option (see PARAMS.h).
2936 o Updated useSingleCpuIO option in mdsio_writefield.F to
2937 work with multi-field files, e.g., for single-file pickup.
2938 o pkg/seaice:
2939 - bug fix in growth.F: QNET for no shortwave case
2940 - added HeffFile for specifying initial sea-ice thickness
2941 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
2942 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
2943 kpp_transport_t.F, forward_step.F, and the_main_loop.F
2944 o pkg/seaice:
2945 - adjoint-friendly modifications
2946 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
2947
2948 checkpoint48e_post
2949 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
2950 o dynamics: change definition of computational domain & adapt mom_fluxform
2951 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
2952 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
2953 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
2954 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
2955 global_ocean.90x40x15 global_with_exf global_ocean_pressure
2956 inverted_barometer solid-body.cs-32x32x1
2957 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
2958
2959 checkpoint48d_post
2960 o in preparation for r*:
2961 a) use pre-computed gradient of hydrostatic potential:
2962 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
2963 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
2964 => affects results of glob_oce_pressure (different truncation error)
2965 update output.txt of ideal_2D_oce & global_ocean_pressure
2966
2967 checkpoint48d_pre
2968 o in preparation for r*:
2969 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
2970 pass the 2 comp. of the grad. as arguments to momentum S/R.
2971 but for the moment, only used if it does not change the results.
2972 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
2973
2974 checkpoint48c_post
2975 Modifications in treatment of initial flux forcing controls
2976 to avoid extra storing of flux fields.
2977
2978 checkpoint48c_pre
2979 o Added tidal_basin_2d experiment (currently 1D!)
2980 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
2981
2982 checkpoint48b_post
2983 o r* coordinate added in #ifdef NONLIN_FRSURF block.
2984 (modification to pressure gradient not yet implemented)
2985 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
2986 (for U & V) that are used for vertical advection of momentum.
2987
2988 checkpoint48a_post
2989 o In preparation for r*, use temp. array to compute vertical transport
2990 in flux-form momentum pkg. => change results of few test-exp.
2991 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
2992 lab_sea, natl_box & plume_on_slope
2993
2994 checkpoint48
2995 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
2996
2997 checkpoint47j_post
2998 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
2999 o moved adexch from forward_step to addummy_in_stepping
3000 o added exch in ctrl_map_...
3001 o aveFreq.=0. at end of cost_final to avoid overwrite in
3002 reverse checkpointing loop
3003 o Yet more changes in gmredi:
3004 * adgmredi_calc_tensor
3005 avoiding all recomputation of gmredi_slope_limit
3006 * adgmredi_x/y/rtransport
3007 added flag for excessive storing to avoid recomp. of
3008 u/v/rtans, dTdx/y/z
3009 -> this is not really necessary and very memory-consuming
3010 * adgmredi_slope_psi:
3011 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
3012 * gmredi_slope_limit
3013 re-activated full calculation of taperfct for case 'ac02'
3014 o updating verification/ adjoints of carbon, global_ocean.90x40x15
3015
3016 checkpoint47i_post
3017 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
3018 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
3019 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
3020 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
3021 o gmredi: fix few bugs.
3022
3023 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
3024 This will be a good checkpoint to plug into the ecco-branch.
3025 o few modif.'s to get latest version adjointed
3026 (mainly kick out code in ini_linear_phisurf)
3027 o modif's to run adjoint with exactConserv
3028 o case GM_BOLUS_ADVEC should be cleaned
3029 S/R gmredi_slope_psi should be cleaned
3030 o verification/carbon now has exactConserv=.TRUE.
3031
3032 checkpoint47g_post
3033 o time-average AIM output: becomes independent from statvars time-average
3034 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
3035 o After TAF bug fix:
3036 Tested adjoint of gmredi package.
3037 Tests were done with checkpoint47 rather than with latest
3038 checkpoint47f_post since the latter is broken for the adjoint
3039 verification/carbon/ contains both ADM and TLM gradient checks.
3040 Here they are, before they get changed/lost/stolen.
3041 Mostly modif.'s to fix numerical sensitivities.
3042 Gradient checks OK for
3043 - GM_taper_scheme:
3044 * clipping
3045 * ac02
3046 * linear
3047 * glw91
3048 * dm95
3049 * ldd97
3050 - GMREDI_OPTIONS:
3051 * GM_VISBECK_VARIABLE_K
3052 * GM_NON_UNITY_DIAGONAL
3053 * GM_EXTRA_DIAGONAL
3054 * GM_BOLUS_ADVEC
3055 in conjunction with data.gmredi parameters to be checked in
3056 in a few minutes under verification/carbon/code/
3057
3058 checkpoint47f_post
3059 Merging from release1_p10:
3060 o modifications for using pkg/exf with pkg/seaice
3061 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
3062 and SEAICE_EXTERNAL_FLUXES
3063 - pkg/exf CPP options EXF_READ_EVAP and
3064 EXF_NO_BULK_COMPUTATIONS
3065 - usage examples are Experiments 8 and 9 in
3066 verification/lab_sea/README
3067 - verification/lab_sea default experiment now uses
3068 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
3069
3070 checkpoint47e_post
3071 o created a tag prior to creating a branch
3072
3073 checkpoint47d_post
3074 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
3075 at the bottom boundary had an erroneous half slip boundary condition
3076 o added bottom drag and no slip boundary condition capabilities to
3077 oceanic pressure coordinates code
3078 o added new verification experiment global_ocean_pressure, this experiment is
3079 also described in the tutorial section of the manual
3080 checkpoint47d_pre
3081
3082 checkpoint47c_post
3083 o Added a verification experiment for a global cubed-sphere ocean run
3084 - verification/global_ocean.cubed32x32x30
3085 - uses pkg/therm_seaice and pkg/bulk_forcing
3086
3087 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
3088 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
3089 when using P-coordinate; only implemented for atmospheric config.
3090 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
3091 NOTES: requires option NONLIN_FRSURF to be "#define".
3092 o update advect_xz/results/output.txt (left from checkpoint44g_post)
3093
3094 checkpoint47b_post
3095 Merging from release1_p9:
3096 o pkg/seaice
3097 - removed GOTO's and added taf directives
3098 - double precision constants to reduce the g77 (Linux)
3099 to F77 (SGI) differences reported in release1_p8
3100 o tools/genmake
3101 - added SGI options
3102 o verification/testscript
3103 - updated to that of checkpoint47a_post
3104 o verification/global_ocean.90x40x15/input/eedata
3105 - modified for SGI f77 compatibility
3106 o verification/lab_sea
3107 - added description of sea-ice model
3108 - added missing matlab routines
3109 - added test of thermodynamics parallelization
3110
3111 checkpoint47a_post
3112 o new pkg: aim_v23
3113 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
3114 for now, keep the same surface forcing as before.
3115 - Part-Cell implemented into AIM; check that Heat & Water are conserved
3116 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
3117 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
3118 o add diagnostic of surface correction term in monitor output
3119
3120 o bulk_force and therm_seaice
3121 - Two packages: bulk_force (Bulk forcing)
3122 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
3123 - Earlier integration from Stephaine Dutkiewicz
3124 and Patrick Heimbach.
3125 - Two ifdef statements for compile time,
3126 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
3127
3128 checkpoint47
3129 differentiable version of checkpoint46n_post
3130 o bug fix in quasihydrostaticterms
3131 o * "clean" adjoint code (in terms of extensive recomputations)
3132 can now be obtained for all GMREDI options (i.e. for
3133 - GM_VISBECK_VARIABLE_K
3134 - GM_NON_UNITY_DIAGONAL
3135 - GM_EXTRA_DIAGONAL
3136 - GM_BOLUS_ADVEC )
3137 * However, wrong gradient check problem remains unsolved.
3138 * New CPP options have been introduced for different
3139 tapering schemes
3140 o external_fields_load now part of differentiation list
3141 o pressure needs multiple storing;
3142 would be nice to have store_pressure at beginning or
3143 end of forward_step, e.g. by having phiHyd global (5-dim.)
3144 (NB: pressure is needed for certain cases in find_rho,
3145 which is also invoked through convective_adjustment).
3146 o recomputations in find_rho for cases
3147 'JMD95'/'UNESCO' or 'MDJWF' are OK.
3148 o #define ATMOSPHERIC_LOADING should be differentiable
3149 o ini_forcing shifted to begining of initialise_varia
3150 o Incorporating QNVS line search routines into MITgcm
3151 (this is separate code, and therefore not under pkg)
3152 lsopt/, optim/
3153 o Updated verification/carbon/
3154 - #define GM_VISBECK_VARIABLE_K
3155 - GM_taper_scheme = 'ldd97'
3156
3157 checkpoint46n_post
3158 Merging from release1_p8:
3159 o verification/natl_box:
3160 updating new external_fields_load routine
3161 o New package: pkg/seaice
3162 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
3163 The sea-ice code is based on Hibler (1979-1980).
3164 Two sea-ice dynamic solvers, ADI and LSR, are included.
3165 In addition to computing prognostic sea-ice variables and diagnosing
3166 the forcing/external data fields that drive the ocean model,
3167 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
3168 The implied surface heat flux is then stored in variable
3169 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
3170 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
3171 non-local transport term. Because this call precedes model
3172 thermodynamics, temperature under sea-ice may not be "exactly" at
3173 the freezing point by the time theta is dumped or time-averaged.
3174 N.B.: fairly large differences in accuracy occur across
3175 different platforms/compilers; comparison between
3176 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
3177 generated output gives:
3178 T S U V
3179 C D M c m s m s m s m s
3180 n p a R g m m e . m m e . m m e . m m e .
3181 f n k u 2 i a a d i a a d i a a d i a a d
3182 g d e n d n x n . n x n . n x n . n x n .
3183
3184 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
3185 o GAD:
3186 - generated new common blocks to account for call of
3187 same gad routines with differing traceridentities
3188 (needed to modify tracerIdentity indices in GAD.h)
3189 - generated separate common blocks for case useCubedSphereExchange
3190 (Department of Futurology)
3191 - parameter lists to gmredi_?transport: added tracerIdentity
3192 - added new key indices to tamc.h
3193 o external_fields_load:
3194 - added this routine to TAF list
3195 - needed to make some common blocks global and additional storing
3196 along the same lines as exf package (checkpoint_lev?_directives.h)
3197 o exf:
3198 updated external forcing package
3199 - bug fixes carried over from ecco-branch
3200 (missing OBCS_OPTIONS.h in two routines)
3201 - enable easy to use "no forcing".
3202 - added exf I/O for atmospheric loading
3203 - added exf I/O for runoff data
3204 - transfered scaling between exf <-> MITgcm to exf namelist
3205 o Adding new verification experiment global_with_exf.
3206 This verification experiment is almost identical to the
3207 global_ocean.90x40x15 experiment, except that it uses
3208 the exf (and cal) package instead of the
3209 external_fields_load routine (cf README file).
3210
3211 checkpoint46m_post
3212 o modified testscript to return -- when there are no lines of "%MON" output
3213 o added new flag "quasiHydrostatic" for QH mode
3214 and new routine quasihydrostaticterms()
3215 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
3216 New routine: mom_u_coriolis_nh()
3217 o fixed sign of non-hydrostatic metric terms in u and v equations.
3218 Depend on correct sign of gravitySign.
3219 o added work.pc* to .cvsignore in aim directories using ifc
3220 o introduced flag for controllin non-hydrostatic metric terms
3221 o removed gravitySign from PARM04
3222 o switched to g77/ifc from pgf77 in aim experiments
3223
3224 checkpoint46l_post
3225 o made convective adjustment work with pressure coordinates:
3226 - changed the direction of k-loop in convective_adjustment.F for the
3227 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
3228 - adjusted the reference pressure k-index in convective_adjustment.F
3229 - adjusted the convection condition in convect.F (in analogy to
3230 calc_ivdc.F)
3231 - convective_adjustment no longer computes anything on the halos
3232 - removed the warnings about negative salinity from find_rho.F and
3233 find_alpha.F; instead the new routine look_for_neg_salinity, called
3234 at the beginning of find_rho, find_alpha, and find_beta, does a
3235 check of the entire slice, if CPP-option
3236 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
3237 checkpoint46l_pre
3238
3239 checkpoint46k_post
3240 o fixed the verification/global_ocean.90x40x15 experiment:
3241 - new bathymetry (the world according to A., JMC, and M.)
3242 - new initial fields and forcing fields (*.bin files)
3243 - new POLY3.COEFFS (for the next release one should switch to a full
3244 equation of state: JMD95P or MDJWF)
3245 - fixed several errors and redundancies in the data file
3246 - experiment uses looped cells
3247 - added matlab directory with diagnostic scripts for plotting of output
3248
3249 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
3250 - read AIM physics parameters from a file (data.aimphys)
3251 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
3252
3253 checkpoint46j_post
3254 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
3255 o move wVel computation at the end of the time step, in S/R integr_continuity
3256 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
3257 o update timeave pkg for wVel diagnostic.
3258 checkpoint46j_pre
3259
3260 checkpoint46i_post
3261 o Clean up AIM package (and keep the results unchanged):
3262 include CPP_OPTION and use IMPLICT NONE in all routines ;
3263 declare all the variables _RL ; use _d 0 for all numerical constants.
3264 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
3265
3266 checkpoint46h_post
3267 o cleaned up the use of rhoNil and rhoConst.
3268 - rhoNil should only appear in the LINEAR equation of state, everywhere
3269 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
3270 and the dynamical equations are all divided by rhoConst
3271 o introduced new parameter rhoConstFresh, a reference density of fresh
3272 water, to remove the fresh water flux's dependence on rhoNil. The default
3273 value is 999.8 kg/m^3
3274 o cleanup up external_forcing.F and external_forcing_surf.F
3275 - can now be used by both OCEANIC and OCEANICP
3276 checkpoint46h_pre
3277
3278 Added code to convert surface volume flux (fresh water) into
3279 a mass flux when using P coordinates in the ocean (OCEANICP).
3280 Note: It assumes you have set rho0=rhoConst=density of fresh water.
3281
3282 checkpoint46g_post
3283 o Include a new diagnostic variable phiHydLow for the ocean model
3284 - in z-coordinates, it is the bottom pressure anomaly
3285 - in p-coordinates, it is the sea surface elevation
3286 - in both cases, these variable have global drift, reflecting the mass
3287 drift in z-coordinates and the volume drift in p-coordinates
3288 - included time averaging for phiHydLow, be aware of the drift!
3289 o depth-dependent computation of Bo_surf for pressure coordinates
3290 in the ocean (buoyancyRelation='OCEANICP')
3291 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
3292 Theta, Salinity, and Pressure in the parameter list. This routine is
3293 presently contained in find_rho.F. This routine does not give the
3294 correct density for 'POLY3', which would be a z-dependent reference
3295 density.
3296 o cleaned up find_rho
3297 - removed obsolete 'eqn' from the parameter list.
3298 o added two new verification experiments: gop and goz
3299 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
3300 checkpoint46g_pre
3301
3302 checkpoint46f_post
3303 o Enable tangent linear (forward mode) gradient checks:
3304 - extended active file handling to g_... files
3305 - added TANGENT_SIMULATION to theSimulationMode
3306 - extended grdchk package accordingly
3307 o added tangent linear setup in verification/carbon/code_ftl
3308 o added adjoint setup in verification/front_relax/code_ad
3309
3310 checkpoint46e_post
3311 o Added new equation of state -> MDJWF
3312 - EOS of McDougall et al., 2002, JAOT, submitted
3313 - caveat: the equation of state is only valid for a smaller (more
3314 realistic?) range of values than JMD95P/Z and UNESCO
3315 - added masks to the calculation of pressure in store_pressure
3316 - added more check values for density in check_eos (ini_eos.F), some of
3317 the old check values are out of the range of the MDJWF-eos, so don't
3318 expect perfect matches for those
3319 checkpoint46e_pre
3320
3321 checkpoint46d_post
3322 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
3323 'OCEANICP', also initialised field pressure correctly in ini_eos in the
3324 case of pressure coordinates. eosType='JMD95Z' in
3325 combination with buoyancyRelation='OCEANICP' now causes an error.
3326 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
3327 in find_alpha/beta.
3328 checkpoint46d_pre
3329
3330 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
3331 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
3332
3333 checkpoint46c_post
3334 o Changes necessary for ocean in p-coordinates
3335 - Added new buoyancy relation = 'OCEANICP'
3336 - Added new parameters = gravitySign (this used to be contained inside
3337 the factor dRdZ which I added when we first switched to R coordinates).
3338 X GM/Redi is not compatible (yet)
3339 X bottom drag and no-slip need to be debugged.
3340 checkpoint46c_pre
3341
3342 checkpoint46b_post
3343 o Added new equation of state -> JMD95Z and JMD95P
3344 - EOS of Jackett and McDougall, 1995, JAOT
3345 - moved all EOS parameters into EOS.h
3346 - new routines ini_eos.F, store_pressure.F
3347 o Added UNESCO EOS, but not recommended because it requires
3348 in-situ temperature (see JMD95)
3349 o Modified formatting for knudsen2.f in utils/knudsen2 and added
3350 unesco.f to be used with POLY3
3351 checkpoint46b_pre
3352
3353 checkpoint46a_post
3354 o Added (atmospheric) pressure loading
3355 - new field in FFIELDS.h, etc...
3356 - new cpp flag ATMOSPHERIC_LOADING
3357 o Changed hFacC to _hFacC in calc_phi_hyd.F
3358 o Added SHORTWAVE_HEATING to some files for consistency
3359 checkpoint46a_pre
3360
3361 checkpoint46
3362 further merges from release1_p5
3363 o new ctrl package
3364 - adopted from ECCO environment to enable optimization
3365 - added Eliassen Palm fluxes to controls
3366 o added Eliassen Palm flux controls to gradient check package
3367 o cost package
3368 - Compatible with new ctrl package
3369 - added Eliassen Palm cost hooks
3370 - modif's of existing cost functions
3371 o Adjoint-related bug fixes in kpp:
3372 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
3373 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
3374 o autodiff package
3375 - flow directives:
3376 + new for S/R do_the_model_io
3377 + enhanced for S/R checkpoint
3378 + new gmredi.flow
3379 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
3380 disable adcommon.h/g_common.h by default.
3381 - fixed problem for adjoint of global_max
3382 o modified verification/carbon/
3383 o New setup for adjoint of global_ocean
3384 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
3385 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
3386 o incorporated hooks for sponge layer code (external_forcing.F)
3387
3388 checkpoint45d_post
3389 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
3390 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
3391 (affects plume_on_slope "cg2d" output)
3392 o add new parameter deltaTfreesurf for free-surface time stepping
3393 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
3394 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
3395 o change phiMin in exp1 (to agree with documentation)
3396 o add new flags:
3397 - T,S forcing inside/outside Adams-Bashforth
3398 - turn off temp,salt advection and/or forcing
3399 - for each tracer, define internal flag for multiDimAdvection & A-B
3400 o monitor: change definition of KE to check conservation of Energy
3401
3402 checkpoint45c_post
3403 o Removed f90 comments ("!")
3404 o Modified initialisations to enable exf package for MITgcm
3405 (without invoking ECCO_PACKAGE).
3406 o modifications to gradient check package (Martin Losch)
3407 - enable centered differences
3408 - modified format of standard output
3409
3410 checkpoint45b_post
3411 o cleaned exchange calls in cg2d
3412 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
3413 o included CPP option SINGLE_LAYER_MODE in thermodynamics
3414 to configure barotropic setup (Martin Losch)
3415 o moved some initialisations within bi,bj loop in dynamics
3416 (TAF flow dependency)
3417 o in initialise_varia, moved call packages_init_variables
3418 before convective_adjustment_init
3419 (corresponding adjustment of TAF tape initialisation).
3420 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
3421
3422 checkpoint45a_post
3423 o compute Rho over the whole domain (extend iMin,jMin indices)
3424 o specific exchange for X-slice domain (case Ny=1)
3425 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
3426 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
3427
3428 checkpoint44h_post = checkpoint45
3429 o Fix to restore differentiability:
3430 place at which packages_init_variables is called in
3431 initialise_varia is crucial for reverse control flow.
3432 o modifications in GMRedi to enable stable adjoint
3433 (corresponding modif's in thermodynamics, dynamics)
3434 o added missing hook for sponge layer code in external_forcing
3435 o modified test cost functions
3436 o storing in gad_advection (plus removal of write(0,*)!
3437 o missing headers TR1.h added in convective_adjustment routines
3438 o errorMessageUnit set non-equal zero in eeboot
3439 (conflict on some platforms, e.g. IBM SP3)
3440 o modified carbon verif.
3441
3442 checkpoint44h_pre
3443 o vertical grid option: allow to put the Interface at the middle between
3444 2 cell-centers ; replace delZ in pkg/kpp by drF.
3445 o GM Advective form: Tracers are advected using the residual transport (=
3446 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
3447
3448 checkpoint44g_post
3449 o fix surface correction term in multiDimAdvection (affects plume_on_slope
3450 results) ; ifdef missing in thermodynamics.F
3451
3452 checkpoint44f_pre,checkpoint44f_post
3453 o added PTRACERS package
3454 This allows an arbitrary number of passive tracers to be integrated
3455 forward simultaneously with the dynamicaly model.
3456 + Implemented so far:
3457 - basic forward algorithm (time-stepping, advection, diffusion, convection)
3458 - I/O and checkpointing
3459 - GM/Redi *but* using the GM/Redi coefficient of Salt
3460 + Not implemented so far:
3461 - KPP
3462 - OBCS
3463 + No specific example supplied (yet) but global_ocean.90x40x15 has the
3464 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
3465 line in data.pkg.
3466 + This package is disabled by default since it increases storage.
3467
3468
3469 o testscript: added -cleanup option
3470 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
3471 b) enable to filter 2D fields.
3472
3473 checkpoint44e_pre,post
3474 o re-wrote convective adjustment to use pre-calculated weights
3475 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
3476 Adds: model/src/convective_weights.F, convectively_mixtracer.F
3477 Original calls to convect() still in place.
3478
3479 chkpt44d_pre,post
3480 o added missing EXCLUDE_MONITOR flags
3481 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
3482 (incompatible typ in MIN/MAX expressions caused problems
3483 on IBM SP3)
3484 o in genmake added variable MAKEDEPEND
3485 plus resetting for case SunOS
3486 o added timer_stats.c routine for IBM SP3
3487 o removed variables in dynamics
3488 !!! I forgot to create tag chkpt44d_pre !!!
3489 !!! But chkpt44d_pre = chkpt44c_post !!!
3490
3491 o real fresh water flux implemented with non-linear free-surface.
3492
3493 chkpt44c_pre,post
3494 o few fix (mask in shap_s2, EmPmR in external_field_load,
3495 USE_NATURAL_BCS in solve_for_P);
3496 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
3497
3498 checkpoint44b_pre/_post
3499 o merge of relevant stuff from the ecco-branch:
3500 - genmake: removed $S64 overwrite for case SunOS
3501 - pkg/exf: update and corrections for field swapping and obcs
3502 - pkg/ecco: parameter lists for the_model_main, the_main_loop
3503 harmonized between ECCO and MITgcm
3504 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
3505 updated checkpointing_lev... lists for obcs
3506 - model/src: minor changes in forward_step, plot_field
3507 added directive for divided adjoint in the_main_loop
3508 - pkg/mdsio: added mdsio_gl_slice
3509
3510 o check parameters & config (chkpt44a_pre,post)
3511 o OBC and NonLin_FrSurf.
3512
3513 checkpoint44
3514 o fix bug in mom_vi_del2uv
3515 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
3516 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
3517 o update AIM experiments (NCEP input files)
3518 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
3519 o added some stuff for AD
3520
3521 checkpoint43
3522 o added two new advection tests
3523 o added global 4x4 degree ocean test
3524 o added test of H&S94 with free surface on cube
3525 o some final mods for gradient check, adjoint,...
3526
3527 checkpoint42
3528 Fixed AD-related problems:
3529 o Store directives up-to-date with re-arranged Adams-Bashforth
3530 (mainly thermodynamics.F)
3531 o New store directives for multi-dim. advection schemes
3532 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
3533 * new common block and key passkey
3534 (mainly gad_advection.F)
3535 o Modified store directives for split of dynamics/thermodynamics
3536 for the case ALLOW_KPP
3537 o Cleaned argument list for timestep_tracer.F
3538
3539 checkpoint41
3540 o re-formatted/added comments in prologues of key subroutines
3541 to work with protex
3542
3543 checkpoint40
3544 o moved calc_gs, calc_gt and calc_tr1 back to model/src
3545 o added FLT (floats) package from Arne along with demo. experiment
3546 o re-arranged Adams-Bashforth scheme for tracers to allow easier
3547 implementation of forward-in-time forcing terms
3548 o more mods for non-linear free-surface including new variable
3549 o modified multi-dim method to work on cube
3550 o bug fix in KPP (from DM)
3551
3552 checkpoint40pre9
3553 o added DST advection schemes
3554 o fix MPI bug on SGI's
3555 o modifications for non-linear free-surface
3556 o fixed conditionals for fixed flow/passive tracer only mode
3557 o added tension/strain form of stress tensor
3558 o changes to commenting of arguments for TAF/TAMC
3559 o added/updated many matlab scripts
3560 o added multi-dimensional advection method for tracers
3561
3562 checkpoint40pre8
3563 o new package rw/
3564 Added method for dumping intermediate local arrays:
3565 mdsio_writetile - same as mdsio_writefield except works from inside
3566 bi,bj loop
3567 mdsio_writelocal - same as mdsio_writetile except works for local
3568 arrays
3569 write_local_r? - higher-level wrapper for mdsio_writelocal
3570 Controlled by diagFreq. Defaults to zero (ie. no dumps)
3571 Example given at end of mom_vecinv.F that dumps some local arrays.
3572 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
3573 control flux-form versus vector invariant code.
3574 Switch is runtime flag vectorInvariantMomentum (defaults to false)
3575 or genmake -DISABLE ...
3576 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
3577 (additional storing is now needed for case vecinv;
3578 currently nothing implemented to switch this storing off
3579 in case fluxform is used since no CPP flag available).
3580
3581 checkpoint40pre7
3582 o bug fix in dynamics.F
3583 calc_viscosity called before k=1,Nr loop.
3584 o added some #ifdef's ALLOW_PASSIVE_TRACER
3585 o cleaned initialisations in ctrl_map_ini
3586 related to TAF
3587
3588 checkpoint40pre6
3589 o split dynamics into thermodynamics & dynamics
3590 o corresponding split of calc_diffusivity into
3591 calc_diffusivity, calc_viscosity
3592 (kpp_calc_diff, kpp_calc_visc).
3593 o Added diffkr, kapgm to control variables
3594 o bug fix in gmredi_slope_limit for ldd97
3595
3596 checkpoint40pre5
3597 o proper initialization of Adams-Bashforth time stepping
3598 + uses forward step for very first step of model (iter=0)
3599 o re-generated *all* output since almost all output is modified by this
3600 change (sorry but we've been putting this one off for about 2 years)
3601 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
3602 *not* regenerated since they are already out of date and I don't
3603 want to create the impression that they are suddenly working.
3604 o removed KAP stuff for DEC's
3605 o modified/added many .cvsignore files in */code and */input
3606 o added new expt "solid-body.cs-32x32x1"
3607 + this uses an alternative form of ini_curvilinear_grid.F which
3608 is not necessarily any better than the current one...
3609
3610 checkpoint40pre4
3611 o added re-initialisations of utrans,vtrans,rtrans in
3612 calc_common_factors which are crucial for TAF.
3613 o extended iMin,jMin range for calc_common_factors,
3614 calc_diffusivity
3615 o added option ALLOW_PASSIVE_TRACER
3616 o a few minor updates and fixes
3617
3618 checkpoint40pre3
3619 o created calc_gtr1.F for gad package
3620 o split the_main_loop and re-introduced forward_step
3621 o some recomputations of nIter0 for TAMC
3622
3623 checkpoint40pre2
3624 o Updated to latest branch of AJA, JMC
3625 o Added gradient check package
3626 o Added routines for passive tracer handling
3627 o Added carbon sequestration sensitivity experiment
3628
3629 checkpoint39
3630 o Modifications and fixes to support TAMC
3631 (mainly missing or wrong directives)
3632 o Corrected common blocks when fooling TAMC to produce adjoint I/O
3633 in addummy_in_stepping
3634 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
3635 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
3636 o Included following packages:
3637 cal: calendar
3638 exf: external forcing
3639 ecco: essential routines to control use of cal, exf
3640 (NB: this is not the full ECCO environment)
3641 o disabled some packages by default in genmake
3642
3643 checkpoint38
3644 o see notes_c37_adj.txt
3645 o corrected wrong layer index in external_forcing_t
3646 o replaced the_main_loop/forward_step by the_main_loop
3647 o removed forceoutput from write_state
3648 (replaced criteria for initial/final state)
3649 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
3650
3651 checkpoint37
3652 o mdsio.F routine split and packaged in pkg/mdsio
3653 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
3654 used unless genmake -disable=mdsio)
3655 o allow a more precise surface-geopotential gradient for the atmosphere
3656 taking into account the change in space of Alpha (=1/rho) at the surface.
3657 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
3658 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
3659 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
3660 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
3661 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
3662 o Time-Average diagnostics defined as a pseudo package "timeave".
3663 o pickup files : old pickup (before c35) did not work with new code (c35
3664 and after) unless activating 2 commented lines in initialise-varia.
3665 o Non-Hydrostatic pickup file Pb fixed.
3666 o bug with Rigid-lid version (since c35) fixed.
3667
3668 checkpoint36
3669 o implement Crank-Nickelson barotropic time-stepping
3670 o recover Time-Average diagnostics
3671 o fix Pb in checkpoint (PR#19)
3672 o AIM become a standard package ; clean unused CPP_kees
3673
3674 checkpoint35
3675 o subtantial rewrite of dynamics.f
3676 o allows staggered time-stepping
3677 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
3678 o added bottom drag (linear + quadratic)
3679
3680 checkpoint34
3681 o Modified exchange routines for correct reverse simulation.
3682 o Added verification output to comply with bug fix in impldiff.F
3683 as of c33 (exp2, natl_box).
3684 o Corrected store directives in dynamics.F
3685 o Corrected array boundaries in impldiff.F
3686 o Corrected array dimensions in gmredi.
3687 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
3688 o Added routine GLOBAL_SUM_INT to global_sum.F
3689 o Added mdsio_gl.F for ECCO purposes.
3690
3691 checkpoint33
3692 o Fixed bug in lower BC in impldiff.F
3693 o Fixed confusion about units of forcing arrays in FFIELDS.h
3694 namely Fu,Fv,Qnet,Qsw,EmPmR:
3695 - Removed verification/natl_box/code/external_fields_scale.F
3696 (did not differ from that in model/src)
3697 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
3698 (see FFIELDS.h for description)
3699 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
3700 kpp_calc.F and kpp_transport_t.F
3701 - Removed model/src/external_fields_scale.F and calls to it
3702 - verification/natl_box uses flux data with "atmospheric" sign so
3703 a special version of external_fields_load.F is used to
3704 change the data as it's read in. This way, the arrays
3705 have the right units and signs at all times tha a user could
3706 possibly use them.
3707 o Corrected genmake to delete a temporary file during configuration
3708
3709 checkpoint32
3710 o Scaling of forcing fields moved from external_forcing.F to
3711 external_fields_scale.F, called directly after loading fields.
3712 o Surface relaxation terms added to surface tendency fields in
3713 extra subroutine.
3714 o impldiff.F changed to avoid storing by TAMC of huge intermediate
3715 fields.
3716 o Changes in GMRedi to comply with packaging structure.
3717 o Modifications and bug fixes in KPP package.
3718 o Verification experiment for KPP added (verification/nat_box/)
3719
3720 checkpoint31
3721 o Packages interface brought in line with defined standard
3722 -> new routines packages_...F
3723 -> changes in initialise_fixed.F, initialise_varia.F
3724 -> enables initialisation interface for ECCO package
3725 o Rescaling of external forcing fields immediately after read
3726 (removed from external_forcing.F)
3727 -> new: surface_fields_scale.F
3728 -> affects ini_foorcing.F, external_fields_load.F
3729 o Computation of surface tendencies before tendency updates.
3730 -> new: external_forcing_surf.F
3731 o Change of variable names useGMRedi, useKPP, useECCO
3732 o Further changes in dynamics.F, impldiff.F for TAMC
3733 o Tested for experiments 0, 2, 4.
3734 - not yet tested for GMRedi.
3735 - not yet tested for KPP.
3736
3737 checkpoint30
3738 o Updates for OBCs
3739 o New experiment for test OBCs (internal_wave)
3740 o New output.txt in verification/exp4/results/
3741 o Updates for KPP: calculation of viscosity corrected, new variables
3742 kpp_dumpFreq and kpp_taveFreq
3743 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
3744 and entry for T90 in genmake
3745
3746 checkpoint29
3747 o packaged KPP and GM/Redi
3748
3749 checkpoint28
3750 o Corrected initialization of hFacMin for difference vertical coordinates
3751 o Modified calculation of partial cell thickness to more robust algorithm
3752 o config_summary.F: replaced write_1D_... by write_0D_...
3753 read_write.F: added subroutines write_0D_...
3754 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
3755 included some initialisations required for TAMC.
3756 o routine calc_isoslopes: modified sqrt computation to make it
3757 differentiable for zero argument.
3758 o routines dynamics, impldiff:
3759 included store directives and tape key computations required for TAMC.
3760 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
3761
3762 checkpoint27
3763 o fixed calc_isoslopes() to so that cancellation of terms in tensor
3764 formulation works properly with variable resolution.
3765 o restructured the calling tree between the_model_main() and dynamics()
3766 o split initialise() into initialise_fixed() and initialise_varia()
3767 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
3768 in new routine ini_psurf()
3769
3770 checkpoint26
3771 o moved some #ifdef in optional routines to encompass everything
3772 except the argument declarations. This was using up some memory.
3773 o fixed macros like _ADT to work with both versions of Linux cpp
3774 o cleaned up some unused and uninitialized variables
3775 (helps when debugging with strict compile options)
3776 o split up CPP_EEOPTIONS.h into options and macros
3777 (macros are now in eesupp/inc/CPP_EEMACROS.h)
3778 o patch for 2 processor JAM mode
3779
3780 checkpoint25
3781 o updates for OBCs and NH
3782 o dramatically reduced memory usage
3783 o added "JAM" routines for use on Artic network
3784 o parameterization of convection by implicit vertical diffusion
3785 o added a diagnostic of convective index
3786 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
3787 (this is was partly for OBCs and NH but also in anticipation of
3788 an explicit free-surface option)
3789 o initial state input files for U and V
3790
3791 checkpoint24
3792 o Removed some spurious "REAL"s
3793 o Updated KPP to latest version from JPL
3794 o Added a COS(latitude) in horizontal viscosity
3795
3796 checkpoint23
3797 o Added del^4 diffusion for salt and temperature
3798 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
3799
3800 checkpoint22
3801 o Made many small changes: implicit none, format(i5), etc...
3802 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
3803
3804 checkpoint21
3805 o Introduced new I/O package that supports direct-access records (mdsio.F)
3806 o Split-up mid-level I/O routines
3807 o Updated input data for experiments 0,1,2,4 and 5
3808 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
3809
3810 checkpoint20
3811 o Tidied up open-boundaries some more
3812 o Added non-hydrostatic code
3813 o Fixed some input data
3814 o Modified MPI start-up to work in "coupled" context.
3815
3816 checkpoint19
3817 o Tidied up directory structure for verification experiments.
3818 o Added new code for open boundaries.
3819 o Corrected advective terms near boundaries.
3820 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
3821 o Implemented free-slip/no-slip BCs and del^4 dissipation.
3822 o Split default parameters out of ini_parms.F into set_defaults.F.
3823
3824 checkpoint18
3825 o Further changes for optional code generation with
3826 CPP - ugh!
3827
3828 checkpoint17
3829 o Beginning to incorporating modularity
3830 for supporting atmos. and ocean configs.
3831 o Small changes for TAMC complinace
3832 o New ultra simple test case. Barotropic box
3833 configuration "exp0".
3834
3835 checkpoint16
3836 o Minor changes to exchange routines to support
3837 accumulation in reverse mode. Adjoint of an
3838 assignment is an addition.
3839 o Changes to support compilation by TAMC (LR(1)
3840 syntax) and by g77 under Linux ( 72 character
3841 limit ).
3842
3843 checkpoint15
3844 Rewrote exchange routines to allow
3845 o General tile <-> tile connectivity.
3846 o TAMC reverse mode flag ( is this really needed? )
3847 o Variable width overlap and exchange region widths.
3848 o Hooks for sharing data via DMA, Arctic, Memory Channel,
3849 shmput/shmget, VIA, SYSV shmem and every other cool
3850 communication method.
3851
3852 checkpoint14
3853 Consistent isomorphism chages made. These allow dynamical core
3854 to support both pressure and meters as a vertical coordinate.
3855
3856 checkpoint13
3857 Release which corrects global_max problem and a couple
3858 of KGM time-averaging diagnostic errors. Also contains
3859 a double-gyre experiment setup as well as the baseline
3860 4 degree global template. The double gyre template is
3861 organised to allow it to be applied automatically to
3862 the baseline configuration.
3863
3864 branch-point-rdot
3865 A few tidy-ups have been made bt the real point of this
3866 check-point (excuse the pun) is to allow a branch to be
3867 made for the purposes of adding the rDot alterations.
3868 I don't want to commit the rDot to the main-trunk until
3869 we've actually tested it...
3870
3871 checkpoint12
3872 Tidy up and added generic genmake script (formerly
3873 configure script).
3874 Released to testers.
3875
3876 checkpoint11
3877 Re-arranged initialise() and introduced ini_vertical_grid()
3878 and ini_masks_etc().
3879
3880 checkpoint10
3881 Introduced the configure script.
3882 Separated out the diags package.
3883 Added template for writing time-averages of tile/intermediate quantities.
3884 Updated SIZE.h in exp2 and made the data big-endian.
3885
3886 checkpoint9
3887 MPI fix. Filename changes (meta/data). salbin*y stuff.
3888 General tidy-up.
3889 SST.bin SSS.bin added to verification/exp2
3890
3891 checkpoint8
3892 Inludes time-dependant forcing and time-averaging.
3893 Works at 4x4 and 2.8125x2.8125 global
3894
3895 checkpoint7-4degree-ref
3896 Branch from checkpoint7. Released for application to
3897 global modeling and general modeling - process studies, regional
3898 model etc..
3899 Configured for verification/exp2 - 4 degree global, two process.
3900
3901 checkpoint7
3902 Created by cnh
3903 Simple 4 degree global simulation
3904 configuration.
3905 Includes climatological wind,
3906 hydrography, bathymetry etc
3907 Does not include Heat Flux and E-P
3908
3909 checkpoint6
3910 Created by cnh
3911 merged checkpoint5 with CD and
3912 spherical polar code.
3913 Still some problems with GM Redi
3914 abd full topography.
3915
3916 checkpoint5
3917 Created by AJA
3918 contains updates to GM Redi
3919 and reordered timestepping loop
3920 for Implicit Diffusion.
3921
3922 checkpoint4
3923 Created by cnh
3924 Contains memory saving macros ( _rdxc etc..) for when
3925 grid variations are limited.
3926 Contains polynomial coeffs for EOS and knudsen program
3927 for generation.
3928
3929 checkpoint3
3930 Created by cnh
3931 Added extra flags for runtime options
3932 Added this file
3933 Added implicit free-surface
3934 Added pre-conditioner
3935 Put compare01 into repository ( compare01/... )
3936 Put data and eedata into repository ( verification/exp1 )
3937
3938 checkpoint2
3939 Created by AJA
3940 Added GM/Redi
3941
3942 checkpoint1
3943 Created by AJA
3944 Restructured kloop in dynamics.F
3945 Added non-linear EOS
3946
3947 baseline
3948 Original checked in code

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