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Revision 1.954 - (show annotations) (download)
Sat Feb 9 16:34:49 2008 UTC (16 years ago) by jmc
Branch: MAIN
CVS Tags: checkpoint59n
Changes since 1.953: +2 -1 lines
checkpoint59n

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.953 2008/02/05 15:49:01 jmc Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 checkpoint59n
8 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
9 number in dedicate array "hdiag":
10 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
11 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
12 - many small changes (integer format) for large number of diagnostics
13 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
14 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
15 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
16 usingSphericalGrid, this allows to define the rotated grid coordinates
17 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
18 geographical coordinates according to the inverse of the rotation defined
19 by the Euler angles, so that Coriolis parameter and online-interpolation by
20 exf works with the geographical coordinates on XC/YC/XG/YG.
21 Naturally, this feature does not work with all packages, so some
22 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
23 profiles), because there the coordinates are assumed to be regular
24 spherical grid coordinates.
25 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
26 - introduce isopycnal diffusion coefficient control.
27 o tools/adjoint_options:
28 - additional control vector components.
29 o pkg/mnc: have mnc create marginally meaning full coordinate variables
30 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
31 o pkg/mypackage:
32 - add example of read/write pickup for state-var ;
33 - add entry points to the main code for state-vars diags & write-pickup.
34 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
35 transitions for useExfYearlyFields
36 - add new subroutine that determines the file to read from for
37 use*YearlyFields = .TRUE. and .FALSE.
38 - add a verification experiment to global_with_exf that tests
39 useExfYearlyFields with USE_EXF_INTERPOLATION defined
40 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
41 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
42 subroutines (which could be generated from a template, because they are
43 almost identical), for now they are included in obcs_prescribe_read.F for
44 simplicity
45 o pkg/exf:
46 - add a little more diagnostic to exf_interp_read (in analogy to
47 mds_read_field, can be turned off with debugLevel < debugLevA=1)
48 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
49 ugly but fast by unrolling short inner loops, inserting a unroll=8
50 directive in routine lagran, and splitting a loop and making do while the
51 outermost loop (the latter requires the intoduction of index arrays)
52 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
53 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
54 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
55 o verification/seaice_obcs: updated for restart test and latest options
56 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
57 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
58 for now this is only available for the C-grid code and also within
59 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
60
61 checkpoint59m
62 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
63 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
64 o gad_som : fix flux output (& diagnostics) to have same units as other
65 advection scheme fluxes (was previously multiplied by deltaT).
66 o added verification/seaice_obcs both to test seaice open boundaries
67 and to provide an example matlab scrpt for generating them
68 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
69 o pkg/salt_plume: clean up salt_plume_frac.F to
70 remove redundancy in PlumeMethod 1 and 4
71 o pkg/kpp: added saltplume diagnostics
72 o pkg/obcs and pkg/seaice:
73 - do not set uice and vice to zero when OB*icefile are unspecified
74 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
75 - moved seaice tracer obcs after call to seaice_growth
76 o pkg/salt_plume: added various options for salt plume depth
77 criterion and for vertical distribution of the salt
78
79 checkpoint59l
80 o pkg/ptracers: new version of ptracers pickup:
81 read meta file and write only fields which are needed to restart.
82 ( same logic as main pickup file ; also using pickupStrictlyMatch )
83 o pkg/seaice:
84 - add timescale for melting due to warm mixed layer as a means of
85 setting SEAICE_availHeatFrac more conveniently
86 - add a CPP-flag/runtime parameter check for flooding algorithm
87 - reformulated availHeat in seaice_growth.F to be independent of AREA
88 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
89 unit changes
90 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
91 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
92 SX vector computer.
93 o pkg/seaice:
94 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
95 seaice forcing fields can now be read only through pkg/exf
96 - removed some unused halos
97 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
98 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
99 or U/VICE from U/VWIND before computing U/VSTRESS
100
101 checkpoint59k
102 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
103 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
104 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
105 all experiments pass when compile with un-initialised var. checking option.
106 o added pkg/salt_plume
107 o script to test restart (for now, in MITgcm_contrib/jmc_script)
108 o pkg/seaice: new read/write pickup version.
109 read meta file and write only fields which are needed to restart.
110 ( same logic as main pickup file ; also using pickupStrictlyMatch )
111 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
112 o lab_sea.hb87: modify the domain & update output.hb87.txt :
113 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
114 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
115 process. Fixed here by closing the domain at the Northern boundary.
116 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
117 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
118 a set of consecutive levels in/from a 3-D array.
119 o pkg/ptracers:
120 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
121 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
122
123 checkpoint59j
124 o in pkgs: dic, obcs, offline, rbcs:
125 standard way to compute coeff. for time interpolation between 2 time reccords
126 which retains full precision (& make results less dependent on compiler).
127 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
128 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
129 packages instead of reading ice cover and wind speed separately
130 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
131 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
132 to allow to compile customized code before the update)
133 o cleaning-up:
134 - fix CPP instruction syntax in pkg/obcs
135 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
136 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
137 - fix some threads issue in IO parts.
138 o pkg/dic:
139 - add tons of "_d 0" (--> much better testreports !)
140 and then update outputs of tutorial_global_oce_biogeo
141 o pkg/mom_fluxform:
142 add a special version of momentum advection intended to conserve momentum
143 next to a bathymetry step or a coastline edge. (default = off = #undef)
144 o new read/write pickup version:
145 - for now, only implemented for main (mdsio) pickup file.
146 - write out only what is needed to restart; merge pickup_nh , pickup_ph
147 and main pickup together.
148 - read meta file; read only what is needed to restart; stop if a field
149 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
150 if it make sense (even if the restart is not perfect).
151 - if no meta file, assume that pickup to read corresponds exactly to
152 a pickup that would currently be written.
153 - read pickup written in the old format (until checkpoint59i) if it
154 recognizes an old meta file (no field-list).
155 - add a meta file in exp. which starts from a pickup: 2 cases:
156 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
157 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
158 b) a meta file describing the content of the associated pickup file
159 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
160 o pkg/mdsio & pkg/rw:
161 - new routine to read a meta file ; new set of routine to read
162 Multiple-fields file (with meta file).
163 o added open boundary conditions capability for seaice
164 HSNOW, HSALT, UICE, and VICE
165
166 checkpoint59i
167 o adjoint:
168 * fix multiDimAdvection adjoint
169 (partial recomputation problem by TAF for fVerT(:,:,kDown)
170 and comlev1 size definition (maxpass vs. max. number of tracers)
171 * verification/global_ocean.90x45x15 adjoint now tests
172 NLFS and multiDimAdvection using DST3 (=30)
173 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
174 o pkg/kpp: add "_d 0" to real constant (if missing);
175 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
176 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
177 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
178 for internal parameters related to restart process (formerly from PARAMS.h)
179 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
180 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
181 as argument. (only atm2d & obcs write_pickup have not yet been updated)
182 o pkg/monitor:
183 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
184 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
185 - account for deep Atmosphere factor and density factor (anelastic)
186 o added open boundary conditions capability for seaice HEFF and AREA
187 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
188 thermodynamics
189 - requires a little reorganization, which affects the testreport results
190 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
191 so that now the conservative form is tested
192 - add a few comments
193 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
194 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
195 o add new diagnostics to seaice: advective, diffusive fluxes (only for
196 multidim-advection, for scheme 2 they are not filled) and transports,
197 thermodynamic growth rates
198 o change units of EmPmR (inside the code, + within coupling interface)
199 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
200 Affects results @ truncation level (cg2d match) and update output of
201 experiments: lab_sea(6), global_ocean.90x40x15(10),
202 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
203 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
204 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
205 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
206
207 checkpoint59h
208 o pkg/exf:
209 - improve vectorization by moving if-statement out of loops in
210 exf_mapfields, exf_radiation
211 - exf_bulkformulae.F: introduce 2D fields and vectorize code
212 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
213 o testreport:
214 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
215 monitor & update offline_exf_seaice exp. output.
216 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
217 o pkg/seaice:
218 - bug fix in the evp solver: boundary conditions were affected be
219 masking of zMax/zMin (changes results)
220 - minor bug fix in boundary conditions in seaice_calc_strainrates
221 (changes results for no_slip)
222 - seaice_lsr.F: make interpolation of eta dependent on boundaries
223 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
224 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
225 stress formulation and no-slip boundary conditions
226 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
227 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
228 o pkg/seaice: a first HSALT time stepping equation has been checked in
229 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
230 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
231 without requiring DO-IF statements
232 o pkg/thsice:
233 use continuous power-law function for partition of energy between lateral
234 melting/freezing and thinning/thickening ; old code using step function
235 still available with #undef THSICE_FRACEN_POWERLAW
236 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
237 o testreport: change AD testing : check against results/output_adm.txt
238 using same scripts as for forward test.
239
240 checkpoint59g
241 o adjoint testing: in preparation for changing testreport:
242 - output format: cost and grad written on separated lines
243 - ad output results in directory "results" (instead of "results_ad")
244 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
245 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
246 o pkg/ecco: allow user defined cost function contributions
247 o testreport:
248 Allow to choose (per experiment) the list of tested output variables
249 and the main variable (used to issue a pass/FAIL ) ;
250 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
251 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
252 Also modify printing of summary:
253 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
254 b) echo the list of tested variables in the individual summary.txt of
255 each experiment.
256 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
257 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
258 (but still depend on the tile decompostion of the domain).
259 o pkg/seaice: change a discretization detail to make the B-grid code
260 "more symmetric". This change is likely to remove all "ridges/leads" that
261 where quasi-aligned with the grid in B-grid solutions. It may also be
262 the solution to the stress coupling issues with the B-grid.
263 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
264 remove .cvsignore from input dir. (since testreport no longer run here).
265 o pkg/thsice:
266 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
267 - fix reshaping of sea-ice just after advection:
268 melt all the ice only if ice-volume is too small.
269 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
270 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
271 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
272 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
273 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
274 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
275 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
276 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
277 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
278 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
279 -> update output.txt
280 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
281 this affects truncation error: -> update output.txt of exp:
282 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
283 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
284
285 checkpoint59f
286 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
287 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
288 a bounded range (in forward mode)
289 o pkg/ecco, ctrl, autodiff and mom_common:
290 internal parameter controls, completements of implementations
291 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
292 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
293 (not seem any difference in testing results).
294 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
295 at face corners.
296 o pkg/generic_advdiff:
297 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
298 loop range indices for computing vertical advection tendency
299 and do the calculation in the interior only (no overlap) ;
300 for now, only implemented for SOM advection (to save CPU time).
301 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
302 o exch2 adjoint
303 First set of changes:
304 - add exch2 hand-written adjoint templates
305 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
306 This will require cleanup in pkg/autodiff/*.F
307 (changed routines currently kept separate in verif. code/)
308 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
309 that used to hide exch2 or cubed-sphere specific code
310 (commented via 'cph-exch2')
311 o pkg/seaice
312 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
313 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
314 output of global_ocean.cs32x15.thsice .
315
316 checkpoint59e
317 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
318 for B-grid vector (not yet tested) and C-grid vector (<- only used
319 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
320 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
321 (#ifdef ALLOW_SALT_PLUME)
322 o gather_2d/scatter_2d: removed halo regions
323 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
324 scheme and the corresponding test case (under front_relax dir). For now,
325 only available with Skew-flux form and not yet tested in realistic set-up.
326 adjoint: store directives updated, but gradient checks deteriorated,
327 so maybe GM/Redi adjoint is now broken.
328 o seaice adjoint
329 * add AREA, HEFF, HSNOW as control variable
330 (should not change lab_sea results)
331 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
332 o pkg/seaice:
333 * added computation of saltFlux in seaice_growth;
334 For time being, sea ice salinity is assumed constant
335 contribution of snow flooding to freshening of sea ice is neglected.
336 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
337 defaults to 0.0 in order to maintain backward compatibility.
338 Typical values for SEAICE_salinity are 4 to 10 g/kg.
339 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
340 * added SEAICE_availHeatFrac, which specifies fraction of surface level
341 heat content used to melt or grow ice
342 * commented out cap of HICE: it helps keep ice thinner
343 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
344 * applied OBCS T/S mask to HEFFM sea ice mask
345
346 checkpoint59d
347 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
348 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
349 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
350 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
351 and change default value of parameter "GM_Small_Number";
352 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
353 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
354 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
355 o pkg/ecco: cost function when applying pkg/smooth to controls
356 o pkg/ctrl: add forcingPrecond run time parameter
357 o pkg/seaice:
358 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
359 - fix bug in metric terms of u-equation in LSR solver (implicit part),
360 changes verification/lab_sea
361 - rearrange implicit part of u-equation in LSR solver to make it easier to
362 read, understand, and debug. This causes changes at the truncation level.
363 - fix (serious) bug in the boundary conditions (sign error in the implicit
364 part) of the LSR solver. Changes all LSR results.
365 - fixed problem with HSNOW initialization to avoid thick snow when AREA
366 is initilized with small values - does not change lab_sea results.
367 - added HsnowFile initialization capability
368 o pkg/smooth: addition to model/src and pkg/ctrl so allow
369 initialization of pkg/smooth and application to control vector
370 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
371 o dependencies: pkg/profiles requires pkg/cal
372 o pkg/profiles:
373 - added option ALLOW_PROFILES_GENERICGRID
374 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
375 that interpolation information (grid points and coefficients) is provided
376 within the netcdf input files.
377 -> sample matlab scripts can be found in MITgcm_contrib/gael
378 that allow you to prepare netcdf input files.
379 - also modified: cleaner include statements, cleaner error print statements,
380 cleaner stops when error, and more tests of the netcdf input files consistency.
381 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
382 o pkg/seaice:
383 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
384 requires a new routine: seaice_diagnostics_fill.F
385 - make sure that seaice does not move if not forced (pressure replacement
386 method, Hibler and Ip, 1995), changes results
387 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
388 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
389 It is turned off by default (=-1.), because it changes the results.
390 - make it possible to read AREA from a file, too.
391
392 checkpoint59c
393 o add S/R and diagnostics for oceanic mixed-layer depth
394 o move GMRedi call after all vertical mixing schemes (including KPP)
395 o pkg/thsice:
396 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
397 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
398 o pkg/obcs:
399 - bug fix for balance code
400 o pkg/seaice:
401 - allow values of SEAICE_elasticParm > 1
402 - add new parameter SEAICE_evpTauRelax as an alternative
403 to SEAICE_elasticParm
404 - make lsr boundary conditions free slip (by default), changes result
405 - add code for no slip boundary conditions for lsr
406 - set minimum of zeta to zero (and not 4e8) (changes results)
407 - add a cap on AREA after advecting AREA if seaice_growth is not called
408 o change calculation of Visbeck K:
409 - no longer depend on tapering scheme; instead, compute slope (limited
410 by GM_maxSlope). this is equivalent to what was comuted before with
411 clipping or linear tappering.
412 - fix vertical averaging (wrong by 1/2 level)
413 - leave the old version (but will not be maintained) within
414 #ifdef OLD_VISBECK_CALC / #endif
415 - update output of exp. ideal_2D_oce
416 o change error catch in calc_r_star to improve vectorization
417 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
418 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
419 o adjoint:
420 Re-organized adjoint checkpointing according to Matt Mazloff
421 (but with modifs/completions/cleanups)
422 Storing is now bundled into large arrays to optimized I/O
423 (and second step in cleanup of the_main_loop)
424
425 checkpoint59b
426 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
427 - export/import (between ocean & coupler) fields needed for ocean DIC.
428 o pkg/seaice:
429 - get rid of three more exchanges seaice_calc_viscosities (required
430 different loop boundaries in seaice_lsr and seaice_ocean_stress)
431 - bug fix in seaice_ocean_stress (update of lab_sea required)
432 - reduce loop boundaries to necessary minimum also in seaice_evp
433 - go back to the old way of computing deltaC/Z as the adjoint likes that
434 better
435 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
436 passive tracer to an Age Tracer) + update output.txt
437 o pkg/exf:
438 - implement A-grid / C-grid selection for wind-stress input files.
439 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
440 for now, in exf_bulk_largeyeager04.F only :
441 - change implementation for case where windspeed + 2. components wind-stress
442 are read-in. AND use rhoConstFresh to convert evap.
443 o pkg/seaice:
444 - use correct EXCH_UV for wind-forcing (on A-grid).
445 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
446 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
447 o pkg/exf:
448 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
449 EXF_INTERPOLATION:
450 - merge global_with_exf/code version of exf_interp_read.F
451 to the main code ;
452 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
453 reading the file ; Important: This options needs to be defined to recover
454 previous code.
455 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
456 - no longer loose real*8 precision along the way when using exf_iprec=64.
457 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
458 - change discretisation of evp-solver in order to avoid another exchange
459 (changes lab_sea) and clean up a little
460 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
461 help the adjoint (this also changes the results slightly)
462 - add a few "_d 0" where they had been missing in seaice_evp.F
463 - cleaning up: remove unused seaice_calc_rhs.F
464 o pkg/exf: some cleaning-up:
465 - change various "constants" into runtime parameters
466 - cleaned-up Large&Yeager04 routine which should eventually
467 replace exf_bulkformulae.F (changed names of S/R and CPP)
468 and merged various ALLOW_ATM_WIND options
469 only used with thsice pkg (in thsice_get_exf.F):
470 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
471 which are used when useStabilityFct_overIce=TRUE (= the default)
472 - change default values of ice & snow emissivity and scale downward LW
473 by ice & snow emissivity.
474 o pkg/thsice:
475 fix few little problems, in thsice_calc_thickn.F:
476 - growth vertically (and not laterally) if iceFrac == iceMaskMax
477 - melt only laterally if hIce < hThinIce (as the comments say)
478 and in thsice_extend.F:
479 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
480 - start to form ice as soon as the minimum ice-volume is reachable.
481 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
482 and cpl_aim+ocn
483 o pkg/kpp
484 - move computation of surface related input fields to KPP into a new
485 subroutine kpp_forcing_surf.F
486 - remove wrong (within bi,bj loops) EXCH calls.
487 - little cleaning (add argument myThid in last position, cvs header ...)
488 - for now, fix conservation problem by exchanging KPPviscAz (may not
489 be the best fix)
490 o pkg/seaice
491 - check for inconsistent evp parameter/cpp-flag combination
492 - remove leftover errIO flat for obsolete name list error handling
493 o OpenAD
494 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
495
496 checkpoint59a
497 o pkg/seaice: some parameter clarifications and a little bit of clean up
498 o pkg/thsice: rename run-time parameters:
499 himin -> hIceMin
500 himin0 -> hThinIce
501 hihig -> hThickIce
502 i0 -> i0swFrac
503 transCoef -> bMeltCoef
504 frac_energy -> fracMelting
505 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
506 with default values (for now) that do not change the results.
507 remove old version of thsice vars advection in pkg/seaice.
508 o in FFIELDS.h:
509 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
510 - make pLoad & sIceLoad always available (but still only used if
511 ATMOSPHERIC_LOADING is #define).
512 o pkg/kpp: replaced _KPP_RL with _RL
513 o bug fixes for vertical diffusivity computations when both KPP and
514 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
515 are no longer updating the vertical diffusivity array
516 (passed as argument) but are (re-) setting those arrays.
517 o pkg/seaice: fix bug in evp solver, while doing that
518 - change (improve?) discretization of stress computations for both
519 cgrid-lsr and evp solver
520 - add a new routine to compute strain rates
521 - the above changes lab_sea results
522 - add no slip conditions for evp solver (off by default), lsr-version
523 may follow
524 - fix exchange for shear at Z-points (does not change lab_sea)
525 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
526 (to force the user to pick a time step since there is not "safe" way
527 of choosing it)
528 - add principal stress diagnostics
529 - rearrange fields for evp a little to avoid having to call a: too many
530 exchanges and b: exchanges for stress trensor components which we do
531 not have.
532 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
533 of evp, complete rewrite for lsr case (latter is does not yet work
534 in all cases)
535 o pkg/kpp: add code to have mixing in shelf ice caverns
536 - add myThid to all kpp routines (long overdue)
537
538 checkpoint59
539 o pkg/exf:
540 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
541 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
542 - move exf header files from lower_case.h to UPPER_CASE.h ;
543 add missing cvs Header & Name
544 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
545 - add namelist param. selectStressGridPosition, exf_monFreq
546 - retire many _CLIM routines, and remove data.exf_clim
547 + params moved to data.exf
548 + climsst, climsss now handled by exf_set_gen, i.e.
549 climss?period=0 refers to constant field,
550 climss?period=-12 to monthly forcing
551 - split up namelists in data.exf
552 o pkg/seaice:
553 - remove seaice_exch and seaice_exch_uv
554 - remove superfluous exchange of theta
555 - add myThid to seaice_budget_ocean/ice
556 - add new interface for atmospheric wind forcing (C-grid only)
557 + new routine
558 + two new field (taux, tauy for stress over ice)
559 + removed one global field (DAIRN) for C-grid case only
560 o pkg/thsise
561 - 2nd set of modifs for thsice adjoint in conjunction with exf
562 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
563
564 checkpoint58y_post
565 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
566 vertical diffusivity, similar to that in MOM4; turned on using
567 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
568 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
569 o Added capability for 3D specification of background vertical diffusion
570 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
571 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
572 "data" file that contains the 3D vertical diffusivity coefficients.
573 o ice dynamics (pkg/seaice) with thsice thermodynamics:
574 - add code within pkg thsice to advect & diffuse sea-ice fields
575 similar to (and will replace) what has been added in seaice_advdiff.F,
576 but: - conserving Mass, Heat & Salt.
577 - better when using non-linear advection scheme (not yet fully tested)
578 - can also be used in atmospheric set-up (for now, only the diffusion).
579
580 checkpoint58x_post
581 o IO option for global-file compact format:
582 - add options when generating topology (utils/exch2/matlab-topology-generator)
583 - add I/O capability (pkg/mdsio).
584 - adapt utils/matlab/rdmds.m to read this format.
585 for now long-line format not yet supported by pkg/mdsio (& exch2).
586 o shelfice: add a few diagnostics
587
588 checkpoint58w_post
589 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
590 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
591 (and replace horiVertRatio in NH code).
592 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
593 and tutorial_plume_on_slope (sensitive to truncation)
594 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
595 directly to drive seaice model (C-grid only)
596 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
597 - reintroduce computation of wind from stress,
598 - compute tau (in exf_bulkformulae.F) from windstress averaged to
599 mass points to avoid tau = 0
600 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
601 o rdmnc.m: make it work with "global" files created with gluemnc
602 o rdmnc.m : some improvements in dealing with singleton dimension
603 (tested on all testreport mnc output files).
604 o genmake2: disable pkg/profiles if netcdf test fails.
605 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
606 o move call to cal_readparms up to make calendar parameters/variable available
607 to all packages
608
609 checkpoint58v_post
610 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
611 useDynP_inEos_Zc tested.
612 o pkg/exf: changes to properly interpolate/mask/scale initial fields
613 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
614 and portions thereof. See read_cs.txt for description and examples.
615 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
616 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
617 following the great-circle arc between those 2 points.
618 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
619 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
620 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
621 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
622 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
623 - still needs work (not working with some options ; efficiency to improve)
624 and serious testing.
625 - use this scheme for temperature & salinity in 2 advection test exp.:
626 advect_xy & advect_xz, respectively.
627
628 checkpoint58u_post
629 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
630 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
631 o testreport: add option "-skipdir" to skip some test.
632 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
633 momentum calculation.
634 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
635 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
636 remove checkpoint.F and the_correction_step.F (no longer used);
637 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
638 o add option (linFSConserveTr) to correct for tracer source/sink due to
639 Linear Free surface
640 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
641 o pkg/thsice: fix reading mnc-pickups
642
643 checkpoint58t_post
644 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
645 o pkg/mdsio:
646 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
647 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
648 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
649 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
650 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
651 either MDS_READ_FIELD or MDS_WRITE_FIELD )
652 - new S/R (to replace MDSWRITEMETA), which allows to write more
653 informations (variable names, time ...) to meta files.
654 - modify rdmds.m to give back the meta file content.
655 o pkg/diagnostics: change vertical interpolation to be safer, and more
656 flexible (define p-levels to interpolate to in data.diagnostics);
657 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
658 diagnostic pointer.
659 o pkg/seaice: more cleaning up of seaice_growth, added many comments
660 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
661 o fix multi-category seaice:
662 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
663 SEAICE_MULTICATEGORY
664 - fix short wave heat flux
665 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
666 and allow to use EVP solver. Change forward lab_sea: test both EVP
667 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
668 o Initial check-in of lab_sea adjoint
669 (very similar to natl_box_adjoint/code_seaice)
670 * used C-grid and EVP solver
671 * used KPP, GM/Redi
672 * uses inAdExact=.TRUE.
673 * gradient checks fail for both ADM and TLM
674 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
675 f.d. gradients actually seem more problematic than ADM, TLM gradients;
676 issue is related to forward mismatch between g77 an ifort
677 o pkg/seaice: overhaul of thermodynamics
678 - growth.F and groatb.F are replaced by new routine seaice_growth.F
679 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
680 - move a few global fields out of SEAICE.h into seaice_growth.F and
681 make them 2D (FICE/QNETO/ ...)
682 - remove FO (it is the same as QNETO)
683 - introduce a few local fields to avoid modifying external fields such
684 as atemp, etc.
685
686 checkpoint58s_post
687 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
688 changed exf_set_gen.F so that
689 genperiod=0 means input file is one time-constant field and
690 genperiod=-12 means input file contains 12 monthly means
691 o CG2D: use pre-computed solver main-diagonal (stored in common block);
692 this affects truncation error ; generate new output file for exp. which
693 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
694 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
695 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
696 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
697 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
698 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
699 o start implementation of deep-atmosphere and anelastic formulation
700 o verification: remove 2nd copy of input files and use script "prepare_run"
701 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
702 o mom_common/vecinv/fluxform: fix a few initialisation isssues
703 o profiles: fix for multithreaded case
704
705 o diagnostics: rename few diags:
706 s/'PRESSURE'/'RCENTER '/g
707 s/'TICE '/'oceFreez'/g
708 s/'TAUX '/'oceTAUX '/g
709 s/'TAUY '/'oceTAUY '/g
710 s/'SWFLUX '/'oceQsw '/g
711 s/DIFx/DFxE/g
712 s/DIFy/DFyE/g
713 and add few ocean-forcing diagnostics:
714 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
715 o modifications to pkg/seaice/growth.F and budget.F, which change results of
716 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
717 as actual snow thickness. It now refers everywhere to effective snow
718 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
719
720 checkpoint58r_post
721 o modifications to pkg/seaice/growth.F, which change results of
722 lab_sea experiment: fixes pertain to melting snow over open water, to
723 masking EVAP under sea ice, and to using the correct AREA variable for
724 computations of EVAP, PRECIP, HSNOW, and GHEFF
725 o add ability to read bathy, salt, and theta using MNC (off by def)
726 o add flooding algorithm and advection of HSNOW for pkg/seaice;
727 both are turned off by default and do no change any results
728 o seaice advection with pkg/thsice: a step toward the use of non-linear
729 advection scheme, but #ifdef or commented out for now (requires more EXCH).
730 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
731 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
732 in natl_box (affects results @ truncation level: update output.txt)
733 o multi-threading and IO:
734 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
735 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
736 (needed to work with SingleCpuIO): tested in all verif. exp.
737 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
738 affects the results (but none of the verification test uses this scheme).
739 o Adding some pkg/diagnostics capability to pkg/seaice
740 (will certainly be subject to changes)
741 o ctrl: adding new control variables:
742 lwflux, lwdown, evap, snowprecip, apressure, runoff
743
744 checkpoint58q_post
745 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
746 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
747 high_res_cube configuration by 4% on Columbia.
748 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
749 add (in global_with_exf/code) a version of EXF_INTERP_READ without
750 dynamical allocation (seems to work in multi-threaded).
751 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
752 single CPU io) so that TAF does not have to see EESUPPORT.h
753 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
754
755 checkpoint58p_post
756 o obcs: stop if obcs is used with useCDscheme = .true.
757 o shelfice:
758 - fix a sign error so that no slip at shelfice interface works
759 - remove stop for combination non-hydrostatic code and shelfice. That does
760 not mean, that the results are correct, but at least they are numerically
761 stable
762 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
763 o added adjoint exch routined for all exch*3d* routines
764 and updated flow directives
765
766 checkpoint58o_post
767 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
768 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
769 o change controling S/R for writing pickup file (new S/R do_write_pickup)
770 and clean-up reading/writing of pickup files.
771 o fix local version of read/write pickup (NH part) in rotating_tank/code
772 o simplify EXCH interface:
773 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
774 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
775 o added the regrid package
776 o shelfice:
777 - add a simple boundary layer scheme to reduce noise
778 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
779
780 checkpoint58n_post
781 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
782 local variable (not in common block).
783 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
784 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
785 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
786 to work with SingleCpuIO.
787 o add "_d 0" to real constant of pkg/cfc subroutines ;
788 update exp. cfc_exemple & tutorial_cfc_offline output files.
789 o multi-threading and IO:
790 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
791 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
792 - barrier before and after reading.
793 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
794 - avoid using MDS_WRITELOCAL for LAND pkg output.
795 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
796 common-block variables ; Allows multi-threading with master-thread IO.
797 o change default MAX_NO_THREADS from 32 to 4 ;
798 and stop cleanly when MAX_NO_THREADS is too small.
799 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
800
801 checkpoint58m_post
802 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
803 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
804 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
805 keep global_ocean.90x40x15 (for AD testing) with former secondary test
806 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
807 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
808 add MITgcm_tutorials (= code + all the tutorials)
809 o ecco, option to compute cost for total ssh (mean+anom)
810 o consistent with addition of ptracer and ssh in pkg/profiles
811 o profiles: adding ptracer and ssh
812 o testreport: change multi-test output-file name
813 (from output.txt.{name} to output.{name}.txt)
814 o profiles: now ok for mutli-tiles case
815 o seaice: add 4 parameters for different advection schemes for area,
816 (effective) seaice thickness, enthalphy, and snow height. Their default
817 is the standard parameter SEAICEadvScheme
818 o calc_gw:
819 - add cosFacU in zonal viscous flux (harmonic.visc.).
820 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
821 of tutorial_plume_on_slope.
822 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
823 o calc_gw: true flux-form, account for horizontal grid spacing.
824 update rotating_tank results, but not plume_on_slope (affected at
825 truncation level, 11 digits).
826
827 checkpoint58l_post
828 o calc_gw:
829 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
830 - remove side-drag for now (need to fix it); update plume_on_slope results.
831 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
832 o commit code to make SST/SSS weights spatially variable
833 (based on either variable in-situ or variable initial T/S weights)
834 o pkg/ecco:
835 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
836 now based on horizontally varying weights wthetaLev, wsaltLev
837 * cost_averagesflags now returns year indices in addition to day, month
838 * sflux balance is performed on annual basis
839 (sflxumm, sfluxmm2, bal_sfluxmm)
840 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
841 including separate counting and multipliers
842 o pkg/rbcs
843 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
844
845 checkpoint58k_post
846 o testreport:
847 - always build in dir. "build" (if not there, mkdir build instead of building
848 & running in input)
849 - run in dir run (if it exists), in build otherwise.
850 - call prepare_run (if input/prepare_run exists)
851 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
852 o pkg/exf modifications to interpolation and rotation routines for more
853 reasonable treatment of North Pole singularity: for tracers North Pole
854 value is set to northernmost zonal-mean value, for zonal velocity it is
855 set to zero, and for meridional velocity it is set to northernmost value.
856 o pkg/exf/exf_check_range.F
857 - add tile index to diagnostics and move stop statement to the very
858 end of the routine.
859 o pkg/diagnostics: (diagnostics_main_init.F)
860 define title of isomorphic variables according to the current config.
861 o pkg/thsice with pkg/seaice dynamics:
862 - fix domain of computation (interior only, required for exf) and do exchanges
863 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
864 o towards a standard way of dealing with multi-threading in MONITOR
865 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
866 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
867 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
868 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
869 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
870 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
871 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
872 o tracer advection:
873 - clean-up and simplify calc_common_factors.F
874 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
875 advection subroutine (but still not used within DST advection S/R)
876 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
877
878 checkpoint58j_post
879 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
880 from file (collects calls previously in FORWARD_STEP)
881 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
882 o adjoint store dir. adjusted accordingly
883 o genmake2
884 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
885
886 checkpoint58i_post
887 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
888 on wind stress (SEAICEstressFactor defaults to 1.)
889 o Total number of Timers is finite (<=40): comment out 2 non-essential one
890 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
891 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
892 on CS-grid: no longer loosing mass.
893 o exf & curvilinear-grid: no longer modify longitude xC & xG.
894 o pkg/ggl90: fix sloppy output and fix a bug
895 o pkg/seaice: added SEAICEuseEVPpickup parameter
896 - Set to false in order to start EVP solver with
897 non-EVP pickup files when using SEAICEuseEVP
898 - fix sign error in diffusion in seaice_calc_rhs
899
900 checkpoint58h_post
901 * Modifications for bottom topography control
902 o replace hFacC by _hFacC at various places
903 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
904 o add non-self-adjoint cg2d_nsa
905 o update autodiff support routines
906 o re-initialise hfac after ctrl_depth_ini
907 o works for 5x5 box, doesnt work for global_ocean.90x40x15
908 * Adding verification for 5x5 box (4-layer) bottom topography control
909
910 checkpoint58g_post
911 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
912 used for mean seasonal cycle, mean diurnal cycle); add an example
913 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
914 o pkg/ggl90:
915 - add parameter (minimum surface kinetic energy)
916 - fix bug (avoiding division by zero)
917 o couple pkg/thsice to pkg/seaice:
918 - modify advection in seaice to accomodate new scalar fields to be advected
919 - only muliDimAdection scheme work with seaice/thsice
920 - mapping of thsice-variables to seaice-variables, back and forth
921 - does not break the verification experiments, but does not give the
922 desired results either
923 o pkg/seaice
924 - make (default) second order advection a bit less confusing?
925
926 checkpoint58f_post
927 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
928 to pkg/seaice):
929 - new routines thsice_map_exf and thsice_get_exf provide the interface
930 - add an additional formal parameter to thsice_solve4temp
931 o pkg/exf:
932 - add new fields wspeed, snowprecip (to be able to couple to thsice)
933 - correct Stefan-Boltzmann constant
934 - new parameter for longwave surface emittance
935 - separate some stuff from exf_bulkformulae into new routines
936 exf_radiation, exf_wind
937 - add new parameters and constants: longwave emissivity for ocean, ice
938 and snow, evaporation parameters over ice
939 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
940 either wind from stress or stress from wind
941 o pkg/thSIce:
942 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
943 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
944 and THSICE_CALC_THICKN
945 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
946 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
947 to make debugging easier.
948 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
949 o pkg/bulk_force:
950 - clean-up comments and parameters ;
951 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
952 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
953 generate new output for test-experiment: aim.5l_cs.thSI
954 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
955 testreport accordingly
956
957 checkpoint58e_post
958 o SEAICE_CGRID adjoint done
959 o R_STAR adjoint implemented.
960 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
961 * need to sort out init. of h0facc, etc.
962 o Make pkg/profile fully independent of ecco,cost, etc. stuff
963 to be able to use it in pure forward.
964
965 checkpoint58d_post
966 o upgrade simple test-experiment to tutorial example:
967 step.1: duplicate the experiment and (step.2) will remove the old copy.
968 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
969 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
970 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
971 tutorial_global_oce_biogeo <- copy of dic_example
972 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
973 tutorial_plume_on_slope <- copy of plume_on_slope
974 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
975 tutorial_global_oce_optim <- empty for now (David ?)
976 tutorial_global_oce_in_p <- copy of global_ocean_pressure
977 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
978 o correct a sign problem in cost_scat.F
979 o obcs and ptracers: fix boundary conditions for advections schemes
980 with larger stencil
981 o thsice adjoint: start
982 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
983 completeness
984 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
985 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
986 o ptracers adjoint:
987 * avoid extensive recomputatations
988 * fix missing re-init. of gptr (missed by TAF)
989 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
990 me to turn off the excessive output to STDOUT that this package produces
991 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
992 and add those terms in Vector-Invariant formulation.
993 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
994 if the control period (xx_hfluxperiod etc) is 0
995 o in profiles pkg, clean routines and fix details
996 o in ecco pkg, reading ssh data:
997 fix problem in case the model does not start at iter0=0
998 o fix mnc-pickup/restart for ptracers
999 o new package prifiles:
1000 code to compute profile-based cost by Gael Forget
1001 (modifs in ecco, ctrl, autodiff)
1002 o Benign bug fix in initialization (spotted by M. Mazloff) of
1003 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
1004
1005 checkpoint58c_post
1006 o adjoint: finish NLFS adjoint and provide reference output in
1007 verification/global_ocean.90x40x15/results_ad_nlfs
1008 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
1009 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
1010 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
1011 with SEAICE_CGRID defined.
1012 o move calendarDumps from "data" to "data.cal" and clean-up the code
1013 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
1014 o add useEXF & useCAL flags (for now, set in hard-coded way)
1015 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
1016 (were missing in NH mode, and wrong in quasihydrostatic mode).
1017 waiting for Chris updated version of calc_gw to add those CALLs.
1018 o fix bug in quasihydrostatic S/R ;
1019 add a test for this option: global_ocean.90x40x15.qshyd
1020 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
1021 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
1022 o add on/off flag useOffLine for package OFFLINE
1023 o seaice:
1024 - modify advection so that it works also on the C-grid
1025 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
1026 problem in multi-tile runs with C-grid
1027 - add flags for clipping ice velocities and/or masking solver forcing
1028 - fix drag (ocean on ice) formulation and a bug that caused noise in the
1029 C-grid solver
1030 - added a few comments to seaice_diffusion.F
1031 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
1032 are now exclusive)
1033 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
1034 required re-ordering the code a little:
1035 + make DAIRN global variable (defined in SEAICE)
1036 + move computation of the viscosities eta and zeta into a new separate
1037 routine (because I need to recompute them in seaice_ocean_stress.F)
1038
1039 checkpoint58b_post
1040 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
1041 update output.txt of exp. aim.5l_cs.thSI
1042 o various mnc cleanups and improvements:
1043 + shrink lookup tables by factor of ~4
1044 + better error reporting when running out of lookup space
1045 + able to handle longer path/file names (up to 500 chars)
1046 o adjoint:
1047 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
1048 - TBD: "hidden" mom_vecinv recomp. in dynamics
1049 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
1050 (allow to differentiate between forcing components using new integer flags:
1051 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
1052 and add new flag to put Dissipation tendency out of Adams-Bashforth.
1053 o ecco
1054 - enable trend removal from SSH anomaly obs.
1055 o adjoint
1056 - a fix for PmEpR when #undef EXACT_CONSERV
1057 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
1058 - try to fix "hidden" recomp. in forward_step for NLFS
1059 (NLFS seems broken sometimes after I checked it in)
1060 o seaice:
1061 - add c-grid version of the dynamic solver:
1062 + three new routines that are the c-grid substitute lsr, dynsolver
1063 and ostres
1064 + put a few fields that were local to dynsolver into global common
1065 blocks, so that I can move the computation of stresses etc into
1066 seaice_lsr (saves coding but may break the adjoint).
1067 - replace more hardwired parameters by runtime parameters
1068 - add ice masks that mask the rhs of the implicit solvers where there
1069 is no ice (commented out in seaice_dynsolver, because i am not sure
1070 if this works properly), eventually this should replace the clipping
1071 of ice velocities in seaice_dynsolver to +/-40cm/s.
1072 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
1073 include it only where its needed
1074 o move balancing of fluxes before the call of external_forcing_surf
1075 o seaice:
1076 - correct units of turning angles (now they are really in degrees)
1077 - move computation of GWATX/Y out of main routine into dynsolver
1078 - initialize GWATX/Y in seaice_init
1079 o Apply mask on Fresh-Water flux (needed for SSH forcing).
1080 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
1081 o seaice: add runtime flags for turning angles (default to zero)
1082 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
1083 and trend from exf forcing and ctrl control adjustments
1084 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
1085 (since checkpoint57x_post)
1086 o change the default rotation period to 86164.s = the Earth rotation
1087 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
1088 and based on a reference stratification. Tested within hs94.cs-32x32x5.
1089 o seaice advection: add code for choosing between the default (2nd order
1090 central differences) and multiDim advection schemes provided by
1091 pkg/generic_advdiff
1092 o seaice:
1093 - removed all references to SEAICE_GRID.h fields from
1094 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
1095 (cubed-sphere configuration will change a little)
1096 - grid computations in seaice_init are obsolete now.
1097 - cleaned up code a little so that is easier to read (hopefully).
1098 - added new (better?) discretizations of default advection and diffusion
1099 (turn on with SEAICEuseFluxForm)
1100 - replace 1 in 3d global fields by kSurface in growth.F
1101
1102 checkpoint58a_post
1103 o seaice:
1104 - bug fix in advect.F
1105 o shelfice:
1106 - separate shelfice load anomaly from pload (breaks with time
1107 dependent forcing), => introduce constant field shelficeLoadAnomaly.
1108 Its default is 0., but it may be computed more cleverly from (unknown)
1109 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
1110 done offline. A good approximation of the pressure load anomaly is
1111 necessary to avoid large initial adjustment processes underneath
1112 deep-reaching shelfice.
1113 - small fix in ISOMIP shelfice_thermodynamics
1114 - add more sophisticated thermodynamics of Hellmer (1989), this is
1115 now the default
1116 - give a few constants more intuitive names
1117 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
1118 if bulk formulae are used in long integration (especially EmPmR). Turn
1119 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
1120 if balancePrintMean, the imbalance that is substracted is printed to
1121 STDOUT.
1122 o fix bug (typo) in obcs_apply_eta.F
1123 o add a new package shelfice which enables us to model the circulation
1124 underneath shelf-ice with draughts of hundreds of meters.
1125 - works
1126 - to do: + include improved thermodynamics
1127 + check whether kSurfC (from model/inc/SURFACE.h) can be used
1128 instead of new field kTopC
1129 + can we use topoFile, Ro_surf and existing code in ini_depth.F
1130 instead of new field R_shelfIce and new code in ini_depth.F
1131 and ini_mask_etc.F?
1132 + adjust vertical mixing schemes?
1133 o seaice pkg:
1134 - add a cpp-flag to include a simple formula for a salinity dependent
1135 freezing point of sea water at the surface
1136 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
1137 meridional stresses are now different (and hopefully correct)
1138 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
1139 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
1140 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
1141 o pkg/diagnostics: add options and parameters for regional-statistics
1142 diagnostics ; define regions by reading a region-mask from a file
1143 (might add other options later)
1144 o pkg/bulk_force:
1145 - add option and parameters to use AIM surface-flux formulae.
1146 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
1147 others forcing fields (defined in PARM05, parameter file "data") are loaded
1148 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
1149 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
1150 - use the right EXCH call for uwind,vwind (to work on CS-grid).
1151 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
1152 and parameters (note: calcWindStress replaces .NOT.readwindstress).
1153 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
1154
1155 checkpoint58
1156 o add "--embed-source" option to genmake2 which, when the supporting
1157 tools can be compiled (as determined by genmake2) will turn on the
1158 embed_files package which then embeds the entire MITgcm source code
1159 (*.[fFhc] + Makefile) used for the build within the executable
1160 - requested by CNH but off by default
1161 - adds a paltry <9MB to the mitgcmuv executable in most cases
1162 - only writes the output when useEMBEDSRC in eedata is true
1163 o clean up 3-dim. relaxation codes:
1164 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
1165 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
1166 * Thanks to Tom Haine for testing!
1167
1168 checkpoint57z_post
1169 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
1170 affects output (@ truncation level) of exp. plume_on_slope ; updated.
1171 o fix the pickup behavior for obcs in combination with ptracers
1172 o fix a bug in ptracers_external_fields_load
1173 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
1174 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
1175 o transfered surface NH pressure to eta field (if exactConserv).
1176 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
1177 and update lab_sea output.txt file.
1178 o completing 3-dim. relaxation code: additional term
1179 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
1180 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
1181 * At compile time, in "EXF_OPTIONS.h" set
1182 #define ALLOW_CLIMTEMP_RELAXATION
1183 #define ALLOW_CLIMSALT_RELAXATION
1184 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
1185 tauThetaClimRelax3Dim = 15552000.0,
1186 tauSaltClimRelax3Dim = 15552000.0,
1187 * 3 cases:
1188 1) Use a constant-in-time 3-dim. field
1189 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
1190 3) Real-time relax. to time-evolving prescribed field
1191 o Adding Laplacian-type smoothness constraint on
1192 initial and boundary (forcing) controls (ic, bc)
1193 * enable at compile-time via
1194 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
1195 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1196 * Absolute scale somewhat unclear so far
1197 * no area weighting was included since no other cost term does so far
1198
1199 checkpoint57y_post
1200 First step for a NLFS adjoint
1201 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
1202 o new init. routines for calc_r_star, calc_surf_dr
1203 o still need to deal with ini_masks_etc
1204 o testreport seemed happy
1205 checkpoint57y_pre
1206
1207 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1208 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1209 o add new offset feature to offline pkg (plus minor cleanup)
1210 o cfc fixes for final year of integration
1211 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1212 be in GCHEM_OPTIONS).
1213
1214 checkpoint57x_post
1215 o fix testreport Pb in multiple test experiment.
1216 o cleanup our namelist syntax in verification:
1217 - make it more F95 standards compliant (some work still needed)
1218 - allows the vast majority of our tests to work with gfortran
1219 o Non-Hydrostatic:
1220 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1221 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1222 o Allow to apply AB on T,S rather than on AB(gT,gS):
1223 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1224 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1225 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1226 - need a "clever" read_pickup to restart from the other AB formulation
1227 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1228 o remove some unused variables (reduces number of compiler warnings)
1229 o adjoint
1230 * Disable useVariableViscosity for adjoint for time being
1231 (there are a number of extensive recomputations)
1232 * Initialize certain variables needed for adjoint
1233
1234 checkpoint57w_post
1235 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1236 fix the singleCpuIO RS version of MDSWRITEFIELD
1237 and add a WARNING if using globalFiles=T with multi-processors.
1238 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1239 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1240 o tracer advection scheme:
1241 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1242 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1243 was not very convenient).
1244 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
1245 (further tests needed for the implicit DST & Flux-Limiter schemes).
1246 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1247 and sRef for convenience, handy, when you want to initialize
1248 ptracers in a large domain with a constant non-zero value. Also,
1249 untangle ptracers_init.F a little.
1250
1251 checkpoint57v_post
1252 o change dome exp. to use variable viscosity in side-drag terms.
1253 o remove all the files from the cfc_offline test since they are now
1254 incorporated into tutorial_cfc_offline which has been producing
1255 identical results for a few days of testing
1256 o add new parameter: sideDragFactor to enable half-slip-side BC
1257 and change side-drag S/R to use viscosity from mom_calc_visc
1258 (can switch back by setting sideDragFactor=0.); affects results at
1259 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1260 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1261 o vorticity & strain are now computed without masking, to account for
1262 no-slip-side BC in variable viscosity calculation ; mask is applied
1263 anyway later on, before computing advection/coriolis terms.
1264 o modify exp4 to test new obcs support for reading from external files
1265 and for passive tracers
1266 o fix behavior of ptracers_monitor when monitor output is written to a
1267 netcdf-file; still not independent of monitor.F (writes in the same
1268 file).
1269 o change default value of tRef (put a uniform, meaningful value for ocean
1270 & atmos) and initialize sRef (was missing, as Martin mentioned).
1271 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
1272 to be proportional to enstrophy dissipation length. Thus,
1273 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1274 This is now consistent with Smagorinsky and with the manual.
1275
1276 checkpoint57u_post
1277 o OBCS and PTRACERS: add open boundary support for passive tracers
1278 - either use homogenous (pseudo) v.Neumann conditions or prescribe
1279 OB-values from file; this is not different from the way theta and salinity
1280 are treated
1281 - however, Orlanski-radiation conditions are not supported, and the model
1282 will stop if you use pTracers and Orlanski at the same time.
1283 - beefed up the rountine obcs_external_fields_load: now only those open
1284 boundary values are overwritten with values from files for which there
1285 are really files, otherwise the OB-fields remain untouched. This makes
1286 it possible to use different OBs at different ends of the domain (as
1287 with EXF)
1288 o reduce number of exch calls in shap_filt (s2).
1289 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1290 truncation level) 4/5 MLAdjust test results (11&12 digits match).
1291
1292 checkpoint57t_post
1293 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1294 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1295 same truncation, independent of the face number: affects affects several
1296 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1297 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1298 note that biharmonic viscosity + no-slip was not tested in any experiment.
1299 o fix bug in non-linear free-surf side-drag ; generate new output for
1300 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1301 o make mnc honor the writeBinaryPrec flag for most kinds of output
1302 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1303 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1304 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1305 o add brackets in multi-terms sum to get same truncation, independent of
1306 the face number (manage to get exactly same value of gU,gV at the cs-edge)
1307 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1308 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
1309 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1310 a maximum grid-scale Reynolds number. Also, changes all length calculations
1311 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1312 Suggested values of viscosity parameters found in mom_calc_visc.
1313 Many new viscosity diagnostics available.
1314
1315 checkpoint57s_post
1316 o Add clearing-house for viscosity calculations, mom_calc_visc and
1317 correct numerous bugs in LeithD and Smagorinsky discretizations.
1318 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1319 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1320 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1321 and with Strain-Tension viscous term calculation (mom_hdissip.F).
1322 The Strain-Tension form is now called with useStrainTensonVisc=.true.
1323 ViscAhStrain and viscAhTension are now retired.
1324 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1325 o In response to JMC's bug report, genmake2 now ignores any soft-links
1326 that it finds in the *current* directory when searching for files.
1327 Soft-links found in any other source directories will still work as
1328 they did before.
1329 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1330 a C routine to unlimit the stack size
1331 o mnc-ify pkg/aim snapshot vars
1332 o mnc-ify pkg/land as requested by Daniel
1333 o various changes to mnc including:
1334 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1335 - output can now be grouped so that all files within a group
1336 change the ITER portion of their names in lock-step together
1337 - can now read ("global") PER-FACE (in addition to PER-TILE) files
1338 and works with both EXCH1 and EXCH2 (but needs more testing)
1339 - writing works for all verification test cases w/ g77 on Linux
1340
1341 checkpoint57r_post
1342 o make MNC variable initialization happen earlier
1343 o add diagnostics for (almost) each term of the momentum Eq.
1344 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1345 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1346 o remove MINIMAL_TAVE_OUTPUT option ;
1347 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1348 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1349 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1350 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1351 o add time-dependent SST, SSS control
1352 o cost terms in ecco/ modularized (new cost_generic.F)
1353 o cost_averages routines are modularized (new cost_averagesgeneric.F)
1354 o new infrastructure for seaice model vs. obs misfits in seaice/
1355 * driver from the_main_loop.F is seaice_cost_driver.F
1356 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1357 * gradient check in Exp. 6a of natl_box_adjoint/
1358 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1359 (see README file)
1360
1361 checkpoint57q_post
1362 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1363 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1364 - bug was reported by Jean-Michel and Ian Fenty
1365 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1366 update exp. cpl_aim+ocn output.
1367 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1368 Needed for high-res. runs with large global files
1369 to be able to limit tapelev size
1370 o Changed some tests for adjoint:
1371 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1372 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1373 * global_ocean.90x40x15/ back to default 3-level checkpointing
1374 o Modifications to enable scripted COMMON to MODULE conversion
1375 * verification/OpenAD/code/ has necessary scripts and description;
1376 * converts, compiles and runs successfully;
1377
1378 checkpoint57p_post
1379 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1380 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1381 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1382 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1383 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1384 (was already the case for dissipation with mom_vecinv,
1385 and also the case for grad.PhiHyd when staggered-timeStep)
1386 This will allow to put dissipation out-off the AB time-stepping.
1387 Unfortunately, affects truncation error. Update output of exp. that "fails"
1388 (cg2d matching number) and leave the others for later: front_relax(10),
1389 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1390 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1391
1392 checkpoint57o_post
1393 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1394 (2) its ready to be documented during the 20050801 DocFest
1395 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1396 for ideal_2D_oce and lab_sea on linux_ia32_g77
1397 o set to #undef CTRL_SET_OLD_MAXCVARS_30
1398 in global1x1_tot/code_seaice_adj to access indices 32, 33
1399 (worth another tag)
1400
1401 checkpoint57n_post
1402 o adding precip control xx_precip 32
1403 o adding swflux control xx_swflux 33
1404 o Replacing 10 forcing penalty cost routines by 1 generic.
1405 o Implementing partitioning in time-mean and variable adjustment
1406 for atmos. state.
1407 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1408 o in natl_box_adjoint:
1409 * updated exp 1 to 10
1410 (but does not have time-mean vs. variable split results yet)
1411 o updated global1x1/*_seaice_adj/
1412 to incorporate latest changes
1413 o enable useSingleCpuIO for mdsio vector routines
1414 (applies in particular to tapelev I/O)
1415 o removed inefficient K-loop in all active_file*control*.F
1416
1417 checkpoint57m_post
1418 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
1419 and advect_cs (use EXCH-2 and standard cs-32 grid files).
1420 o pkg/exch2: filling of face-corner halo regions is optional
1421 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
1422
1423 checkpoint57l_post
1424 tag before updating tutorials (pre-release-2)
1425 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
1426 for output and interpolation of input fields onto model grid)
1427 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
1428 Affects results of exp. rotating_tank ; update output.txt.
1429 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
1430 and taking the square quantity and/or using a fraction-weight field.
1431 o fix aim_diagnostics_init.F mate numbers.
1432 o add mnc output capability to diagnostics/diagstat and update
1433 our cvsignore files for the ACSII output generated
1434
1435 checkpoint57k_post
1436 o lab_sea now uses diagnostics package and provides a suite of
1437 new EXF diagnostics output.
1438
1439 checkpoint57j_post
1440 o exf
1441 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
1442 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
1443 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
1444 * extended diagnostics output
1445 - now includes all EXF variables
1446 - hs, hl moved to common block
1447 - separate S/R for diagnostics, called after ctrl vector is added
1448 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
1449 - EXFqnet contains true Qnet (i.e. includes qsw)
1450 * updated verif. lab_sea, global_with_exf
1451 * Rearranging hflux (exf_mapfields -> exf_getforcing)
1452 to ensure that diagnostics sees a true EXFqnet
1453 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
1454 o diagnostics pkg: change pointers so that 1 diagnostic can be used
1455 several times with different frequencies.
1456 o mnc-ify the thsice package as requested by Daniel Enderton
1457 - the monitor--MNC output needs work
1458 - many attributes need to be added (most are currently blank)
1459 o mnc-ify theaim_v23 package as requested by Daniel Enderton
1460 - many attributes need to be added (most are currently blank)
1461 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
1462 o add Sadourny like discretization to the 4th.O vorticity advection scheme
1463 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
1464 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
1465 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
1466 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
1467 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
1468
1469 checkpoint57i_post
1470 o Diagnostics package was changed: diagnostic allocation is now deactivated
1471 by setting an empty file name in the namelist (used to be by setting 0 frequency)
1472 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
1473 add 1rst Order upwind vertical Shear.
1474 o add a quick fix for A/B checkpointing in OFFLINE mode
1475 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
1476 end-run around the C/Fortran linking horror in eesup/src/timers.F
1477 o added pkg/runclock: allows user to terminate run based on wall clock
1478 o added non-hydrostatic scaling parameter: nh_am2
1479 o pkg/my82: futile attempt to make results compiler-independent by adding
1480 some "_d 0", etc. no effect.
1481 o for mnc output, fill the 'T' coordinate var with myTime and create a
1482 separate 'iter' variable for iteration count
1483 o pkg/diagnostics:
1484 add new capability: output of Global/Regional & per-level statistics ;
1485 tested against monitor output (including land & thSIce) on various exp.
1486 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
1487
1488 checkpoint57h_done
1489 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
1490 data.diagnostics, data.gchem, data.ptracers) is done.
1491
1492 o pkg/diagnostics: prepare for Global/Regional statistics.
1493 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
1494 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
1495 and rename it: DIFFERENT_MULTIPLE
1496
1497 checkpoint57h_post
1498 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
1499 o pkg/diagnostics: change output frequency, now in seconds (instead
1500 of Nb of iterations). This requires to change data.diagnostics.
1501 checkpoint57h_pre
1502
1503 o in mnc, let the user create the output dir if both mnc_outdir_date
1504 and mnc_outdir_num are false
1505 o add fflags() to pkg/diagnostics which allows one to specify, on a
1506 per-file basis, the file precision [default behavior is unchanged]
1507 o added diagnostics to pkg/kpp, including computation of mixed layer
1508 depth based on a temperature/density criterion
1509 o updated verification/natl_box to test the new pkg/kpp diagnostics
1510 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
1511 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
1512 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
1513 not mnc -- this mistake was found by JMC and is now corrected
1514
1515 checkpoint57g_post
1516 o add Adams-Bashforth 3rd Order time stepping:
1517 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
1518 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
1519 checkpoint57g_pre
1520
1521 o make lambda[Theta,Salt]ClimRelax spatially varying
1522 (default remains spatially uniform constant based on tau)
1523 o added new control variables
1524 * init. uVel, vVel, etanN
1525 * lambda[Theta,Salt]ClimRelax
1526 o separate masks used for ctrl_pack/unpack 'from write_grid' output
1527 (suggested by G. Forget)
1528
1529 checkpoint57f_post
1530 o add parameter "baseTime" = model base time = time at iteration zero
1531 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
1532 account for baseTime shift
1533 o move Coriolis arrays from PARAMS.h to GRID.h
1534 checkpoint57f_pre
1535
1536 o mnc-ifying the seaice package
1537 o introduced an alternative length scale calculation for use in the limiting
1538 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
1539 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
1540 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
1541 as well as grad(vort3). Made it compatible with both approximate form
1542 for the cubed sphere and full form of these gradients. Added flag
1543 useFullLeith to select between approximate and full form.
1544 o add "d0" in getcon.F to reduce differences between compilers/platforms
1545 update output.txt of exp. fizhi-gridalt-hs
1546 o change port_rand funtion to allow to set the seed.
1547 o fix obscure MNC bug involving conversion between reals and integers
1548 - it caused no problems with certain (eg. gcc, ifc) compilers but the
1549 new version is now more standards-compliant
1550 o adjoint-related modifications
1551 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
1552 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
1553 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
1554
1555 checkpoint57e_post
1556 o Adding eddy stress controls a la Ferreira et al.
1557 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
1558
1559 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
1560 update output.txt of exp. fizhi-gridalt-hs
1561 o add more "Z" dimensions and associated coordinate vars to MNC
1562 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
1563 o parameter calendarDumps: when set, approximate months (30-31 days) and years
1564 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
1565 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
1566 months and years. Requires pkg/cal.
1567 o diagnostics: add pickup functionality
1568 - off by default for backwards compatibility
1569 - current version only uses MDSIO -- MNC will be added
1570 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
1571 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
1572
1573 checkpoint57d_post
1574 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
1575 o modify verification/ideal_2D_oce so that it tests the creation of mnc
1576 output from the diagnostics package
1577 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
1578 o make genmake2 more portable by using ".$FS" instead of ".f" for more
1579 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
1580 o add coordinate variables to the MNC output from the diagnostics package
1581 o change MNC-flags default value: true when useMNC=TRUE
1582 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
1583 the ability (off by default) to read the grid information using MNC
1584 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
1585 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
1586 o do snap-shot diagnostics at the middle of the time-interval (instead of
1587 at the end).
1588 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
1589 new test for AIM with thSIce + slab-ocean
1590 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
1591 o move state variable diagnostics to the beginning of the time step ;
1592 (note: still needs some work specially for snap-shot diagnostics)
1593 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
1594
1595 checkpoint57c_post
1596 o Change testing option (-ieee) to get closer agreement between g77 & ifort
1597 o generate new output.txt files on faulks with g77 & the new -ieee option
1598 checkpoint57c_pre
1599
1600 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
1601 update output.txt of exp. global_ocean.90x40x15
1602 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
1603 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
1604 o add saltFlux(+File) forcing capability with periodicExternalForcing
1605 o allow to use pkg diagnostics for GM-Redi & ThSIce output
1606 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
1607 o improvements for the MNC output from DIAGNOSTICS:
1608 - correct handling of the unlimitied dimension
1609 - all dims now have associated coordinate variables
1610 - variables located at U, V, and Corner ("Z") points are now written
1611 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
1612 *all* data points are output
1613 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
1614 o added pkg/seaice/seaice_monitor.F
1615 o mdsio_readfield.F can now read files visible only to master MPI process.
1616 o pkg/seaice: some test code for ice-modified ocean stress
1617 o exf_getffields interpolation defaults to bilinear for all scalar forcing
1618 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
1619 spurious negative numbers for precipitation and humidity. Will cause
1620 some small numerical differences for integrations using pkg/exf/exf_interp.F.
1621 o pkg/ctrl/
1622 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
1623 May be enabled via doPackDiag
1624 * introduce z-scaling of
1625 + gradient (doZscalePack) and
1626 + control (doZscaleUnpack)
1627 o pkg/mdsio/
1628 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
1629 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
1630
1631 checkpoint57b_post
1632 o simplify options in diagnostics_fill arguments (remove weird combinations)
1633 o fix MNC coordinate variables so that they now contain per-face index
1634 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
1635 general, EXCH2 grids are only aligned to a "local" coordinate system
1636 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
1637 o Implement instantaneous output within pkg diagnostics:
1638 setting a negative frequency in data.diagnostics produces
1639 "snap-shot" output (as opposed to time-average if freq > 0)
1640 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
1641 NOTE: change ptracer diagnostics name: use 2 characters to work with
1642 more than 9 tracers. Add also diagnostics of advect & diffus flux.
1643 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
1644 becomes the coordinate variable for the 'T' dimension
1645 o add CF-style coordinate variables to MNC
1646 - just a first cut: numbers are meaningless on the cubesphere and
1647 missing along the T axis but otherwise it works!
1648 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
1649 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
1650 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
1651 this is based directly on what the model compute, so that the content of
1652 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
1653 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
1654 o clean up build options files for SunOS, in particular
1655 - remove -traditional from xmakedepend
1656 - change -xarch=v9 to -xarch=native for f77
1657 - restore use of make (not gmake)
1658 - add CC=gcc if using g77
1659 o changes per discussion of AM, JMC, & EH3 today:
1660 - move redundant "grid" variables out of "state" -- in preparation of
1661 creating proper CF-style coordinate variables and in recognition
1662 that any/all grid variables can be easily copied (eg. w/NCO) from
1663 the grid files into any of the other NetCDF files
1664 - *always* output grid variables with MDSIO (this will eventually be
1665 changed)
1666 - output MNC grid file if useMNC is true
1667 o every instance of _END_MASTER() has been found and replaced with
1668 _END_MASTER( myThid ) in order to satisfy certain picky Sun
1669 preprocessors
1670 o re-arrange diagnostics pkg initialisation:
1671 - allow each package to extend the available diagnostics list
1672 - add some checking and fix small problems (multi-threaded, ...)
1673 - new S/R diagnostics_fill (replace fill_diagnostics):
1674 look through the short list of active diag. (instead of the long list)
1675 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
1676
1677 checkpoint57a_post
1678 o this set of changes restores TAMC compatibility
1679 tested for global_ocean.90x40x15 adjoint on trough
1680 (what a pain)
1681
1682 checkpoint57a_pre
1683 o some modifs in tools/build_options for sunos
1684 o call ctrl_pack for ctrl at end for optimcycle=0
1685
1686 checkpoint57
1687 o add horizontal bi-harmonic viscosity for vertical velocity
1688 - new parameter viscA4W (defaults to viscA4)
1689 - affects only non-hydrostatic code
1690 - to be done: no-slip lateral boundary conditions
1691 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
1692 o implement Implicit Vertical advection for pTracers
1693 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
1694 (implemented also for implicit vertical diffusion & advection)
1695 o OBCS: extend application of tracer open boundary conditions
1696 to a strip beyond the boundary of width Olx/Oly
1697 o add call monitor to TAF set of required calls (flow directives)
1698 and include in natl_box_adjoint
1699 o untangle a few ifdefs related to cost, ctrl, autodiff
1700 untangel a few ALLOW_ECCO_OPTIMIZATION
1701 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
1702 (theta2, salt2 in ecco_cost_weights)
1703
1704 checkpoint56c_post
1705 o OBCS as control variables
1706 - update ctrl_ad_diff.list, obcs_ad_diff.list
1707 - remove balance of obcs controls from default
1708 - fix index bug nobcs in ctrl_init
1709 - fix dummy fields filen in ctrl_pack
1710 - add dummy weights for obcs
1711 o lsopt: comment out fort.94 output
1712 o optim:
1713 - remove unnecessary header files
1714 - adjusted namelists
1715 - add xerbla.F to Makefile
1716 o exf:
1717 - multiple modifications of exf_check_range
1718 - unit change in exf_init_runoff from [m/year] to [m/s]
1719 o mdsio:
1720 - i/o-vector change debugLevel from debLevA to debLevB
1721
1722 checkpoint56b_post
1723 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
1724 is called from DO_THE_MODEL_IO
1725 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
1726 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
1727 - clean up PTRACERS_WRITE_TIMEAVE a little
1728 o add another verification experiment that tests both the cfc-pkg and
1729 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
1730 reactive tendencies treated inline with regular timestepping
1731 o testreport previously did a lousy job of comparing small numbers, so
1732 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
1733 implemented in the little c-progam tmp_cmpnum.c which is embedded in
1734 testreport.
1735 o ptracers_monitor: bug fix for MPI
1736
1737 checkpoint56a_post
1738 o GCHEM: finish reorganizating the package
1739 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
1740 (introduces another 3D-array for each passive tracer, but only if
1741 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
1742 gchemTendency is not needed because the timestep is done separately)
1743 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
1744 - GCHEM is now---more or less cleanly---separate from PTRACERS
1745 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
1746 so clear to me how that should be done in a general way.
1747 o CFC: improve formatting of output in CFC_ATMOS
1748 o PTRACERS:
1749 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
1750 that ALL experiments with ptracers enable can be checked. This makes
1751 GCHEM_MONITOR obsolete.
1752 - include a runtime parameter PTRACERS_monitorFreq that defaults to
1753 monitorFreq
1754 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
1755 o add PTRACERS (PTR0[1-5]) to testreport output
1756 o exf_check_range:
1757 * default changed to .TRUE.
1758 * will check values for niter0 if debLevA, every timestep if debLevB
1759 * STOP in exf_check_range if 'out of range'
1760 * range chosen generous to allow for potential extema
1761 TBD: a version with stricter range
1762 permitted range would be runtime parameters
1763 o GMredi:
1764 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
1765 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
1766 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
1767 o GCHEM:
1768 - move call to GCHEM_FORCING_SEP, so that it is now called before
1769 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
1770 - introduced a useGCHEM runtime flag and applied it everywhere.
1771 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
1772 this flag is now only visible within GCHEM-pkg routines.
1773 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
1774 be replaced by a 3D array that is computed before thermodynamics; for
1775 this, the tracer ID iTracer had to be included into the parameter list
1776 of ptracers_forcing
1777 - set up forward_step to call gchem_forcing, that will replace
1778 gchem_forcing_int in ptracers_forcing
1779 - cleaning up
1780 o small cleaning of exch2: remove files that are also in eesupp/src
1781
1782 checkpoint56
1783 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
1784 o mnc: cleanup "full" files--fixes out-of-memory problem
1785 o ECCO-GODAE
1786 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
1787 * fully merged and updated from SIO code
1788 windstress sign change affects
1789 - exf_inscal_[u/v]stress
1790 - sign of xx_tau[u/v] adjustments
1791 - signs in cost_scat
1792 * ctrl_get_gen: avoid update of tau[u/v] for first few days
1793 * natl_box_adjoint updated and compressed
1794 * 2-level checkpoint switch added
1795 (tested in EXP. 1 of natl_box_adjoint)
1796 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
1797 o SVD
1798 * first complete, non-hacked version for SVD calculations
1799 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
1800 performed via direct access files admtlm_vector.it????
1801 (via ctrl_[un]pack)
1802 * optimcycle is used for ARPACK iteration counter
1803 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
1804 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
1805 and add linear transforms where necessary
1806 * controls are initial/final SST, SSS (can be extended; need to check
1807 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
1808 o mdsio: filename info to both stderr, stdout
1809 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
1810 from sign change
1811
1812 checkpoint55j_post
1813 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
1814 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1815 o add consistent build directories and .cvsignore files to verification
1816 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
1817 o make all subroutines 30 or less characters in length for certain older
1818 compilers to work (a thorough search only turns up two routines in
1819 pkg/ptracers)
1820 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
1821 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1822
1823 checkpoint55i_post
1824 o change arrays for total vertical diffusivity (2.D if explicit,
1825 3.D if implicit) ; each ptracer uses its own background value.
1826 o added mnc/NetCDF output capability to ocn_compon_interf
1827 - added bits to verification/cpl_aim+ocn so that it can run on
1828 ITRDA and other clusters without the mpirun "-wd" option
1829 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
1830 configuration
1831 o give MNC the ability to create additional files rather than
1832 exceeding a specified file size limit "MNC_MAX_FILESIZE"
1833 - the default is just less than 2GB which is a practical limit
1834 on many systems
1835 o Compute the non-local term using either KPP vertical diffusivity (=default)
1836 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
1837
1838 checkpoint55h_post
1839 o add verification test "vermix"
1840 o remove all the *_ioinc flags and replace with the single global
1841 outputTypesInclusive flag
1842 o allow to set a vertical profile of vertical diffusivity for T & S
1843 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
1844 o useMNC moved from data.mnc to data.pkg
1845
1846 checkpoint55g_post
1847 o Renaming carbon AD experiments to comply with testreport conventions
1848 o Updating adjoint of Held-Suarez hs94.1x64x5
1849 o Fixing directives for non-ECCO forward_step, after ECCO directives
1850 have been fixed to avoid recomp. of do_oceanic_phys
1851 Works well for global_ocean.90x40x15,
1852 but recomp. issue remains for carbon
1853 o Updating adjoint output for natl_box_adjoint after
1854 pkg/ecco has been modified (see taga c55d_post)
1855
1856 checkpoint55f_post
1857 o rename to timeave_init_fixed
1858
1859 checkpoint55e_post
1860 o some delicate re-shuffle of store directives to avoid one
1861 extra call of do_oceanic_physics
1862 affects ecco_the_main_loop.F, do_oceanic_physics.F
1863 checkpoint_lev1_directives.h
1864 o NB: this may break global_ocean adjoint temporarily,
1865 but it is clear how to fix it. Will do later, need this now.
1866
1867 checkpoint55d_post
1868 o ECCO specific cost function terms (up-to-date with 1x1 runs)
1869 o ecco_cost_weights is modified to 1x1 runs
1870 o modifs to allow observations to be read in as
1871 single file or yearly files
1872 o enable to read exf forcing fields as either
1873 single file or yearly files (flag useExfYearlyFields)
1874 checkpoint55d_pre
1875
1876 o switch between 2-level and 3-level checkpointing
1877 o add ability of MNC to write local and "partial" (eg. 2D slices where
1878 the full 3D field is never actually stored) arrays to NetCDF files
1879 with the correct (that is, the complete multi-dimensional) set of
1880 array indicies
1881 - used in mom_vecinv() to write the diagFreq output
1882 - tested (demonstrated) in verification/aim.5l_cs
1883 o further mnc-ification
1884 - add verification/lab_sea to the list with mnc setups
1885 - fix undefined mnc v-names in cd_code
1886 - add kpp to mnc output (both snapshot and timeave)
1887 o non-hydrostatic code
1888 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
1889 in calc_gw.F
1890 - defaults to viscAh
1891 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
1892 friction or Leith) in non-hydrostatic mode, as long as there is
1893 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
1894 o pkg/cost
1895 extend simple cost functions to treat time mean quantities
1896 (T,U,V) via cost_accumulate_state from cost_tile
1897 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
1898 be 2 times larger than the minimum size the advection scheme requires.
1899 now get a perfect conservation of salt in advect_cs test-exp (updated)
1900 o GGL90 (Gaspar's TKE mixed layer)
1901 - add horizontal diffusion of TKE, requires exchanges in
1902 do_fields_blocking_exchanges, horizontal diffusivity is zero by
1903 default. In OPA there is no horizontal diffusion of TKE but the
1904 mixing coefficients are computed from a horizontal average of TKE of
1905 6 points or so. I think that diffusion has a little more physical
1906 justification.
1907 - clean up ggl90_calc in the hope of reducing memory usage (this hope
1908 was in vain)
1909 - mask tke-variable in ggl90_init
1910 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
1911 o fix biharmonic diffusion on CS-grid.
1912 o more obcs stuff
1913 - added obcs_external_fields_load as an alternative to the EXF-pkg option
1914 for reading boundary values. This routine is called from
1915 obcs_prescribe_read
1916 - updated obcs_check
1917 - changed sponge layer relaxation parameter units for days to seconds
1918 - turned off sponge layer by default
1919 - changed argument list of OBCS_CALC to myTime+deltaTclock
1920 - fixed about 35 bugs in obcs_external_fields_load
1921
1922 checkpoint55c_post
1923 o obcs stuff
1924 - new runtime flags useOBCSprescribe, useOBCSbalance
1925 - re-arranged obcs_calc
1926 - moved exf_getobcs to obcs_prescibe_read
1927 obcs_prescibe_read is called after ORLANSKI stuff
1928 and independent of it (executable can contain all).
1929 - updated obcs_check
1930 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
1931 These may be necessary only if tangential velocities are
1932 prescribed at OB, not sure, needs testing.
1933 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
1934 which simplifies the calls and passes the ifc check-bounds test
1935
1936 checkpoint55b_post
1937 o add a 2D scalar, Z location, exchange_2 routine.
1938 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
1939 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
1940 affects advect_cs results (for the wrong reason): update output.txt
1941 o use a more standard discretization for biharmonic viscosity ;
1942 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
1943 affects results of dome set-up: update output.txt
1944 o fix gad_advection.F (CubedSphere part), back to version 1.23
1945 o fix bug in mom_vi_del2uv.F (CubedSphere part).
1946
1947 checkpoint55a_post
1948 o merged code to
1949 * prescribe/read time-dependent open boundaries
1950 (works in conjunction with exf, cal)
1951 * sponge layer code for open boundaries
1952 * each boundary N/S/E/W now has its own CPP option
1953 (healthy for the adjoint)
1954
1955 checkpoint55
1956 o up-to-date adjoint of previous breaks
1957 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
1958 - global_ocean_ebm: adjoint still needs fix (TLM ok)
1959 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
1960 - carbon: * remove tr1-related adjoint verification
1961 * add ptracer as control variable
1962 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
1963 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
1964
1965 checkpoint54f_post
1966 o in verification/carbin/ remove experiment related to
1967 ALLOW_PASSIVE_TRACER (array tr1 etc)
1968 code_ad/ input_ad/ results_ad
1969
1970 o add two new packages
1971 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
1972 + subject to optimization (memory)
1973 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
1974 + subject to reordering (many GOTOs in the original code)
1975 + so far opps is called for every (i,j) point, and then operates in
1976 the vertical; one may want to reorder the scheme in order operate in
1977 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
1978 fields)
1979 o overhaul of IO so that we now have flags for MDSIO and/or MNC
1980 - all verification tests compile and run with linux_ia32_g77
1981 - defaults are compatible with current input files--nothing
1982 should change if you were not previously using MNC
1983 - MNC output has been added in numerous places (eg. timeave)
1984 but there are still a few writes not yet do-able with MNC
1985 (this is in progress)
1986 - flags now allow for either/or/both use of MDSIO and MNC and
1987 documentation will soon follow
1988 - numerous small formatting cleanups for ProTeX
1989 o add version info (via BUILD_INFO.h) to MNC and stdout
1990
1991 checkpoint54e_post
1992 o add two new packages
1993 - pp81 (Packanowski and Philander, 1981), Richardson number and
1994 stratification dependent mixing
1995 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
1996 - these scheme operate in a similar manner as KPP (without ghat, of
1997 course), however there is only one diffusivity that is used for both
1998 temperature and salinity (and passive tracers)รง
1999 o add offline package
2000 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2001 provided by Stephanie Dutkiewicz
2002 o genmake2: add ability to search for C compilers and cleanup test output
2003 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
2004
2005 checkpoint54d_post
2006 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
2007 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
2008 leading to additional shift by 5 days each year of integration
2009 (i.e. leading to considerable offset over the years)
2010 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
2011 o start with no AB and no initial filtering (staggerTimeStep):
2012 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
2013 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
2014 (external loading & cpl import/export stay in forward_step.F)
2015 o update coupling interface to work with new staggerTimeStep
2016 o change MDSIO ptracers_pickup.
2017 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
2018 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
2019 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
2020
2021 checkpoint54c_post
2022 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
2023 this affects (truncation error) output.txt of test-exp:
2024 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
2025 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
2026 o change Qnet to always be the net heat flux, (+upward).
2027 affects (truncation error) output of natl_box exp.: updated
2028 o define the max number of passive tracers in PTRACERS_SIZE.h
2029 o start to test mnc routinely in exp0
2030 o add sea-ice loading (sIceLoad) as a new forcing field.
2031
2032 checkpoint54b_post
2033 o add testreport "-j JOBS" option for parallel builds (tested and pretty
2034 impressive on Altix and Opteron systems)
2035 o diagnostics can now write NetCDF files through the mnc package
2036 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
2037 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
2038 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
2039 affects (truncation error) output of lab_sea & natl_box exp.: updated
2040 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
2041
2042 checkpoint54a_post
2043 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
2044 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
2045 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
2046 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
2047 + internal_wave (shift in writing cg2d_ini_res)
2048 checkpoint54a_pre
2049
2050 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
2051 - modified verification/lab_sea and natl_box_adjoint accordingly
2052
2053 checkpoint54
2054 checkpoint53g_post
2055 o prepare splitting of thermodynamics: store convect.counter in common block
2056 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
2057 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
2058 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
2059 o new parameter "nShapS": allow to treat differently S from T (nShapT)
2060 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
2061 o restore adjointability
2062
2063 checkpoint53f_post
2064 o modifications that affect AIM experiment results (update output.txt):
2065 - no advection of S at top interface Nr (pkg/generic_advdiff)
2066 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
2067 o AIM pkg:
2068 - include stability function into surf.Flux derivative relative to Tsurf
2069 - calculate clear-sky radiation & surface temp. change (for diagnostics)
2070
2071 checkpoint53e_post
2072 o merged cylindrical coord configuration
2073 o added rotating_tank experiment
2074 checkpoint53e_pre
2075
2076 checkpoint53d_post
2077 o faulks upgraded: re-generate output.txt that have changed:
2078 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
2079 o Added Bryan and Lewis, 1979, vertical diffusivity profile
2080 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
2081 o added Sadourny discretization of Coriolis
2082 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
2083 - re-enabled use of omega3 (useAbsVorticity)
2084 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
2085 vector-invariant equations
2086 - note: does *NOT* yet use same variable visc. for no-slip BC's.
2087 o recoded the lateral boundary conditions for non-hydrostatic w, this time
2088 hopefully without new bugs
2089 - still to do: biharmonic friction for non-hydrostatic w
2090 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
2091 o regenerated output for global_ocean_ebm (using -ieee)
2092 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
2093 of mom_common/
2094 - simple re-arrangement of instructions within computing loop
2095 checkpoint53d_pre
2096
2097 checkpoint53c_post
2098 o new version of coupler for AIM+thSIce and Ocean models
2099 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
2100 - land: change Evaporation of snow
2101 - aim with thSIce: fix bug in snow-precip.
2102 o changes to calc_gw.F
2103 - bug fix for w^2 term near the bottom boundary
2104 - (hopefully) improve the lateral slip boundary condtions for use with
2105 partial/looped cells
2106 - because the bug fix changes two verification experiments anyway (exp5
2107 and plume on slope), change the lateral boundary condition from half slip
2108 to the value of no_slip_sides
2109 o ebm package wasnt quite up to the parallel task. Fixed that.
2110 o Adjoint of EBM package + verification
2111 * TLM OK
2112 * ADM not sufficient accuracy yet (needs further testing)
2113
2114 checkpoint53b_post
2115 o Commiting new energy balance model to repository
2116 * package is pkg/ebm
2117 * verif. is verification/global_ocean_ebm
2118 * references are in ebm_driver.F
2119 C * X. Wang, P. Stone and J. Marotzke, 1999:
2120 C Global thermohaline circulation. Part I:
2121 C Sensitivity to atmospheric moisture transport.
2122 C J. Climate 12(1), 71-82
2123 C * X. Wang, P. Stone and J. Marotzke, 1999:
2124 C Global thermohaline circulation. Part II:
2125 C Sensitivity with interactive transport.
2126 C J. Climate 12(1), 83-91
2127 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
2128 C Destabilization of the thermohaline circulation
2129 C by atmospheric eddy transports.
2130 C J. Climate 7(12), 1870-1882
2131 o Will need long integration testing.
2132 checkpoint53b_pre
2133
2134 o created pkg/mom_common in preparation for variable viscosity code
2135 o renamed and split ini_mnc_io
2136 o pkg/land: only liquid water can diffuse or run-off
2137 o AIM using land: soil wetness availability account for snow
2138 o added printMapIncludesZeros to EEPARMS namelist
2139
2140 checkpoint53a_post
2141 o restore TAMC compatiility for exf_constants.h
2142 (no usage of _d in .h)
2143 o Additional storing in KPP in an attempt to fix
2144 TAMC problem with adjoint of KPP code.
2145 (no success...)
2146 Identical code works fine with TAF.
2147 o Fixed verification/natl_box_adjoint experiments.
2148 Initial conditions for Experiments 4 and 5 are now
2149 set to "SEAICE_initialHEFF=0", which is more reasonable,
2150 and hence gives results closer to that of Experiment 2.
2151 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
2152
2153 checkpoint53
2154 o stable checkpoint with up to date adjoint
2155 TLM tests only run for 1st grdchk at the moment. Its unclear if
2156 this is a code problem or a problem with resetting code for g_
2157 variables that is being autogenerated wrong.
2158 Otherwise:
2159 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
2160 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
2161 are both still in chaos following their security messes.
2162
2163 checkpoint52n_post
2164 o various build (mostly genmake2) changes including:
2165 - ability to build/run more easily within Cygwin and MacOS X
2166 - more complicated Makefiles with a stronger dependence on Gnu Make
2167 o pkg/seaice modifications
2168 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
2169 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
2170 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
2171 - changed proxy for geostrophic velocity and updated
2172 verification/lab_sea/results/* accordingly
2173 - removed ADI dynamic solver from pkg/seaice
2174 - replaced all occurrences of 1/CSTICE or 1/CSUICE
2175 they caused a segmentation fault under certain circumstances
2176 - removed unused field WATR
2177 o bug fix in exf-package:
2178 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
2179 now reflect that.
2180 o small fixes in the cal-package:
2181 - set reference date to first of January for the 'model'-calendar
2182 - failing of cal_CheckDate in cal_FullDate now actually results in a
2183 warning
2184 o small modifications in exf-package to increase flexibility:
2185 - change climtempfreeze from a constant to a runtime parameter that
2186 is specified in data.exf_clim (default = -1.9)
2187 - introduce runtime parameter windstressmax (default = 2.0) that is
2188 specified in data.exf
2189 o fix in pkg/thsice:
2190 - update Evap (Tsf changes) to be consistent with Latent heat flux
2191 - maintain snow precipitation unchanged (even if Tsf >=0).
2192 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
2193
2194 checkpoint52m_post
2195 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
2196 this does not change any of the results, because myIter=0 in swfrac always
2197 lead to jwtype=2 (the default anyway), but the call makes little sense
2198 as a default
2199 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
2200 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
2201 atmospheric model (AIM) to use it ; add a "slab ocean" component.
2202 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
2203 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
2204 o extending useSingleCpuIO option to work with new exch2 I/O format
2205 - old-style, missing-tile I/O is still accessible by defining CPP
2206 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
2207 o monitor package can write to NetCDF files and/or STDOUT
2208 o fix re-definition bug in MNC_GRID_INIT_ALL()
2209 o doc/api_reference added
2210 - a framework for building an API Reference Manual using all
2211 the "protex" comments embedded in the code
2212 - see pkg/generic_advdiff, pkg/mnc for examples
2213 o MNC:
2214 - make myThid the last argument for all subroutines
2215 - new default for the grid files: NO halos
2216 - add useMNC and other run-time flags
2217 - separate per-file-group handling of the unlimited dimension
2218 - early initialization of MNC w/ flags read at the eeboot stage
2219 and lookup tables set in initialize_fixed
2220 - write all MNC output to a freshly-created directory
2221 o thermodynamics sea-ice (thsice) is now tested with testreport.
2222 o test exp. advect_cs: use the standard cs32 grid ; update output.
2223 o Added functionality to grdchk:
2224 pick global i,j,k position (or nearest wet) where to perform check.
2225
2226 checkpoint52l_post
2227 o new land formulation:
2228 a) use ground enthalpy as prognostic variable to ensure exact
2229 energy conservation.
2230 b) account for water temperature and for latent heat of freezing
2231 in all processes (rain, run-off, ground storage)
2232 c) compute surface and ground temperature implicitly.
2233 o aim_v23 modification for new land model:
2234 a) Treat separately land / ocean / sea-ice surface fluxes
2235 to allow implicit computation of land & sea-ice surface temp.
2236 b) add snow precipitation.
2237 checkpoint52l_pre
2238
2239 o fix problem (when 1 tile is empty) in min/max monitor.
2240 o fix bug in timeAve (u,vZetatave in common block)
2241 o no restoring terms under ice for pkg/seaice
2242 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
2243 o bug fix for pkg/seaice pickups
2244 o change MNC call locations and add coordinate attributes
2245 o mask vorticity at the corner ; affects global_ocean.cs output
2246 o fix ini_curvilinear_grid ; test CS experiments with mpi
2247 o aim.5l_cs: modify sea-ice fraction input file ; update output
2248 o exf: Adding simple range check routine for exf fields after read
2249
2250 checkpoint52k_post
2251 o removed top-level directory "diags"
2252 - we migrated these functions to pkg/timeave a long time ago
2253 o fixed bug introduced in pkg/monitor
2254 o accuracy ctrlprec = 32 insuffient for gradient checks using
2255 averaged fields (I/O via cost_averages)
2256 -> use ctrl.h in active_file*.F to control I/O precision.
2257 o paramter list of CALL ADTHE_MAIN_LOOP
2258 o added initial do_the_model_io to ecco
2259 o set all ...Freq to zero after cost_final
2260 taveFreq, dumpFreq, pChkptFreq
2261 o MAIN and ECCO differentiability restored
2262
2263 checkpoint52j_post
2264 o fix nchklev in tamc.h for global_ocean...
2265 o Bringing flow and store directives up-to-date
2266 o Really weird thing!
2267 call do_the_model_io from the_main_loop with parameters
2268 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
2269 TAF places a faulty re-call of initialise_varia
2270 after cost_final call which should not be there!
2271 checkpoint52j_pre
2272
2273 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
2274 error messages
2275 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
2276 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
2277 debug output
2278 o modfied mdsio_writefield.F to handle non-global files under exch2
2279 o update AIM Cubed-Sphere exp (aim.5l_cs):
2280 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
2281 o update AIM Equatorial Channel exp:
2282 use standard aim_v23 pkg and change the SST fields to be more realistic.
2283 o globalFile now works with exch2
2284 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
2285 mon_vort3.F to make exch2 friendly with >1 tile per cube face
2286 o limit timeave output for hi-res integrations
2287
2288 checkpoint52i_post
2289 o removed CPP_EEOPTIONS.h from verification/*/code
2290 o updated the tiling for global_ocean_pressure
2291 checkpoint52i_pre
2292
2293 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
2294 the old pkg/aim).
2295
2296 checkpoint52h_pre
2297 o shortened offending lines in exch2_send_rx?.template
2298 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
2299 o genmake2: add build & execute test for NetCDF code
2300 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
2301 old grid files, moved CPP_EEMACROS.h to pkg/exch2
2302 o added useSingleCPUIO flag to monitor.F and mon_out.F
2303 o added temporary hack for sea-ice dynamics on the cube:
2304 metric terms are ignored and it is assumed that
2305 there is no sea-ice on cube faces 1, 2, 4, and 5.
2306
2307 checkpoint52f_post
2308 o added exch2 cube routines to pkg/exch2
2309 o modified hs94.cs-32x32x5 to use it
2310 o added new grid files to hs94.cs-32x32x5
2311 checkpoint52f_pre
2312
2313 checkpoint52e_post
2314 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
2315 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
2316 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
2317 to work with implicit vertical advection and AB ;
2318 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
2319 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
2320 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
2321 checkpoint52e_pre
2322
2323 o fix bug in impldiff when Nr=1 or Nr=2.
2324 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
2325 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
2326 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
2327 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
2328 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
2329 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
2330 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
2331
2332 checkpoint52d_post
2333 o re-tiled many expts to allow comparison in multi-processor mode
2334 - updated output accordingly
2335 - changed hs94.128x64x5 to use intial T from file rather than use the
2336 random number generator
2337 o add infrastructure in model routines for fizhi and gridalt packages
2338 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
2339 o changes to permit hi-res, cubed-sphere, configuration
2340 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
2341 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
2342 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
2343 of surface winds for the cube
2344 (A verification experiment, based on global_ocean.cs32x15, but with
2345 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
2346 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
2347 complete with example surface forcing files and matlab scripts to look
2348 at the output and compare it with that of global_ocean.cs32x15.)
2349 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
2350 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
2351 to conform to the common rule.
2352 o check-in the first version of the coupler + interfaces for multi-components
2353 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
2354 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
2355 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
2356 - ocean and atmos. share the same horizontal grid (no interpolation).
2357 - exchanges between component and coupler is done in forward_step
2358 o new verification experiment, cpl_aim+ocn:
2359 coupled ocean - AIM atmosphere on cs32 grid.
2360
2361 checkpoint52d_pre
2362 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
2363 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
2364
2365 checkpoint52c_post
2366 o Fixing OPTIONS files for use of exf:
2367 - ALLOW_ECCO not needed
2368 - ECCO_CPPOPTIONS.h should not be included from
2369 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
2370 as has been the case in the past
2371 - All cal/exf related options are currently set in
2372 single header file. Should remain so until we
2373 agree on a consistent new policy.
2374 o Removed all CPP options for cal package.
2375 cal has no more CPP options.
2376 o modified STOREs in GAD_ADVECTION
2377 o corrected key comp. for passkey
2378
2379 checkpoint52b_post
2380 o new version: "thsice" of thermodynamic sea-ice pkg:
2381 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
2382 - modify fluxes but do not change theta directly;
2383 - light cleaning of bulk_force pkg (still needed with thsice).
2384 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
2385 + output_thsice.txt to test thsice & bulk_force pkgs.
2386 o put back grid & coriolis monitor output.
2387 checkpoint52b_pre
2388
2389 o call "do_the_model_io" at the beginning (=> dump initial state)
2390 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
2391 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
2392 (need info on NUMBER_OF_PTRACERS)
2393 o missing PTRACERS headers in some routines
2394 o default tamc.h in pkg/autodiff supposed to crash
2395 to ensure proper customization
2396
2397 checkpoint52a_post
2398 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
2399 - moved surfaceTendencyTice from pkg/seaice to main code
2400 - subroutine FREEZE_SURFACE now limits only surface temperature
2401 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
2402 => new output.txt for global_ocean.cs32x15 & global_with_exf
2403 - keep the old version of FREEZE for backward compatibility;
2404 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
2405 - corresponding modifs for TAF directives
2406 o added surface flux output variables to TIMEAVE_STATVARS
2407 o time-averaged output for pkg/ptracers
2408 o fix problem with ECCO-related divided adjoint
2409 snapshot file was missing some ad-variables,
2410 but no warning issued by TAF
2411
2412 checkpoint52a_pre
2413 o some bug fixes for #undef REAL4_IS_SLOW
2414
2415 checkpoint52 = ecco_c52_e35
2416 o after testing adjoints of checkpoint51u_post
2417
2418 checkpoint51u_post
2419 o this is the post-merge tag of the ecco-branch
2420 (needs another clean checkout and re-testing)
2421 o various natl_box_adjoint configs and results
2422 but no input fields
2423 o obcs adjoint not yet merged!
2424 o adding ECCO global 1x1 and 2x2 degree configs
2425 o updated/extended some store directives for seaice
2426 o pkg/ecco now containes ecco-specific part of cost function
2427 o top level routines the_main_loop, forward_step
2428 supersede those in model/src/
2429 previous input data.cost now in data.ecco
2430 (new namelist ecco_cost_nml)
2431 o in ctrl/ cleaned some cross-dependencies and updated CPP options
2432
2433 checkpoint51t_post
2434 o this is the pre-merge tag of the ecco-branch
2435
2436 checkpoint51s_post
2437 o cleanup: removed various obsolete #define-s
2438 o pkg/grdchk
2439 - renamed 'ph-grd 3' to 'grad-res'
2440 - merged from ecco-branch
2441 (remaining bug fixes for obcs gradient checks)
2442 - additional high-precision output for testreport
2443 (grep for 'precision_grdchk_result')
2444
2445 checkpoint51r_post
2446 o cleaned up or removed CPP_OPTIONS.h files
2447 o updated results for some of the tests to reflect the new
2448 optfiles (-ieee: -O0 instead of -O3)
2449
2450 checkpoint51q_post
2451 o cd_code:
2452 - moved cd_scheme.F -> cd_code_scheme.F
2453 - separate read_checkpoint from cd_code_ini_vars.F
2454 - separated cd_code part from write_checkpoint
2455 - updated AD_SOURCE, generated .flow
2456 - added CD_CODE_VARS.h to the_main_loop
2457 - Moving cd_code specific store dir.s to pkg/cd_code
2458 o ctrl package totally restructured
2459 - pack/unpack now optional and decoupled from
2460 xx_/adxx_ I/O
2461 - ctrl_pack/unpack cleaned
2462 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
2463 - confined inclusion of AD_CONFIG.h to where necessary.
2464 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
2465
2466 checkpoint51p_post
2467 o create initial cd_code package
2468 - WARNING: the initialization of fields within packages
2469 is broken because INI_FIELDS (where READ_CHECKPOINT is
2470 called) is called *before* PACKAGES_INIT_VARIABLES.
2471 This seems to be backwards since
2472 1) its important to initially zero the entire field including
2473 the "halo" region
2474 2) zeroing needs to be done *before* reading pickup info
2475 and the pickup call might or might not happen in any
2476 particular run
2477 - this needs an overhaul for R2
2478 o cleanup verification/*/code/GMREDI_OPTIONS.h
2479 o cleanup testreport
2480
2481 checkpoint51o_post
2482 o bringing AD-related verif's up to date with genmake2
2483 - carbon/
2484 - global_ocean.90x40x15/
2485 - hs.94.1x64x5/
2486 - (front_relax/ )
2487 o (more) consistent directory structure for AD-related verif.'s
2488 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
2489 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
2490 o bug fix in find_alpha.F for MDJWF:
2491 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
2492 change rho -> rho-rhoConst
2493 - replace call find_rho to find_rhonum
2494 o initialisation of rFlx extended to full array (required by TAF)
2495 and shifted to thermodynamics
2496 o removed PTRACERS.h in ptracers routine
2497 o added surfacetendencyPtr to S/R parameter list pracers_forcing
2498 o Correcting initialisations for fVerU, fVerV.
2499 o helping TAF to recognize dependency on kUp for
2500 fVerU, fVerV
2501 o Replacing delZ by delR in pkg/ctrl/
2502 checkpoint51o_pre
2503
2504 o undid all of cp51 pending some cleanups and discussion
2505 o added the [#include "AD_CONFIG.h"] statement to all files that need
2506 it for adjoint/tl #defines
2507 o re-worked the build logic in genmake2 to support AD_CONFIG.h
2508 o removed tools/genmake since it no longer works
2509
2510 checkpoint51n_post
2511 o modifications to make FREEZE flux visible to pkg/kpp
2512 - moved surfaceTendencyTice from pkg/seaice to main code
2513 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
2514 - subroutine FREEZE now limits only surface temperature
2515 (this means new output.txt for global_ocean.90x40x15,
2516 global_ocean.cs32x15, and global_with_exf)
2517 o added surface flux output variables to TIMEAVE_STATVARS
2518
2519 checkpoint51n_pre
2520 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
2521 o added [#include "AD_CONFIG.h"] to all files that use the following
2522 defines:
2523 - ALLOW_ADJOINT_RUN
2524 - ALLOW_TANGENTLINEAR_RUN
2525 - ALLOW_ECCO_OPTIMIZATION
2526
2527 checkpoint51m_post
2528 o incorporating changes to get TAMC/TAF working in genmake2
2529 - added new TAMC/TAF targets to the Makefile
2530 - various cleanups related to package handling
2531 - these changes should have no impact on the forward model
2532
2533 checkpoint51l_post
2534 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
2535 - faster algorithm for cal_addtime.F
2536 - higher precision arithmetic, where needed
2537 - pkg/exf *startdate variables changed from calendar date to
2538 model integration time
2539
2540 checkpoint51l_pre
2541 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
2542 o enable to apply restoring on S & T only in a latitude band.
2543 o update output (external_forcing_surf modif. change truncation errors)
2544 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
2545
2546 checkpoint51k_post
2547 o change default to: useNHMTerms=.FALSE.
2548 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
2549 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
2550 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
2551 exp1, ideal_2D_oce
2552 - change data file of oceanic exp (leave the results unchanged for now)
2553 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
2554 o set gravitySign automatically according to the vertical coordinate used
2555 (and change sign: back to "logical" value: +1 when R increases downward)
2556 o added an include barrier to the default CPP_OPTIONS.h and
2557 removed the #include "PACKAGES_CONFIG.h" from it
2558 o fix a bug in mom_fluxform (from chk51j_post)
2559
2560 checkpoint51j_post
2561 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
2562 o adjusted some flow directives (dynamics, thermodynamics)
2563 o added cubed-sphere case to test cost function
2564 o heckpoint_lev?_directives.h now include
2565 pkg-specific directives, whenever those are enabled.
2566 o Moving pkg-specific flow directives to corresponding pkg
2567 Moving pkg-specific differentiation list to corresponding pkg
2568 Moving pkg-specific checkpoint-lev storing to corresponding pkg
2569 ---> conventions are
2570 - pkg_ad.flow
2571 - pkg_ad_diff.list
2572 - pkg_ad_check_lev?_dir.h
2573
2574 checkpoint51i_post
2575 o merge of the branch-genmake2
2576 - knowingly breaks the older genmake
2577 - automatic generation of all ALLOW_${PKG_NAME} defines
2578 - new testreport supersedes older testscript
2579 o large number of package inclusion and header cleanups
2580 checkpoint51i_pre
2581
2582 o new output for adjoin of global ocean vector invariant
2583 o fix for checkpoint of thermodynamic seaice and bulk_force
2584 o Steph gchem various cleanups
2585
2586 checkpoint 51h_pre
2587 o fixed some single quotes
2588 o modify gchem pkg to be more versatile
2589 o modifications to clean up dic pkg
2590 o add pkg/cfc
2591
2592 checkpoint51g_post
2593 o provide links for ARPACK and ADM*TLM
2594 o start removing verification/vero/
2595 o update AD-related stuff
2596 (in particular some IF-statements in model/src/ routines)
2597 o adding to verification/global_ocean.90x40x15/ adjoint of
2598 vector invariant setup
2599
2600 checkpoint51f_post
2601 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
2602 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
2603 of tracer Green's fucntions for ocean inversion project.
2604
2605 checkpoint51f_pre
2606 o Added on-the-fly spatial interpolation capability
2607 "USE_EXF_INTERPOLATION" to pkg/exf.
2608 - This is a temporary Cartesian-grid hack until
2609 the super-duper ESMF coupler becomes available.
2610 - See verification/global_with_exf/README for usage example.
2611 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
2612 flags and modified pkg/seaice accordingly.
2613 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
2614 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
2615 non-local transport term.
2616
2617 checkpoint51e_post
2618 o pkg/mom_vecinv:
2619 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
2620 - add time-ave diagnostic of vorticity advection.
2621 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
2622 o atmospheric geopotential: - include water vapor effect;
2623 - use p^kappa in p* scaling.
2624 o land pkg: read initial state from files.
2625 o AIM : add stratospheric drag in the upper level
2626
2627 checkpoint51d_post
2628 o change function ILNBLNK (=> last non-blank char.) to return zero
2629 (instead of the string length) when the string. char is empty
2630 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
2631 o modif's to restore TAMC compatibility
2632 - avoid "_d" constructs in PARAMETER declarations
2633 - avoid interrupting lines by comment lines
2634 o Use cluster local disks for purely local I/O
2635 vs. globally visible disks needed for ctrl stuff
2636 (merged from ecco-branch)
2637 - new active_file_loc... and mdsio_..._loc routines
2638 - affected packages: autodiff, ctrl, grdchk, mdsio
2639
2640 checkpoint51c_post
2641 o introducing integer flag debugLevel
2642 - debLevZero: suppress all output
2643 - debLevA: standard
2644 - debLevB: equivalent to current debugMode=.TRUE.
2645 o introducing pathname variable mdsioLocalDir for mdsio
2646 that can be specified at runtime
2647 (relevant for cluster I/O to local disk)
2648 `
2649 >>>checkpoint51b_post
2650 adjoint of ptracers
2651 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
2652 o extended state in checkpoint_lev?, etc.
2653 o alternative ctrl/cost with tr1 or ptracer
2654 o new comlev1_bibj_ptracers
2655 o new ptracers.flow
2656 o made ptracers_forcing same as external_forcing_s
2657 o added verification for adjoint with ptracers
2658 - adm. grdchk fail so far
2659 - tlm. grdchk OK
2660 - checked tapelev/comlev recomputations: OK
2661 <<<checkpoint51b_pre
2662
2663 checkpoint51a_post
2664 o added code for biogeochemistry package
2665 - new pkgs: dic, gchem
2666 - new subroutine in ptracers
2667 o modify code for biogeo packages
2668 - in model/src and pkg/ptracers
2669
2670 checkpoint51
2671 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
2672 - autodiff, ctrl, exf, grdchk, seaice
2673 kept separate packages
2674 - cost, ecco, obcs
2675 o updating verification/internal_wave, verification/lab_sea
2676 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
2677
2678 checkpoint50i_post
2679 o Preparing next differentiable checkpoint and sync
2680 of MAIN vs. ecco-branch
2681 - 1st step: this one is differentiable
2682 - 2nd step: next(! not this) checkpoint will have updated packages
2683 from ecco-branch)
2684
2685 checkpoint50h_post
2686 o new package "land": provide surface BC for AIM.
2687 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
2688 o AIM: use true log-P extrapolation for near surface temp (= as in
2689 F.Molteni paper) ; update aim.5l_cs output.
2690 o New variable in PARM03 for more flexible pickups
2691 o somewhat cleaned package initialisation sequence for
2692 ctrl/ cost/ ecco/ in packages_... routines
2693
2694 checkpoint50g_post
2695 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
2696 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
2697 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
2698 made the default because of faster convergence than ADI
2699
2700 checkpoint50f_post
2701 o exf totally restructured
2702 - replaced all exf_set_ routines by one generic exf_set_gen.F
2703 and made sure it's still differentiable
2704 - split exf_getffields.F into new exf_bulkformulae.F
2705 - exf_inscal_/exf_outscal_ suffixes consistent with field names
2706 - updated adjoint/makefile and relevant verif. accordingly
2707
2708 checkpoint50f_pre
2709 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
2710 + change Evap over land. (update aim.5l_cs output)
2711 o added missing .cvsignores and made uniform across expts
2712 o changed configuration of tidal_basin_2d expt
2713 o added pkg/debug functions for tracing code in fatal crashes
2714 o tidied pkg/monitor to use MONITOR_OPTIONS.h
2715 o new fn in pkg/monitor to stop model if solution grows too big
2716 o removed lots of single quotes from comments
2717
2718 checkpoint50e_post
2719 o make KPP work with PTRACERS
2720 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
2721 nearly a copy of kpp_transport_s
2722 - there is no analogue to SurfaceTendencyS, so I have to use
2723 gPtr(of the surface layer) instead
2724 o add a new platform SunFire+mpi (SunFire 15000) to genmake
2725 checkpoint50e_pre
2726
2727 checkpoint50d_post
2728 o change kpp output from multiple-record state files to single-record state
2729 files analogous to write_state.F
2730 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
2731 analogous to the cg2d-related output.
2732 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
2733 so that writing to internal file fn (with length 512) fails.
2734 checkpoint50d_pre
2735
2736 checkpoint50c_post
2737 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
2738 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
2739 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
2740 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
2741 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
2742
2743 checkpoint50c_pre
2744 Merging from release1_p13:
2745 o bug fix for pkg/seaice dynamic solver
2746 o Added SEAICE_initialHEFF to pkg/seaice
2747
2748 checkpoint50b_post
2749 o store u*,v* in gU,V instead of in guNm1,gvNm1
2750 o in order to put the momForcing out of the Adams-Bashforth:
2751 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
2752 to timestep.F
2753 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
2754 o re-generate output for highly sensitive test-exp:
2755 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
2756
2757 checkpoint50b_pre
2758 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
2759 o corrected CPP option mismatch in exf_Bulk... functions for case
2760 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
2761
2762 checkpoint50a_post
2763 o Bug fix for merging between c50 and KPP.
2764 ikey was passed from thermodynamics to kpp_calc via
2765 common block rather than being recomputed in kpp_calc,
2766 in contradiction with new key itdkey.
2767 New key ikppkey created, and tamc.h headers updated.
2768
2769 checkpoint50
2770 - 2nd step of merge with ecco-branch:
2771 merge changes in ecco-branch back into main trunk
2772 - bug fix in find_alpha
2773 - more storing in gmredi_calc_tensor.F, kpp_routines.F
2774 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
2775 - merged some sliced AD support routines
2776
2777 checkpoint49
2778 merged from ecco-branch:
2779 o exf:
2780 - Enable initialisation of forcing fields to constant
2781 (runtime) values.
2782 - in exf_getffields.F
2783 Reduce i-/j-loop to interior domain, discarding overlaps.
2784 That also fixes wrong TAF-key computations for key_1, key_2
2785 with bulf formulae.
2786 - exf_init.F modify #ifdef for exf_init_evap
2787 - exf_getffieldrec.F, ctrl_getrec.F
2788 The following INT-usages are not safe:
2789 fldsecs = int(fldsecs/fldperiod)*fldperiod
2790 fldcount = int(fldsecs/fldperiod) + 1
2791 and were modified.
2792 o autodiff: checkpoint_lev...
2793 - updated storing for bulk formulae (some arrays were missing)
2794 - added state for seaice package
2795 - synchronized with main branch
2796 o DIVA:
2797 Modif.s in
2798 - the_main_loop.F
2799 - the_model_main.F
2800 and added cost_final_restore.F cost_final_store.F
2801 o With these changes, it is possible to fully separate
2802 the first forward run to compute the cost function (mdthe_main_loop)
2803 and adjoint runs over individual DIVA intervals (adthe_main_loop)
2804 into separate model executions.
2805 This enables better tuning of DIVA to given queue sizes.
2806 o Loss of cost function value in consecutive DIVA runs is
2807 fixed by storing to 'costfinal' file.
2808 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
2809 beginning/end of adjoint integration is accounted for.
2810 The current changes apply to TAF-1.4.26.
2811 TAF has one remaining bug, requiring one manual change
2812 (see MITgcm manual).
2813 o cal: synchronized between MAIN and ecco-branch
2814
2815 checkpoint48i_post
2816 o Changes to restore differentiability of code w.r.t. previous tag
2817 (mostly adding new routines to make list and replacing
2818 pressure by totPhiHyd).
2819 o Updated and merged grdchk package
2820 - has both ADM and TLM checks
2821 - works for single- and multi-proc.
2822 - output cleaned
2823 - worked successfully for parallel DIVA
2824 o genmake:
2825 - Adding -platform=SP4
2826 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
2827 o Modif. for DIVA:
2828 ctrl_unpack should not be called in intermediate DIVA interval.
2829 (similar thing would apply for active files such as
2830 tbar, sbar, psbar, which should not be reinitialised;
2831 only relevant for ecco-branch)
2832
2833 checkpoint48h_post
2834 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
2835 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
2836 o Added SEAICE_initialHEFF to pkg/seaice
2837 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
2838
2839 checkpoint48g_post
2840 --- EOS:
2841 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
2842 store total Potential in totPhyHyd for diagnostics & EOS.
2843 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
2844 --- Pressure/geopotential gradient:
2845 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
2846 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
2847 ( changes results of global_ocean_pressure )
2848 o NLFS + z-coord.: add eta*Rho' contribution.
2849 o accurate phiHyd when using interface-W at the middle between 2 centers
2850 ( changes results of ideal_2D_oce )
2851 o includes r* 2nd term in potential gradient.
2852
2853 checkpoint48f_post
2854 Merging from release1_p12:
2855 o Modifications for using pkg/exf with pkg/seaice
2856 - improved description of the various forcing configurations
2857 - added basic radiation bulk formulae to pkg/exf
2858 - units/sign fix for evap computation in exf_getffields.F
2859 - updated verification/global_with_exf/results/output.txt
2860 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
2861 (SBO) core products, including oceanic mass, center-of-mass,
2862 angular, and bottom pressure (see pkg/sbo/README.sbo).
2863 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
2864 to avoid negative values in shallow regions.
2865 - updated verification/natl_box/results/output.txt
2866 - updated verification/lab_sea/results/output.txt
2867 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
2868 o Added useSingleCpuIO option (see PARAMS.h).
2869 o Updated useSingleCpuIO option in mdsio_writefield.F to
2870 work with multi-field files, e.g., for single-file pickup.
2871 o pkg/seaice:
2872 - bug fix in growth.F: QNET for no shortwave case
2873 - added HeffFile for specifying initial sea-ice thickness
2874 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
2875 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
2876 kpp_transport_t.F, forward_step.F, and the_main_loop.F
2877 o pkg/seaice:
2878 - adjoint-friendly modifications
2879 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
2880
2881 checkpoint48e_post
2882 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
2883 o dynamics: change definition of computational domain & adapt mom_fluxform
2884 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
2885 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
2886 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
2887 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
2888 global_ocean.90x40x15 global_with_exf global_ocean_pressure
2889 inverted_barometer solid-body.cs-32x32x1
2890 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
2891
2892 checkpoint48d_post
2893 o in preparation for r*:
2894 a) use pre-computed gradient of hydrostatic potential:
2895 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
2896 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
2897 => affects results of glob_oce_pressure (different truncation error)
2898 update output.txt of ideal_2D_oce & global_ocean_pressure
2899
2900 checkpoint48d_pre
2901 o in preparation for r*:
2902 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
2903 pass the 2 comp. of the grad. as arguments to momentum S/R.
2904 but for the moment, only used if it does not change the results.
2905 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
2906
2907 checkpoint48c_post
2908 Modifications in treatment of initial flux forcing controls
2909 to avoid extra storing of flux fields.
2910
2911 checkpoint48c_pre
2912 o Added tidal_basin_2d experiment (currently 1D!)
2913 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
2914
2915 checkpoint48b_post
2916 o r* coordinate added in #ifdef NONLIN_FRSURF block.
2917 (modification to pressure gradient not yet implemented)
2918 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
2919 (for U & V) that are used for vertical advection of momentum.
2920
2921 checkpoint48a_post
2922 o In preparation for r*, use temp. array to compute vertical transport
2923 in flux-form momentum pkg. => change results of few test-exp.
2924 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
2925 lab_sea, natl_box & plume_on_slope
2926
2927 checkpoint48
2928 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
2929
2930 checkpoint47j_post
2931 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
2932 o moved adexch from forward_step to addummy_in_stepping
2933 o added exch in ctrl_map_...
2934 o aveFreq.=0. at end of cost_final to avoid overwrite in
2935 reverse checkpointing loop
2936 o Yet more changes in gmredi:
2937 * adgmredi_calc_tensor
2938 avoiding all recomputation of gmredi_slope_limit
2939 * adgmredi_x/y/rtransport
2940 added flag for excessive storing to avoid recomp. of
2941 u/v/rtans, dTdx/y/z
2942 -> this is not really necessary and very memory-consuming
2943 * adgmredi_slope_psi:
2944 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
2945 * gmredi_slope_limit
2946 re-activated full calculation of taperfct for case 'ac02'
2947 o updating verification/ adjoints of carbon, global_ocean.90x40x15
2948
2949 checkpoint47i_post
2950 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
2951 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
2952 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
2953 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
2954 o gmredi: fix few bugs.
2955
2956 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
2957 This will be a good checkpoint to plug into the ecco-branch.
2958 o few modif.'s to get latest version adjointed
2959 (mainly kick out code in ini_linear_phisurf)
2960 o modif's to run adjoint with exactConserv
2961 o case GM_BOLUS_ADVEC should be cleaned
2962 S/R gmredi_slope_psi should be cleaned
2963 o verification/carbon now has exactConserv=.TRUE.
2964
2965 checkpoint47g_post
2966 o time-average AIM output: becomes independent from statvars time-average
2967 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
2968 o After TAF bug fix:
2969 Tested adjoint of gmredi package.
2970 Tests were done with checkpoint47 rather than with latest
2971 checkpoint47f_post since the latter is broken for the adjoint
2972 verification/carbon/ contains both ADM and TLM gradient checks.
2973 Here they are, before they get changed/lost/stolen.
2974 Mostly modif.'s to fix numerical sensitivities.
2975 Gradient checks OK for
2976 - GM_taper_scheme:
2977 * clipping
2978 * ac02
2979 * linear
2980 * glw91
2981 * dm95
2982 * ldd97
2983 - GMREDI_OPTIONS:
2984 * GM_VISBECK_VARIABLE_K
2985 * GM_NON_UNITY_DIAGONAL
2986 * GM_EXTRA_DIAGONAL
2987 * GM_BOLUS_ADVEC
2988 in conjunction with data.gmredi parameters to be checked in
2989 in a few minutes under verification/carbon/code/
2990
2991 checkpoint47f_post
2992 Merging from release1_p10:
2993 o modifications for using pkg/exf with pkg/seaice
2994 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
2995 and SEAICE_EXTERNAL_FLUXES
2996 - pkg/exf CPP options EXF_READ_EVAP and
2997 EXF_NO_BULK_COMPUTATIONS
2998 - usage examples are Experiments 8 and 9 in
2999 verification/lab_sea/README
3000 - verification/lab_sea default experiment now uses
3001 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
3002
3003 checkpoint47e_post
3004 o created a tag prior to creating a branch
3005
3006 checkpoint47d_post
3007 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
3008 at the bottom boundary had an erroneous half slip boundary condition
3009 o added bottom drag and no slip boundary condition capabilities to
3010 oceanic pressure coordinates code
3011 o added new verification experiment global_ocean_pressure, this experiment is
3012 also described in the tutorial section of the manual
3013 checkpoint47d_pre
3014
3015 checkpoint47c_post
3016 o Added a verification experiment for a global cubed-sphere ocean run
3017 - verification/global_ocean.cubed32x32x30
3018 - uses pkg/therm_seaice and pkg/bulk_forcing
3019
3020 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
3021 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
3022 when using P-coordinate; only implemented for atmospheric config.
3023 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
3024 NOTES: requires option NONLIN_FRSURF to be "#define".
3025 o update advect_xz/results/output.txt (left from checkpoint44g_post)
3026
3027 checkpoint47b_post
3028 Merging from release1_p9:
3029 o pkg/seaice
3030 - removed GOTO's and added taf directives
3031 - double precision constants to reduce the g77 (Linux)
3032 to F77 (SGI) differences reported in release1_p8
3033 o tools/genmake
3034 - added SGI options
3035 o verification/testscript
3036 - updated to that of checkpoint47a_post
3037 o verification/global_ocean.90x40x15/input/eedata
3038 - modified for SGI f77 compatibility
3039 o verification/lab_sea
3040 - added description of sea-ice model
3041 - added missing matlab routines
3042 - added test of thermodynamics parallelization
3043
3044 checkpoint47a_post
3045 o new pkg: aim_v23
3046 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
3047 for now, keep the same surface forcing as before.
3048 - Part-Cell implemented into AIM; check that Heat & Water are conserved
3049 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
3050 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
3051 o add diagnostic of surface correction term in monitor output
3052
3053 o bulk_force and therm_seaice
3054 - Two packages: bulk_force (Bulk forcing)
3055 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
3056 - Earlier integration from Stephaine Dutkiewicz
3057 and Patrick Heimbach.
3058 - Two ifdef statements for compile time,
3059 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
3060
3061 checkpoint47
3062 differentiable version of checkpoint46n_post
3063 o bug fix in quasihydrostaticterms
3064 o * "clean" adjoint code (in terms of extensive recomputations)
3065 can now be obtained for all GMREDI options (i.e. for
3066 - GM_VISBECK_VARIABLE_K
3067 - GM_NON_UNITY_DIAGONAL
3068 - GM_EXTRA_DIAGONAL
3069 - GM_BOLUS_ADVEC )
3070 * However, wrong gradient check problem remains unsolved.
3071 * New CPP options have been introduced for different
3072 tapering schemes
3073 o external_fields_load now part of differentiation list
3074 o pressure needs multiple storing;
3075 would be nice to have store_pressure at beginning or
3076 end of forward_step, e.g. by having phiHyd global (5-dim.)
3077 (NB: pressure is needed for certain cases in find_rho,
3078 which is also invoked through convective_adjustment).
3079 o recomputations in find_rho for cases
3080 'JMD95'/'UNESCO' or 'MDJWF' are OK.
3081 o #define ATMOSPHERIC_LOADING should be differentiable
3082 o ini_forcing shifted to begining of initialise_varia
3083 o Incorporating QNVS line search routines into MITgcm
3084 (this is separate code, and therefore not under pkg)
3085 lsopt/, optim/
3086 o Updated verification/carbon/
3087 - #define GM_VISBECK_VARIABLE_K
3088 - GM_taper_scheme = 'ldd97'
3089
3090 checkpoint46n_post
3091 Merging from release1_p8:
3092 o verification/natl_box:
3093 updating new external_fields_load routine
3094 o New package: pkg/seaice
3095 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
3096 The sea-ice code is based on Hibler (1979-1980).
3097 Two sea-ice dynamic solvers, ADI and LSR, are included.
3098 In addition to computing prognostic sea-ice variables and diagnosing
3099 the forcing/external data fields that drive the ocean model,
3100 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
3101 The implied surface heat flux is then stored in variable
3102 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
3103 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
3104 non-local transport term. Because this call precedes model
3105 thermodynamics, temperature under sea-ice may not be "exactly" at
3106 the freezing point by the time theta is dumped or time-averaged.
3107 N.B.: fairly large differences in accuracy occur across
3108 different platforms/compilers; comparison between
3109 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
3110 generated output gives:
3111 T S U V
3112 C D M c m s m s m s m s
3113 n p a R g m m e . m m e . m m e . m m e .
3114 f n k u 2 i a a d i a a d i a a d i a a d
3115 g d e n d n x n . n x n . n x n . n x n .
3116
3117 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
3118 o GAD:
3119 - generated new common blocks to account for call of
3120 same gad routines with differing traceridentities
3121 (needed to modify tracerIdentity indices in GAD.h)
3122 - generated separate common blocks for case useCubedSphereExchange
3123 (Department of Futurology)
3124 - parameter lists to gmredi_?transport: added tracerIdentity
3125 - added new key indices to tamc.h
3126 o external_fields_load:
3127 - added this routine to TAF list
3128 - needed to make some common blocks global and additional storing
3129 along the same lines as exf package (checkpoint_lev?_directives.h)
3130 o exf:
3131 updated external forcing package
3132 - bug fixes carried over from ecco-branch
3133 (missing OBCS_OPTIONS.h in two routines)
3134 - enable easy to use "no forcing".
3135 - added exf I/O for atmospheric loading
3136 - added exf I/O for runoff data
3137 - transfered scaling between exf <-> MITgcm to exf namelist
3138 o Adding new verification experiment global_with_exf.
3139 This verification experiment is almost identical to the
3140 global_ocean.90x40x15 experiment, except that it uses
3141 the exf (and cal) package instead of the
3142 external_fields_load routine (cf README file).
3143
3144 checkpoint46m_post
3145 o modified testscript to return -- when there are no lines of "%MON" output
3146 o added new flag "quasiHydrostatic" for QH mode
3147 and new routine quasihydrostaticterms()
3148 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
3149 New routine: mom_u_coriolis_nh()
3150 o fixed sign of non-hydrostatic metric terms in u and v equations.
3151 Depend on correct sign of gravitySign.
3152 o added work.pc* to .cvsignore in aim directories using ifc
3153 o introduced flag for controllin non-hydrostatic metric terms
3154 o removed gravitySign from PARM04
3155 o switched to g77/ifc from pgf77 in aim experiments
3156
3157 checkpoint46l_post
3158 o made convective adjustment work with pressure coordinates:
3159 - changed the direction of k-loop in convective_adjustment.F for the
3160 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
3161 - adjusted the reference pressure k-index in convective_adjustment.F
3162 - adjusted the convection condition in convect.F (in analogy to
3163 calc_ivdc.F)
3164 - convective_adjustment no longer computes anything on the halos
3165 - removed the warnings about negative salinity from find_rho.F and
3166 find_alpha.F; instead the new routine look_for_neg_salinity, called
3167 at the beginning of find_rho, find_alpha, and find_beta, does a
3168 check of the entire slice, if CPP-option
3169 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
3170 checkpoint46l_pre
3171
3172 checkpoint46k_post
3173 o fixed the verification/global_ocean.90x40x15 experiment:
3174 - new bathymetry (the world according to A., JMC, and M.)
3175 - new initial fields and forcing fields (*.bin files)
3176 - new POLY3.COEFFS (for the next release one should switch to a full
3177 equation of state: JMD95P or MDJWF)
3178 - fixed several errors and redundancies in the data file
3179 - experiment uses looped cells
3180 - added matlab directory with diagnostic scripts for plotting of output
3181
3182 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
3183 - read AIM physics parameters from a file (data.aimphys)
3184 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
3185
3186 checkpoint46j_post
3187 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
3188 o move wVel computation at the end of the time step, in S/R integr_continuity
3189 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
3190 o update timeave pkg for wVel diagnostic.
3191 checkpoint46j_pre
3192
3193 checkpoint46i_post
3194 o Clean up AIM package (and keep the results unchanged):
3195 include CPP_OPTION and use IMPLICT NONE in all routines ;
3196 declare all the variables _RL ; use _d 0 for all numerical constants.
3197 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
3198
3199 checkpoint46h_post
3200 o cleaned up the use of rhoNil and rhoConst.
3201 - rhoNil should only appear in the LINEAR equation of state, everywhere
3202 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
3203 and the dynamical equations are all divided by rhoConst
3204 o introduced new parameter rhoConstFresh, a reference density of fresh
3205 water, to remove the fresh water flux's dependence on rhoNil. The default
3206 value is 999.8 kg/m^3
3207 o cleanup up external_forcing.F and external_forcing_surf.F
3208 - can now be used by both OCEANIC and OCEANICP
3209 checkpoint46h_pre
3210
3211 Added code to convert surface volume flux (fresh water) into
3212 a mass flux when using P coordinates in the ocean (OCEANICP).
3213 Note: It assumes you have set rho0=rhoConst=density of fresh water.
3214
3215 checkpoint46g_post
3216 o Include a new diagnostic variable phiHydLow for the ocean model
3217 - in z-coordinates, it is the bottom pressure anomaly
3218 - in p-coordinates, it is the sea surface elevation
3219 - in both cases, these variable have global drift, reflecting the mass
3220 drift in z-coordinates and the volume drift in p-coordinates
3221 - included time averaging for phiHydLow, be aware of the drift!
3222 o depth-dependent computation of Bo_surf for pressure coordinates
3223 in the ocean (buoyancyRelation='OCEANICP')
3224 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
3225 Theta, Salinity, and Pressure in the parameter list. This routine is
3226 presently contained in find_rho.F. This routine does not give the
3227 correct density for 'POLY3', which would be a z-dependent reference
3228 density.
3229 o cleaned up find_rho
3230 - removed obsolete 'eqn' from the parameter list.
3231 o added two new verification experiments: gop and goz
3232 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
3233 checkpoint46g_pre
3234
3235 checkpoint46f_post
3236 o Enable tangent linear (forward mode) gradient checks:
3237 - extended active file handling to g_... files
3238 - added TANGENT_SIMULATION to theSimulationMode
3239 - extended grdchk package accordingly
3240 o added tangent linear setup in verification/carbon/code_ftl
3241 o added adjoint setup in verification/front_relax/code_ad
3242
3243 checkpoint46e_post
3244 o Added new equation of state -> MDJWF
3245 - EOS of McDougall et al., 2002, JAOT, submitted
3246 - caveat: the equation of state is only valid for a smaller (more
3247 realistic?) range of values than JMD95P/Z and UNESCO
3248 - added masks to the calculation of pressure in store_pressure
3249 - added more check values for density in check_eos (ini_eos.F), some of
3250 the old check values are out of the range of the MDJWF-eos, so don't
3251 expect perfect matches for those
3252 checkpoint46e_pre
3253
3254 checkpoint46d_post
3255 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
3256 'OCEANICP', also initialised field pressure correctly in ini_eos in the
3257 case of pressure coordinates. eosType='JMD95Z' in
3258 combination with buoyancyRelation='OCEANICP' now causes an error.
3259 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
3260 in find_alpha/beta.
3261 checkpoint46d_pre
3262
3263 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
3264 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
3265
3266 checkpoint46c_post
3267 o Changes necessary for ocean in p-coordinates
3268 - Added new buoyancy relation = 'OCEANICP'
3269 - Added new parameters = gravitySign (this used to be contained inside
3270 the factor dRdZ which I added when we first switched to R coordinates).
3271 X GM/Redi is not compatible (yet)
3272 X bottom drag and no-slip need to be debugged.
3273 checkpoint46c_pre
3274
3275 checkpoint46b_post
3276 o Added new equation of state -> JMD95Z and JMD95P
3277 - EOS of Jackett and McDougall, 1995, JAOT
3278 - moved all EOS parameters into EOS.h
3279 - new routines ini_eos.F, store_pressure.F
3280 o Added UNESCO EOS, but not recommended because it requires
3281 in-situ temperature (see JMD95)
3282 o Modified formatting for knudsen2.f in utils/knudsen2 and added
3283 unesco.f to be used with POLY3
3284 checkpoint46b_pre
3285
3286 checkpoint46a_post
3287 o Added (atmospheric) pressure loading
3288 - new field in FFIELDS.h, etc...
3289 - new cpp flag ATMOSPHERIC_LOADING
3290 o Changed hFacC to _hFacC in calc_phi_hyd.F
3291 o Added SHORTWAVE_HEATING to some files for consistency
3292 checkpoint46a_pre
3293
3294 checkpoint46
3295 further merges from release1_p5
3296 o new ctrl package
3297 - adopted from ECCO environment to enable optimization
3298 - added Eliassen Palm fluxes to controls
3299 o added Eliassen Palm flux controls to gradient check package
3300 o cost package
3301 - Compatible with new ctrl package
3302 - added Eliassen Palm cost hooks
3303 - modif's of existing cost functions
3304 o Adjoint-related bug fixes in kpp:
3305 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
3306 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
3307 o autodiff package
3308 - flow directives:
3309 + new for S/R do_the_model_io
3310 + enhanced for S/R checkpoint
3311 + new gmredi.flow
3312 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
3313 disable adcommon.h/g_common.h by default.
3314 - fixed problem for adjoint of global_max
3315 o modified verification/carbon/
3316 o New setup for adjoint of global_ocean
3317 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
3318 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
3319 o incorporated hooks for sponge layer code (external_forcing.F)
3320
3321 checkpoint45d_post
3322 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
3323 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
3324 (affects plume_on_slope "cg2d" output)
3325 o add new parameter deltaTfreesurf for free-surface time stepping
3326 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
3327 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
3328 o change phiMin in exp1 (to agree with documentation)
3329 o add new flags:
3330 - T,S forcing inside/outside Adams-Bashforth
3331 - turn off temp,salt advection and/or forcing
3332 - for each tracer, define internal flag for multiDimAdvection & A-B
3333 o monitor: change definition of KE to check conservation of Energy
3334
3335 checkpoint45c_post
3336 o Removed f90 comments ("!")
3337 o Modified initialisations to enable exf package for MITgcm
3338 (without invoking ECCO_PACKAGE).
3339 o modifications to gradient check package (Martin Losch)
3340 - enable centered differences
3341 - modified format of standard output
3342
3343 checkpoint45b_post
3344 o cleaned exchange calls in cg2d
3345 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
3346 o included CPP option SINGLE_LAYER_MODE in thermodynamics
3347 to configure barotropic setup (Martin Losch)
3348 o moved some initialisations within bi,bj loop in dynamics
3349 (TAF flow dependency)
3350 o in initialise_varia, moved call packages_init_variables
3351 before convective_adjustment_init
3352 (corresponding adjustment of TAF tape initialisation).
3353 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
3354
3355 checkpoint45a_post
3356 o compute Rho over the whole domain (extend iMin,jMin indices)
3357 o specific exchange for X-slice domain (case Ny=1)
3358 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
3359 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
3360
3361 checkpoint44h_post = checkpoint45
3362 o Fix to restore differentiability:
3363 place at which packages_init_variables is called in
3364 initialise_varia is crucial for reverse control flow.
3365 o modifications in GMRedi to enable stable adjoint
3366 (corresponding modif's in thermodynamics, dynamics)
3367 o added missing hook for sponge layer code in external_forcing
3368 o modified test cost functions
3369 o storing in gad_advection (plus removal of write(0,*)!
3370 o missing headers TR1.h added in convective_adjustment routines
3371 o errorMessageUnit set non-equal zero in eeboot
3372 (conflict on some platforms, e.g. IBM SP3)
3373 o modified carbon verif.
3374
3375 checkpoint44h_pre
3376 o vertical grid option: allow to put the Interface at the middle between
3377 2 cell-centers ; replace delZ in pkg/kpp by drF.
3378 o GM Advective form: Tracers are advected using the residual transport (=
3379 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
3380
3381 checkpoint44g_post
3382 o fix surface correction term in multiDimAdvection (affects plume_on_slope
3383 results) ; ifdef missing in thermodynamics.F
3384
3385 checkpoint44f_pre,checkpoint44f_post
3386 o added PTRACERS package
3387 This allows an arbitrary number of passive tracers to be integrated
3388 forward simultaneously with the dynamicaly model.
3389 + Implemented so far:
3390 - basic forward algorithm (time-stepping, advection, diffusion, convection)
3391 - I/O and checkpointing
3392 - GM/Redi *but* using the GM/Redi coefficient of Salt
3393 + Not implemented so far:
3394 - KPP
3395 - OBCS
3396 + No specific example supplied (yet) but global_ocean.90x40x15 has the
3397 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
3398 line in data.pkg.
3399 + This package is disabled by default since it increases storage.
3400
3401
3402 o testscript: added -cleanup option
3403 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
3404 b) enable to filter 2D fields.
3405
3406 checkpoint44e_pre,post
3407 o re-wrote convective adjustment to use pre-calculated weights
3408 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
3409 Adds: model/src/convective_weights.F, convectively_mixtracer.F
3410 Original calls to convect() still in place.
3411
3412 chkpt44d_pre,post
3413 o added missing EXCLUDE_MONITOR flags
3414 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
3415 (incompatible typ in MIN/MAX expressions caused problems
3416 on IBM SP3)
3417 o in genmake added variable MAKEDEPEND
3418 plus resetting for case SunOS
3419 o added timer_stats.c routine for IBM SP3
3420 o removed variables in dynamics
3421 !!! I forgot to create tag chkpt44d_pre !!!
3422 !!! But chkpt44d_pre = chkpt44c_post !!!
3423
3424 o real fresh water flux implemented with non-linear free-surface.
3425
3426 chkpt44c_pre,post
3427 o few fix (mask in shap_s2, EmPmR in external_field_load,
3428 USE_NATURAL_BCS in solve_for_P);
3429 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
3430
3431 checkpoint44b_pre/_post
3432 o merge of relevant stuff from the ecco-branch:
3433 - genmake: removed $S64 overwrite for case SunOS
3434 - pkg/exf: update and corrections for field swapping and obcs
3435 - pkg/ecco: parameter lists for the_model_main, the_main_loop
3436 harmonized between ECCO and MITgcm
3437 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
3438 updated checkpointing_lev... lists for obcs
3439 - model/src: minor changes in forward_step, plot_field
3440 added directive for divided adjoint in the_main_loop
3441 - pkg/mdsio: added mdsio_gl_slice
3442
3443 o check parameters & config (chkpt44a_pre,post)
3444 o OBC and NonLin_FrSurf.
3445
3446 checkpoint44
3447 o fix bug in mom_vi_del2uv
3448 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
3449 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
3450 o update AIM experiments (NCEP input files)
3451 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
3452 o added some stuff for AD
3453
3454 checkpoint43
3455 o added two new advection tests
3456 o added global 4x4 degree ocean test
3457 o added test of H&S94 with free surface on cube
3458 o some final mods for gradient check, adjoint,...
3459
3460 checkpoint42
3461 Fixed AD-related problems:
3462 o Store directives up-to-date with re-arranged Adams-Bashforth
3463 (mainly thermodynamics.F)
3464 o New store directives for multi-dim. advection schemes
3465 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
3466 * new common block and key passkey
3467 (mainly gad_advection.F)
3468 o Modified store directives for split of dynamics/thermodynamics
3469 for the case ALLOW_KPP
3470 o Cleaned argument list for timestep_tracer.F
3471
3472 checkpoint41
3473 o re-formatted/added comments in prologues of key subroutines
3474 to work with protex
3475
3476 checkpoint40
3477 o moved calc_gs, calc_gt and calc_tr1 back to model/src
3478 o added FLT (floats) package from Arne along with demo. experiment
3479 o re-arranged Adams-Bashforth scheme for tracers to allow easier
3480 implementation of forward-in-time forcing terms
3481 o more mods for non-linear free-surface including new variable
3482 o modified multi-dim method to work on cube
3483 o bug fix in KPP (from DM)
3484
3485 checkpoint40pre9
3486 o added DST advection schemes
3487 o fix MPI bug on SGI's
3488 o modifications for non-linear free-surface
3489 o fixed conditionals for fixed flow/passive tracer only mode
3490 o added tension/strain form of stress tensor
3491 o changes to commenting of arguments for TAF/TAMC
3492 o added/updated many matlab scripts
3493 o added multi-dimensional advection method for tracers
3494
3495 checkpoint40pre8
3496 o new package rw/
3497 Added method for dumping intermediate local arrays:
3498 mdsio_writetile - same as mdsio_writefield except works from inside
3499 bi,bj loop
3500 mdsio_writelocal - same as mdsio_writetile except works for local
3501 arrays
3502 write_local_r? - higher-level wrapper for mdsio_writelocal
3503 Controlled by diagFreq. Defaults to zero (ie. no dumps)
3504 Example given at end of mom_vecinv.F that dumps some local arrays.
3505 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
3506 control flux-form versus vector invariant code.
3507 Switch is runtime flag vectorInvariantMomentum (defaults to false)
3508 or genmake -DISABLE ...
3509 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
3510 (additional storing is now needed for case vecinv;
3511 currently nothing implemented to switch this storing off
3512 in case fluxform is used since no CPP flag available).
3513
3514 checkpoint40pre7
3515 o bug fix in dynamics.F
3516 calc_viscosity called before k=1,Nr loop.
3517 o added some #ifdef's ALLOW_PASSIVE_TRACER
3518 o cleaned initialisations in ctrl_map_ini
3519 related to TAF
3520
3521 checkpoint40pre6
3522 o split dynamics into thermodynamics & dynamics
3523 o corresponding split of calc_diffusivity into
3524 calc_diffusivity, calc_viscosity
3525 (kpp_calc_diff, kpp_calc_visc).
3526 o Added diffkr, kapgm to control variables
3527 o bug fix in gmredi_slope_limit for ldd97
3528
3529 checkpoint40pre5
3530 o proper initialization of Adams-Bashforth time stepping
3531 + uses forward step for very first step of model (iter=0)
3532 o re-generated *all* output since almost all output is modified by this
3533 change (sorry but we've been putting this one off for about 2 years)
3534 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
3535 *not* regenerated since they are already out of date and I don't
3536 want to create the impression that they are suddenly working.
3537 o removed KAP stuff for DEC's
3538 o modified/added many .cvsignore files in */code and */input
3539 o added new expt "solid-body.cs-32x32x1"
3540 + this uses an alternative form of ini_curvilinear_grid.F which
3541 is not necessarily any better than the current one...
3542
3543 checkpoint40pre4
3544 o added re-initialisations of utrans,vtrans,rtrans in
3545 calc_common_factors which are crucial for TAF.
3546 o extended iMin,jMin range for calc_common_factors,
3547 calc_diffusivity
3548 o added option ALLOW_PASSIVE_TRACER
3549 o a few minor updates and fixes
3550
3551 checkpoint40pre3
3552 o created calc_gtr1.F for gad package
3553 o split the_main_loop and re-introduced forward_step
3554 o some recomputations of nIter0 for TAMC
3555
3556 checkpoint40pre2
3557 o Updated to latest branch of AJA, JMC
3558 o Added gradient check package
3559 o Added routines for passive tracer handling
3560 o Added carbon sequestration sensitivity experiment
3561
3562 checkpoint39
3563 o Modifications and fixes to support TAMC
3564 (mainly missing or wrong directives)
3565 o Corrected common blocks when fooling TAMC to produce adjoint I/O
3566 in addummy_in_stepping
3567 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
3568 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
3569 o Included following packages:
3570 cal: calendar
3571 exf: external forcing
3572 ecco: essential routines to control use of cal, exf
3573 (NB: this is not the full ECCO environment)
3574 o disabled some packages by default in genmake
3575
3576 checkpoint38
3577 o see notes_c37_adj.txt
3578 o corrected wrong layer index in external_forcing_t
3579 o replaced the_main_loop/forward_step by the_main_loop
3580 o removed forceoutput from write_state
3581 (replaced criteria for initial/final state)
3582 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
3583
3584 checkpoint37
3585 o mdsio.F routine split and packaged in pkg/mdsio
3586 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
3587 used unless genmake -disable=mdsio)
3588 o allow a more precise surface-geopotential gradient for the atmosphere
3589 taking into account the change in space of Alpha (=1/rho) at the surface.
3590 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
3591 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
3592 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
3593 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
3594 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
3595 o Time-Average diagnostics defined as a pseudo package "timeave".
3596 o pickup files : old pickup (before c35) did not work with new code (c35
3597 and after) unless activating 2 commented lines in initialise-varia.
3598 o Non-Hydrostatic pickup file Pb fixed.
3599 o bug with Rigid-lid version (since c35) fixed.
3600
3601 checkpoint36
3602 o implement Crank-Nickelson barotropic time-stepping
3603 o recover Time-Average diagnostics
3604 o fix Pb in checkpoint (PR#19)
3605 o AIM become a standard package ; clean unused CPP_kees
3606
3607 checkpoint35
3608 o subtantial rewrite of dynamics.f
3609 o allows staggered time-stepping
3610 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
3611 o added bottom drag (linear + quadratic)
3612
3613 checkpoint34
3614 o Modified exchange routines for correct reverse simulation.
3615 o Added verification output to comply with bug fix in impldiff.F
3616 as of c33 (exp2, natl_box).
3617 o Corrected store directives in dynamics.F
3618 o Corrected array boundaries in impldiff.F
3619 o Corrected array dimensions in gmredi.
3620 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
3621 o Added routine GLOBAL_SUM_INT to global_sum.F
3622 o Added mdsio_gl.F for ECCO purposes.
3623
3624 checkpoint33
3625 o Fixed bug in lower BC in impldiff.F
3626 o Fixed confusion about units of forcing arrays in FFIELDS.h
3627 namely Fu,Fv,Qnet,Qsw,EmPmR:
3628 - Removed verification/natl_box/code/external_fields_scale.F
3629 (did not differ from that in model/src)
3630 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
3631 (see FFIELDS.h for description)
3632 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
3633 kpp_calc.F and kpp_transport_t.F
3634 - Removed model/src/external_fields_scale.F and calls to it
3635 - verification/natl_box uses flux data with "atmospheric" sign so
3636 a special version of external_fields_load.F is used to
3637 change the data as it's read in. This way, the arrays
3638 have the right units and signs at all times tha a user could
3639 possibly use them.
3640 o Corrected genmake to delete a temporary file during configuration
3641
3642 checkpoint32
3643 o Scaling of forcing fields moved from external_forcing.F to
3644 external_fields_scale.F, called directly after loading fields.
3645 o Surface relaxation terms added to surface tendency fields in
3646 extra subroutine.
3647 o impldiff.F changed to avoid storing by TAMC of huge intermediate
3648 fields.
3649 o Changes in GMRedi to comply with packaging structure.
3650 o Modifications and bug fixes in KPP package.
3651 o Verification experiment for KPP added (verification/nat_box/)
3652
3653 checkpoint31
3654 o Packages interface brought in line with defined standard
3655 -> new routines packages_...F
3656 -> changes in initialise_fixed.F, initialise_varia.F
3657 -> enables initialisation interface for ECCO package
3658 o Rescaling of external forcing fields immediately after read
3659 (removed from external_forcing.F)
3660 -> new: surface_fields_scale.F
3661 -> affects ini_foorcing.F, external_fields_load.F
3662 o Computation of surface tendencies before tendency updates.
3663 -> new: external_forcing_surf.F
3664 o Change of variable names useGMRedi, useKPP, useECCO
3665 o Further changes in dynamics.F, impldiff.F for TAMC
3666 o Tested for experiments 0, 2, 4.
3667 - not yet tested for GMRedi.
3668 - not yet tested for KPP.
3669
3670 checkpoint30
3671 o Updates for OBCs
3672 o New experiment for test OBCs (internal_wave)
3673 o New output.txt in verification/exp4/results/
3674 o Updates for KPP: calculation of viscosity corrected, new variables
3675 kpp_dumpFreq and kpp_taveFreq
3676 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
3677 and entry for T90 in genmake
3678
3679 checkpoint29
3680 o packaged KPP and GM/Redi
3681
3682 checkpoint28
3683 o Corrected initialization of hFacMin for difference vertical coordinates
3684 o Modified calculation of partial cell thickness to more robust algorithm
3685 o config_summary.F: replaced write_1D_... by write_0D_...
3686 read_write.F: added subroutines write_0D_...
3687 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
3688 included some initialisations required for TAMC.
3689 o routine calc_isoslopes: modified sqrt computation to make it
3690 differentiable for zero argument.
3691 o routines dynamics, impldiff:
3692 included store directives and tape key computations required for TAMC.
3693 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
3694
3695 checkpoint27
3696 o fixed calc_isoslopes() to so that cancellation of terms in tensor
3697 formulation works properly with variable resolution.
3698 o restructured the calling tree between the_model_main() and dynamics()
3699 o split initialise() into initialise_fixed() and initialise_varia()
3700 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
3701 in new routine ini_psurf()
3702
3703 checkpoint26
3704 o moved some #ifdef in optional routines to encompass everything
3705 except the argument declarations. This was using up some memory.
3706 o fixed macros like _ADT to work with both versions of Linux cpp
3707 o cleaned up some unused and uninitialized variables
3708 (helps when debugging with strict compile options)
3709 o split up CPP_EEOPTIONS.h into options and macros
3710 (macros are now in eesupp/inc/CPP_EEMACROS.h)
3711 o patch for 2 processor JAM mode
3712
3713 checkpoint25
3714 o updates for OBCs and NH
3715 o dramatically reduced memory usage
3716 o added "JAM" routines for use on Artic network
3717 o parameterization of convection by implicit vertical diffusion
3718 o added a diagnostic of convective index
3719 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
3720 (this is was partly for OBCs and NH but also in anticipation of
3721 an explicit free-surface option)
3722 o initial state input files for U and V
3723
3724 checkpoint24
3725 o Removed some spurious "REAL"s
3726 o Updated KPP to latest version from JPL
3727 o Added a COS(latitude) in horizontal viscosity
3728
3729 checkpoint23
3730 o Added del^4 diffusion for salt and temperature
3731 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
3732
3733 checkpoint22
3734 o Made many small changes: implicit none, format(i5), etc...
3735 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
3736
3737 checkpoint21
3738 o Introduced new I/O package that supports direct-access records (mdsio.F)
3739 o Split-up mid-level I/O routines
3740 o Updated input data for experiments 0,1,2,4 and 5
3741 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
3742
3743 checkpoint20
3744 o Tidied up open-boundaries some more
3745 o Added non-hydrostatic code
3746 o Fixed some input data
3747 o Modified MPI start-up to work in "coupled" context.
3748
3749 checkpoint19
3750 o Tidied up directory structure for verification experiments.
3751 o Added new code for open boundaries.
3752 o Corrected advective terms near boundaries.
3753 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
3754 o Implemented free-slip/no-slip BCs and del^4 dissipation.
3755 o Split default parameters out of ini_parms.F into set_defaults.F.
3756
3757 checkpoint18
3758 o Further changes for optional code generation with
3759 CPP - ugh!
3760
3761 checkpoint17
3762 o Beginning to incorporating modularity
3763 for supporting atmos. and ocean configs.
3764 o Small changes for TAMC complinace
3765 o New ultra simple test case. Barotropic box
3766 configuration "exp0".
3767
3768 checkpoint16
3769 o Minor changes to exchange routines to support
3770 accumulation in reverse mode. Adjoint of an
3771 assignment is an addition.
3772 o Changes to support compilation by TAMC (LR(1)
3773 syntax) and by g77 under Linux ( 72 character
3774 limit ).
3775
3776 checkpoint15
3777 Rewrote exchange routines to allow
3778 o General tile <-> tile connectivity.
3779 o TAMC reverse mode flag ( is this really needed? )
3780 o Variable width overlap and exchange region widths.
3781 o Hooks for sharing data via DMA, Arctic, Memory Channel,
3782 shmput/shmget, VIA, SYSV shmem and every other cool
3783 communication method.
3784
3785 checkpoint14
3786 Consistent isomorphism chages made. These allow dynamical core
3787 to support both pressure and meters as a vertical coordinate.
3788
3789 checkpoint13
3790 Release which corrects global_max problem and a couple
3791 of KGM time-averaging diagnostic errors. Also contains
3792 a double-gyre experiment setup as well as the baseline
3793 4 degree global template. The double gyre template is
3794 organised to allow it to be applied automatically to
3795 the baseline configuration.
3796
3797 branch-point-rdot
3798 A few tidy-ups have been made bt the real point of this
3799 check-point (excuse the pun) is to allow a branch to be
3800 made for the purposes of adding the rDot alterations.
3801 I don't want to commit the rDot to the main-trunk until
3802 we've actually tested it...
3803
3804 checkpoint12
3805 Tidy up and added generic genmake script (formerly
3806 configure script).
3807 Released to testers.
3808
3809 checkpoint11
3810 Re-arranged initialise() and introduced ini_vertical_grid()
3811 and ini_masks_etc().
3812
3813 checkpoint10
3814 Introduced the configure script.
3815 Separated out the diags package.
3816 Added template for writing time-averages of tile/intermediate quantities.
3817 Updated SIZE.h in exp2 and made the data big-endian.
3818
3819 checkpoint9
3820 MPI fix. Filename changes (meta/data). salbin*y stuff.
3821 General tidy-up.
3822 SST.bin SSS.bin added to verification/exp2
3823
3824 checkpoint8
3825 Inludes time-dependant forcing and time-averaging.
3826 Works at 4x4 and 2.8125x2.8125 global
3827
3828 checkpoint7-4degree-ref
3829 Branch from checkpoint7. Released for application to
3830 global modeling and general modeling - process studies, regional
3831 model etc..
3832 Configured for verification/exp2 - 4 degree global, two process.
3833
3834 checkpoint7
3835 Created by cnh
3836 Simple 4 degree global simulation
3837 configuration.
3838 Includes climatological wind,
3839 hydrography, bathymetry etc
3840 Does not include Heat Flux and E-P
3841
3842 checkpoint6
3843 Created by cnh
3844 merged checkpoint5 with CD and
3845 spherical polar code.
3846 Still some problems with GM Redi
3847 abd full topography.
3848
3849 checkpoint5
3850 Created by AJA
3851 contains updates to GM Redi
3852 and reordered timestepping loop
3853 for Implicit Diffusion.
3854
3855 checkpoint4
3856 Created by cnh
3857 Contains memory saving macros ( _rdxc etc..) for when
3858 grid variations are limited.
3859 Contains polynomial coeffs for EOS and knudsen program
3860 for generation.
3861
3862 checkpoint3
3863 Created by cnh
3864 Added extra flags for runtime options
3865 Added this file
3866 Added implicit free-surface
3867 Added pre-conditioner
3868 Put compare01 into repository ( compare01/... )
3869 Put data and eedata into repository ( verification/exp1 )
3870
3871 checkpoint2
3872 Created by AJA
3873 Added GM/Redi
3874
3875 checkpoint1
3876 Created by AJA
3877 Restructured kloop in dynamics.F
3878 Added non-linear EOS
3879
3880 baseline
3881 Original checked in code

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