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Revision 1.1738 - (show annotations) (download)
Mon Sep 17 22:32:32 2012 UTC (11 years, 8 months ago) by jmc
Branch: MAIN
Changes since 1.1737: +9 -1 lines
document changes in pkg/obcs

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.1737 2012/09/15 23:01:51 jmc Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 o pkg/obcs:
8 - change settings of OB index in case OB coincides with tile edge (shared by
9 2 tiles), so that common OB location is registered by both tiles (instead of
10 only 1). However, for Southern and Western OB, index value = 0 is not
11 recognized as valid OB index (=default null value) and needs to be fixed.
12 - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
13 - new parameter "OB_indexNone" for null index value (for now, still zero)
14 to replace hard-coded null index value of zero.
15 o pkg/exch2:
16 - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
17 always check buffer-size (but outside the loop); move checking for valid
18 index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
19 print each tile and point connection only if |W2_printMsg|>= 2 and 3.
20 o pkg/ctrl (pack & unpack):
21 - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
22 (locally defined) for different variables (+ remove the variable-specific
23 file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
24 (to be extended to other local file names in ctrl.h).
25 o pkg/flt:
26 - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
27 o pkg/mdsio:
28 - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
29 o tools/genmake2:
30 - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
31 (added by Alistair in version 1.51 for building without make depend);
32 - remove Header files list (H_SRC_FILES) from the dependence of targets
33 ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
34 place in version 1.23): this save going through staf when unrelated header
35 file has been modified.
36 Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
37 "make depend" step, still need to do "make links" before "make adtaf".
38 o eesupp/src (+ few pkg src files) & genmake2:
39 - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
40 - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
41 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
42 upper/lower case ; account for space between "#" and undef/define)
43 o pkg/flt (with exch2):
44 - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
45 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
46
47 checkpoint63s (2012/09/05)
48 o pkg/ecco:
49 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
50 - add more relevant #ifdef ALLOW_SMOOTH ones.
51 - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
52 o pkg/ctrl:
53 - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
54 ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
55 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
56 doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
57 ctrlSmoothCorrel3D (new).
58 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
59 - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
60 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
61 controls when useAtmWind, and vice versa.
62 - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
63 - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
64 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
65 - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
66 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
67 - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
68 replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
69 o pkg/smooth:
70 - remove un-necessary includes.
71 - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
72 Those CPP options were never defined, and not necessary.
73 o model/src:
74 - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
75 - standard treatment of useSMOOTH.
76 o pkg/autodiff:
77 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
78 useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
79 o pkg/exch2:
80 - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
81 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
82 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
83 and tiles to process mapping.
84 - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
85 moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
86 rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
87 from w2_eeboot.F to w2_readparms.F.
88 o eesupp/src:
89 - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
90 ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
91 also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
92 - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
93 is defined (remove condition on usingMPI) to match cases where MPI_INIT
94 has been called.
95 - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
96 - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
97 (so that on 1 proc, get same myPid independently of usingMPI)
98 - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
99 useCubedSphereExchange with EXCH-1 (safer).
100 - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
101 o pkg/ggl90:
102 - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
103 used in ALLOW_GGL90_SMOOTH code.
104 o pkg/flt:
105 - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
106 floats at the Southern end of the domain).
107 o eesupp/inc:
108 - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
109 but not used (and not to be used) anywhere, just for documentation.
110 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
111 - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
112 a) can damage previously written records in any other multi-record files.
113 b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
114 o tools/genmake2:
115 - define variable MAKE within Makefile and use it in place of 'make';
116 - update AD_CONFIG.h (if needed) before building any of the executable
117 (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
118 and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
119 - always print usual warning comment 'this file is automatically generated'
120 from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
121 o pkg/cheapaml:
122 - updated to correspond to the code used in accepted paper (Nico Wienders).
123 o pkg/exf:
124 added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
125 ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
126 and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
127 o pkg/exf, autodiff, ctrl, ecco and seaice:
128 remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
129 o pkg/ctrl, ecco:
130 allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
131 Depending on useAtmWind, one is inactive, and the other is active (see
132 exf_getffields.F/exf_getsurfacefluxes.F).
133 o tools/genmake2:
134 - improve error msg when failing in 2nd test of check_for_broken_Ff
135 - fix option '-makefile' short-name (-mf according to genmake2 -help)
136 - source local config file "genmake_local" just after processing the genmake2
137 command arguments (previously done before processing arg).
138 o pkg/grdchk:
139 - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
140 to this routine from cost_final has been dropped in g_cost_final)
141 - improve printed information (more explicit msg, no longer using "print *,"
142 fix fcpertminus printed value).
143 o model/src:
144 - move call to COST_INIT_VARIA out of packages_init_variables.F directly
145 into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
146 this prevents getting cost-funct reset in adinitialise_varia recomputations.
147 o pkg/dic:
148 - move initialisation of "freefe" array from from dic_biotic_forcing.F to
149 fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
150 o pkg/grdchk:
151 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
152 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
153 o pkg/autodiff/ctrl/grdchk :
154 - attempt to sort out what works and what does not,
155 with regard to I/O, and to warn/stop accordingly.
156 o pkg/grdchk:
157 - attempt to fix grdchk in the case of useSingleCpuIO.
158 - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
159 statements were moved from grdchk_main.F and into
160 grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
161 - a global sum is applied to record numbers icvrec/layer
162 out of grdchk_loc so that they be passed to I/O routines.
163 o pkg/smooth:
164 - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
165 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
166 o verification/testreport:
167 - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
168 - can also use compressed (gzip) reference output file;
169 - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
170 to be easier to collect by testreport.
171 - update existing TLM output (half out-of-date by more than 3 yrs).
172 - report NETCDF & LAPACK settings (from genmake2) in output dir.
173 - report run-time in each individual summary (previously only for AD test);
174 for TLM test, add also TAF version.
175 - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
176
177 checkpoint63r (2012/08/15)
178 o tools/genmake2:
179 - fix Makefile for target ftlall (+ update files to clean after make ftlall)
180 o pkg/ecco/ecco_cost_final.F :
181 - fix fc print statements (to stdout and costfunction0000) so
182 that the printed value is always after the global sum.
183 o pkg/seaice/seaice_dynsolver.F :
184 - fix ice strength assymptote at SEAICE_area_max<1
185 (no change for the standard case of SEAICE_area_max=1)
186 o some cleaning:
187 - pkg source files: ensure that all *.F files from each pkg included the
188 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
189 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
190 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
191 includes;
192 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
193 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
194 is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
195 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
196 - update option-file CPP_OPTIONS.h of all AD experiments:
197 * no longer include PACKAGES_CONFIG.h ;
198 * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
199 * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
200 including ECCO_CPPOPTIONS.h).
201 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
202 - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
203 separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
204 not necessary accurate).
205 - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
206 pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
207 deliberately break compilation (a remainder that it needs to be customized)
208 - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
209 - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
210 - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
211 o tools/genamke2:
212 - check for lapack.
213 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
214 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
215 jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
216 from both packages.
217 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
218 - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
219 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
220 of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
221 o pkg/cost : add comments to explain special and/or untested setups.
222 o pkg/exf:
223 - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
224 (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
225 o verification/*/code_ad:
226 mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
227 - reccord when this file is included (define ECCO_CPPOPTIONS_H)
228 - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
229 allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
230 o pkg/seaice :
231 - added possibility to change ice strength/PRESS0 relationship to
232 HEFF, according to the following run time parameters
233 SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
234 SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
235 SEAICEpresH0 :: HEFF threshold for ice strength (m)
236 o pkg/ggl90 :
237 - added run time flag mxlSurfFlag to include the code that ensure
238 mixing between first and second level (previously included as a comment)
239 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
240 - add test of newly added dumpAdByRec=T option where
241 we write all records to one file per variable.
242 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
243 - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
244 to check that this code is ok with taf and compiles in adjoint.
245 o pkg/autodiff :
246 - added run time param dumpAdByRec : ad dump format switch.
247 If true then write all records to one file per variable.
248 Else write one file per record (remains the default).
249 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
250 o pkg/seaice:
251 - Added SEAICEuseTILT run time switch : if set to
252 false then omit the tilt term in seaice dynamics.
253 - Fix free drift calculation.
254 o pkg/shelfice:
255 When initializing SHELFICEDragQuadratic, set default to be
256 consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
257 but retain option to set it independently
258 (inconsistenty spotted by Veronique Dansereau)
259 o eesupp/inc:
260 - in EEPARAMS.h, add real-type constant for some frequently used simple number
261 (0,1,2,1/2), with name explicitly referring to RS/RL type.
262 o model/src:
263 - move balancing of relaxation terms to new S/R balance_relax.F.
264 o pkg/autodiff:
265 re-write active I/O high-level (control) S/R:
266 - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
267 - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
268 - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
269 MDS_READ/WRITE_FIELD); change loops to multi-threads.
270 - update and merge active_file_control_slice.flow into active_file_control.flow
271 - update the calls in lower level S/R (active_file.F, active_file_g.F and
272 active_file_ad.F) keeping the argument list and function unchanged.
273 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
274 =.TRUE.") and remove high-level (control) _loc version (not called anymore).
275 - new low-level active I/O routines, one for each type (RL/RS), for active var
276 of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
277 fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
278 right type.
279 o autodiff and RS=real*4:
280 - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
281 ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
282 - change argument type of 3-D mask argument to _RS to match type in the call
283 (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
284 o pkg/thsice:
285 - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
286 - option to correct ocean fresh-water flux for imbalance of Atmos+Land
287 fresh-water flux: uniform correction or proportional to local precip.
288 o pkg/ctrl:
289 - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
290 - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
291 ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
292 - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
293
294 checkpoint63q (2012/07/30)
295 o pkg/autodiff:
296 note about monitor and snap-shot of ad-variables:
297 a) need to apply ADEXCH before monitor or output of ad-vars to include
298 overlap contributions (was done for adjDump but missing for monitor).
299 b) since ADEXCH implies adding overlap values to interior array, machine
300 truncation error is expected when adding an ADEXCH call in the middle of
301 the time-stepping (although mathematically identical).
302 modifs:
303 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
304 declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
305 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
306 apply ADEXCH before monitor or snap-shot of ad-variables:
307 =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
308 - implement new method (copy+adexch) for snap-shot and monitor of main model
309 ad-vars (initially not used by default -> output unchanged).
310 - change default (set to 2) to use new method and update few output_adm.txt
311 with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
312 and both tutorial_tracer_adjsens tests).
313 - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
314 and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
315 o pkg/ctrl:
316 enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
317 generic control variables via
318 #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
319 Only required customization should be S/R ctrl_map_ini_genarr.F
320 (routine in repository contains example)
321 o pkg/exf:
322 - fix and refine checking of surface-relaxation setting when using EXF
323 o verification (adjoint exp):
324 - reduce length of simulation by half for experiment global_ocean.cs32x15
325 (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
326 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
327 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
328 of KE that can occur with aggressive optimization
329 + put quadratic bottom drag calculation in separated loops (only done if
330 using bottomDragQuadratic)
331 o model/src: CG2D_NSA
332 - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
333 and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
334 - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
335 change cg2d residual target to be expressed in Wunits (=> do not normalise
336 RHS ; this fix global_max Pb with TAF); update output.
337 o verification/tutorial_tracer_adjsens:
338 improve parameter consistency (and get rid of warnings):
339 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
340 - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
341 - use staggerTimeStep (for stability) in som81; use default rotation period.
342 o pkg/exch2:
343 - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
344 reset to 0 = 1 long line in X)
345 o pkg/mdsio:
346 - fix reading of dimensions from meta file for large-size domain
347 o model/src:
348 - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
349 - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
350 Cubed-Sphere Exch with CS-corners inside the domain;
351 make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
352 globalArea and to set hasWetCSCorners.
353 - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
354 metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
355 - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
356 useCDscheme and useCubedSphereExchange).
357 o pkg/seaice/seaice_growth.F :
358 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
359 for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
360 when the previous code was not correct.
361 - in all cases diagnoze the boundary condition mismatch to SIaaflux
362 - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
363 that term to QNET (essentially to set the melt/freeze water to 0degC).
364 when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
365 o verification/global_ocean.cs32x15/input.seaice :
366 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
367 - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
368 - update results (output.seaice.txt) accordingly.
369 o verification/lab_sea/input/data.seaice :
370 - remove SEAICEheatConsFix, which is now be tested
371 in global_ocean.cs32x15. The presently coded fix
372 is only consistent with real fresh water + nlfs.
373 - update results (output.txt) accordingly.
374 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
375 o AD_CONFIG.h file:
376 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
377 - remove #include "AD_CONFIG.h" from all included OPTIONS files and
378 add it explicitly in each fortran src file where it is needed.
379 motivation: header file AD_CONFIG.h is generated/modified after "make depend"
380 thus introducing potentially wrong dependency; therefore, better to include
381 it only where it's really needed, and after any other included OPTIONS file
382 (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
383 or ALLOW_TANGENTLINEAR_RUN).
384
385 checkpoint63p (2012/07/06)
386 o pkg/autodiff:
387 - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
388 - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
389 which are now read from new parameter file "data.autodiff" (inAdExact
390 previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
391 - add file "data.autodiff" in all verification/*/input_ad/ directories.
392 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
393 mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
394 o verification/tutorial_tracer_adjsens/
395 - add extra sub-verification which uses "SOM" advection scheme
396 (2nd Order-Moment Advection Scheme, Prather Limiter) with
397 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
398 and in data:
399 multiDimAdvection=.TRUE.,
400 tempAdvScheme=81,
401 saltAdvScheme=81,
402 o model/src:
403 - introduce ALLOW_BALANCE_RELAX which allow the removal
404 of the global mean of relaxation terms by setting
405 balanceThetaClimRelax and balanceSaltClimRelax
406 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
407 This case is now treated appropriately in seaice_growth.F
408 o pkg/seaice:
409 - do balanceEmPmR and balanceQnet based on the net fluxes
410 (SItflux) that enter the ocean+ice system rather than QNET
411 and EMPMR. Works best in real fresh water.
412 - SIatmFW, SIatmQnet, and SItflux computations had to be moved
413 out of the diagnotics bloc, and stored in global arrays.
414
415 checkpoint63o (2012/06/29)
416 o vertical mixing schemes:
417 - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
418 - replace computation of density (in Function STATE1, opps_calc.F) by a call
419 to S/R FIND_RHO_SCALAR
420 - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
421 and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
422 affects output (vermix.ggl90) at truncation level.
423 o testreport:
424 - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
425 (nSx,nSy) for the number of threads (from eedata.mth)
426 o model/src:
427 - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
428 related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
429 o verification/tutorial_tracer_adjsens/
430 - compile with ALLOW_CG2D_NSA
431 - run with nonlinFreeSurf=3
432 - update reference output_adm.txt
433 o tools/genmake2:
434 - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
435 refine usePROFILES switching off (only when NetCDF is not available).
436 o verification (atmospheric set-up):
437 - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
438 o pkg/profiles : refine profiles and files handling.
439 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
440 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
441 - changes to use model/src/the_main_loop.F rather than the ecco version
442 in ecco type adjoint runs.
443 o model/src:
444 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
445 - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
446 - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
447 o model/src:
448 - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
449 update output of test experiment bottom_ctrl_5x5.
450 o pkg/generic_advdiff:
451 - implement vertical bi-harmonic diffusion (for now, only for T & S and
452 only explicitly).
453 o verification/bottom_ctrl_5x5/
454 update reference output (results changed quite some time ago,
455 not sure when; but new reference results look ok in terms of grdchk)
456 o verification/1D_ocean_ice_column/
457 For verification purposes, the exact adjoint rather than an approx.
458 should be used (e.g., to comare against F.D. or TLM).
459 removed autodiff_inadmode*_ad.F routines in code_ad/
460 Update results/ accordingly.
461 o pkg/cal:
462 - change cal_getdate.F so that output date is function of input time only
463 (less ambiguous, not mixed up with input iteration number).
464 - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
465 o pkg/diagnostics:
466 - implement calendarDumps also for stats-diags
467 - implement calendarDumps also for snap-shot output (negative freq)
468 - for now, ignores calendarDumps if non-zero phase-lag.
469
470 checkpoint63n (2012/06/04)
471 o model/src:
472 - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
473 between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
474 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
475 similar to calc_r_star.F); update results of experiment internal_wave and
476 tutorial_global_oce_in_p (affected @ truncation level).
477 o pkg/shelfice:
478 - add parameterisation of advective-diffusive flux into the ice shelf
479 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
480 - simply eps3/3a computation
481 o eesupp:
482 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
483 between tiles, just fill-in edges assuming locally periodic subdomain) and
484 add corresponding exchange subroutines (EXCH0);
485 - new CG-solver version (_EX0) for disconnected-tiles special case.
486 o model/src (CG-solvers):
487 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
488 (similar final residual output and max-Iter number as with standard version);
489 - allows to store and use lowest-residual solution (standard & _SR versions);
490 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
491 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
492 o eesup/src:
493 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
494 ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
495 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
496
497 checkpoint63m (2012/04/27)
498 o pkg/shelfice:
499 - account for partical cells in surface level below ice-shelf for hydrostatic
500 pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
501 o ad test experiments:
502 - update and rename to "ad_optfile.local" local AD-optfile specific to a
503 particular adjoint verification experiment (in verification/*/code_ad/)
504 o pkg/seaice & pkg/exf:
505 - Part two of ECCO-CLIVAR code merges.
506 Completes merge of seaice area relax. code.
507 Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
508 to be set in EXF_OPTIONS.h since this pkg controls its I/O
509 (and avoids second CPP option in SEAICE_OPTIONS.h)
510 - change default value of costIceStart & costIceEnd to a valid date.
511 - add snowPrecip to HSNOW in seaice_growth
512 o pkg/ptracers:
513 - move ptracers summary and setup check into separated S/R ; add a check for
514 valid PTRACERS_Iter0 value (error+stop or just warning).
515 o pkg/cal (+ pkg/ecco):
516 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
517 as input; and for AD, unless both are not differentiable (e.g., k index)).
518 o model/src:
519 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
520 is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
521 temporary set to usingZCoords value (to be changed to F when using shelfice).
522 - hydrostatic pressure: implement partial cell near the surface also for
523 Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
524 usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
525 o pkg/ctrl/ctrl_init.F:
526 - add a formal parameter to s/r ctrl_init_rec to print
527 xx_$(ctrl_valiable)_file for easier debugging
528 - move call of cal_* routines into the if-block where they are really
529 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
530 to specify a startdate
531 o pkg/seaice:
532 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
533 global_ocean.cs32x15/code versions).
534 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
535 verification experiment global_ocean.cs32x15.seaice and update results.
536 o pkg/exf:
537 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
538 (according to useExfYearlyFields).
539 o pkg/cal:
540 - move calendar setting & summary (previously in cal_readparams.F) into new
541 S/R CAL_INIT_FIXED to be called later in the initialisation process, once
542 length of the simulation is set (after SET_PARMS call); This is an attempt
543 to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
544 - For safety: keep a record of pkg/cal parameter settings status
545 to allow to STOP if one pkg/cal S/R is called too early.
546 - add a stop in all basic pkg/cal subroutines if called before setting is done.
547 - modify cal_getdate.F: stop when nothing was returned;
548 if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
549 this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
550
551 checkpoint63l (2012/04/04)
552 o pkg/bbl:
553 - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
554 update global_with_exf output.yearly.txt file.
555 o pkg/cal:
556 - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
557 - remove 2 unsused and very short (1 line only) functions ;
558 - remove unsused subroutines from AD-Diff list.
559 o model/src:
560 - start to implement clean wait to stop in initialization S/R (config_check.F,
561 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
562 o folowing PRINT_MESSAGE changes:
563 - remove reminder multiple print to the same file (STDOUT) when multi-threads.
564 o pkg/bbl:
565 - modification so it can work with z*
566 - replace deltaT with dTtracerLev(k) for asynchronous time stepping
567 - global_with_exf/input.yearly verification; changes output.yearly.txt
568 o eesupp/src:
569 - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
570 writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
571 - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
572 # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
573 - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
574 - when using MPI, always set usingMPI=T ; set default accordingly and stop
575 if not consistent.
576 - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
577 argument is zero (in case called within single-thread section).
578 o pkg/fizhi:
579 clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
580 in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
581 o pkg/exch2:
582 - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
583 activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
584 - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
585 but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
586 with bad ones coming from a not-yet-updated halo.
587 This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
588 o pkg/frazil:
589 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
590 http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
591 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
592 o verification/lab_sea
593 * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
594 * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
595 * nTimeSteps 3 -> 4
596 * changed reference output accordingly
597 o pkg/ctrl:
598 * fix ctrl_get_gen for xx_sst, xx_sss
599 o pkg/fizhi:
600 - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
601 update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
602 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
603 fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
604 clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
605 o pkg/gmredi:
606 - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
607 o pkg/fizhi:
608 - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
609 (old)aces open64 tuv test.
610 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
611 o pkg/mom_vecinv:
612 - fix 1 loop range in mom_vecinv.F to be like all the other loops which
613 set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
614 with non-lin free-surf).
615 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
616 in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
617 some compilers (gfortran 4.6.0 on MacOS)
618 o momentum:
619 - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
620 & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
621 fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
622
623 checkpoint63k (2012/03/17)
624 o model/src:
625 - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
626 flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
627 - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
628 (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
629 o model/src: solve_*diagonal.F
630 - replace division with multiplication by inverse (similar to original version)
631 update output of AD exp. global_ocean.90x40x15.
632 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
633 to enable the use of the vectorized & differentiable solve_tridiagonal.F
634 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
635 vertical advection (to get solve_tridiagonal tested in AD mode).
636 o pkg/seaice: ECCO-CLIVAR merge:
637 1. seaice AREA relaxation
638 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
639 * runtime flag: SEAICE_tauAreaObsRelax
640 2. modified global mean cost imbalance code: CPP option
641 ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
642 o another iteration on solve_*diagonal.F
643 Make choices independent of AUTODIFF
644 Default will be the adjoinable vectorized version.
645 Alternative choices are:
646 * non-adjoinable original version with low memory footprint:
647 #define SOLVE_DIAGONAL_LOWMEMORY
648 * still adjoinable but does not vectorize (k as inner-most loop):
649 #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
650 o testreport
651 - add option to use a home made wrapper around "make"
652 - remove MITGCM_IEEE env. variable (no longer active)
653 o pkg/shelfice
654 - improve computation of friction velocity for velocity dependent
655 exchange coefficients: include velocities into SHELFICEBoundaryLayer
656 block to average velocities vertically
657 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
658 o Modify diagonal solvers, now three versions (upon request):
659 #ifndef SOLVE_DIAGONAL_AUTODIFF
660 1. default version (dating back a while ago)
661 #else /* def SOLVE_DIAGONAL_AUTODIFF */
662 # ifdef SOLVE_DIAGONAL_KINNER
663 2. adjoinable version with k-innermost loop (G. Forget)
664 # else
665 3. adjoinable vectorized version of 2.
666 # endif
667 #endif /* SOLVE_DIAGONAL_AUTODIFF */
668 All flags are currently set within routines, but could/should be moved to CPP-options.
669 Array bounds for 1. are as before, for 2.,3. cover the entire domain
670 (could be changed for 1. too).
671 o verification/lab_sea (fwd):
672 - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
673 use 7 categories (except hb87), new solve4temp params (except salt_plume),
674 constant salinity (=4) or variable salinity (salt_plume) done through
675 SItracer.
676 o pkg/seaice:
677 - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
678 - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
679 SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
680 from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
681 SEAICE_freeze got retired) but already better than previously with
682 SEAICE_freeze=123456.7 deg.C;
683 - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
684 (safer multi-threaded setting); always set SEAICEuseEVP;
685 - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
686 SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
687 stop if multiple specifications for the same coeff; make sure default
688 SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
689 o pkg/obcs:
690 - allow to switch to upwind 1rst order advection scheme for the advective
691 flux computation at the open-boundary; disabled for adjoint built.
692 o pkg/ptracers:
693 - rename PTRACERS_RESTART.h -> PTRACERS_START.h
694 - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
695 - add parameter to decide when to start a tracer; use internal flag to
696 know which tracer to step-forward; switch this internal flag at the top
697 of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
698 for adjoint built.
699 o pkg/seaice:
700 - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
701 - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
702 - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
703 o pkg/ecco:
704 - fix writing of output file DiagnosCost_ClimSalt/Theta
705 and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
706 o pkg/seaice:
707 - add missing initialisation of COR_ICE array in dynsolver.F
708 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
709 compiled either way, and is tested in all exps (multidim was only tested
710 in lab_sea ad before).
711 - cosmetic change to prepare for future addition of ITD. no change to results.
712 no defaults change.
713 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
714 - by lack of adequate verification experiments, I further used custom versions
715 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
716 should be correct.
717 - avoid recomputations in ad.
718 o array initialisation in adjoint mode:
719 1) pkg/mom_common/mom_calc_ke.F:
720 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
721 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
722 part this initialisation is gone, resulting in Floating Point Exception
723 (caught by open64 compiler with debug option).
724 2) model/src/convective_weights.F
725 set output convectCount over the full array range (instead of doing
726 an update): this fix a similar issue when called within recomputation (adjoint)
727 which could by-pass the initialisation (normally done in the caller S/R).
728 o pkg/seaice:
729 - final version of turbulent flux params, as agreed at MIT ice meet:
730 SEAICE_mcPheePiston (default is ~ 0.000875)
731 SEAICE_mcPheeTaper (default is 0.)
732 SEAICE_frazilFrac (defualt is 1.)
733 SEAICE_mcPheeStepFunc (default is false)
734 - changes results at trunction error level
735 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
736 o added pkg/frazil:
737 - see frazil_description.tex for details
738 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
739 o pkg/shelfice/shelfice_thermodynamics.F
740 - fix exponents for velocity dependent exchange coefficients: change
741 from 2/3(=0) to 0.66666666666666667
742 - move computation of velocity dependent exchange coefficients into
743 separate loop, so that it applies to both thermodynamics
744 - move some divisions by constants out of loops
745
746 checkpoint63j (2012/02/16)
747 o pkg/seaice:
748 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
749 - SItracer: added run time params, and allow coupling to ocn salinity.
750 o pkg/seaice: remove (almost) all divisions by constants within loops
751 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
752 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
753 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
754 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
755 o pkg/seaice :
756 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
757 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
758 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
759 - add permanent SItflux diag that corresponds to TFLUX but includes
760 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
761 - allow activation/testing of a fix for suspected missing term in
762 ocn-ice heat budget (to be confirmed). To test this, you want to
763 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
764 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
765 - no change in results, fwd or ad.
766 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
767 - switch to variable freezing point.
768 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
769 - bug fix : the sublimation term that was missing is now activated.
770 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
771 - bug fix : flooding sign term for SIsal0.NE.0.
772 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
773 o pkg/seaice:
774 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
775 is now the default, and the old default constant freezing point is recovered
776 with SEAICE_tempFrz0 = -1.96,
777 SEAICE_dTempFrz_dS = 0.,
778 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
779 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
780 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
781 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
782 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
783 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
784 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
785 seaice_growth r149 for legacy branch (no results change).
786 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
787 from I. Fenty).
788 - results did not change except for global_ocean.cs32x15, mostly due to the
789 switch to variable freezing point (see above item for detail).
790 o pkg/thsice:
791 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
792 seawater freezing in thsice_calc_thickn (not used).
793 o pkg/seaice: turbulent flux term specification via run time params.
794 - replace CPP switches with run time switches to facilitate testing
795 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
796 GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
797 - added runtime parameter : SEAICEturbFluxFormula
798 - move Mcphee constants to SEAICE_PARAMS.h
799 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
800 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
801 remove seaice_summary call (moved to seaice_init_fixed)
802 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
803 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
804 - seaice_summary.F : add missing report of read turbulent flux term set up
805 and SITRACER.
806 - seaice_check.F : check range; inform and stop if retired CPPs are used
807 (incl. SEAICE_AGE).
808 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
809 CPP switch, same computation as before for the different options.
810 - change results at the truncation level.
811 o pkg/seaice:
812 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
813 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
814 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
815 - update verification/*/input*/data.seaice:
816 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
817 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
818 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
819 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
820 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
821 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
822 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
823 difference in results only due to machine truncation.
824 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
825 MaykutPolySatVap; keep MIN_LWDOWN.
826 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
827 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
828 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
829 o pkg/salt_plume:
830 - isolate saltPlumeFlux array exch into a specific S/R called from
831 do_oceanic_phys.F
832 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
833 o verification:
834 - move untested set-up to MITgcm_contrib/verification_other.
835 o pkg/seaice:
836 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
837 o pkg/seaice:
838 - seaice_solve4temp.F (keeping results unchanged):
839 * add 2 future run-time params to select which saturation vapor pressure
840 formula is used and how post-iteration fluxes are set.
841 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
842 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
843 the linearized expression to stay consistent with tsurf finding.
844 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
845 can be < 0.
846 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
847 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
848 conductive heat flux F_c , and add it explicitly when updating tsurf as
849 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
850 so that now F_ia has a consistent meaning through the entire routine.
851 This causes differences at truncation level: update output of fwd exp.
852 global_ocean.cs32x15.seaice.
853 o pkg/seaice:
854 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
855 of arrays, sign/direction of fluxes; no effect on results.
856 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
857 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
858 note: this should have been done before changing celsius2K default.
859 - to keep results unchanged, add back old value of celsius2K in verification
860 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
861 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
862 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
863 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
864 freezing temp is consistent with value in seaice_growth.F ; this causes
865 differences at machine truncation level: update lab_sea AD output (3/4).
866 o pkg/seaice:
867 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
868 and climsst/sss even when using seaice (to prevent calculation that might
869 use SST on land); does not affect any verification exp.
870 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
871 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
872 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
873 over land (non-legacy code)
874 o vectorize salt_plume package:
875 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
876 - this code computes plumebk everywhere (also over land), thus requires
877 code to avoid divisions by zero and catch the case of kLev=Nr.
878 - efficiency of salt_plume_frac is still sub-optimal
879 o tools (genmake2):
880 - fix makefile NAME specification (option: -makefile NAME) by adding
881 "-f $MAKEFILE" in few places where it was missing including makedepend
882 command (contribution from Paul).
883
884 checkpoint63i (2012/01/24)
885 o model/src:
886 - add factorized versions of some EOS code to find_rho.F,
887 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
888 o model/src:
889 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
890 - change default celsius2K from 273.16 to 273.15
891 - to keep results unchanged, add back old value of celsius2K in verification
892 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
893 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
894 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
895 to make TAF generate vectorizable code
896 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
897 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
898 have flags that do this more efficiently.
899 o pkg/diagnostics/diagstats_calc.F
900 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
901 o pkg/obcs (with exch2):
902 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
903 and remove code (in obcs_readparms.F) which was based on EXCH of indices
904 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
905 o pkg/exf and seaice exp:
906 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
907 so that switching off area & heff advection flags does not affect results.
908 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
909 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
910 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
911 results of verification experiments: 1D_ocean_ice_column(fwd),
912 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
913 and offline_exf_seaice (all 4).
914 o pkg/seaice:
915 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
916 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
917 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
918 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
919 not multi-dim advection;
920 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
921 SHORTWAVE_HEATING #undef.
922 o optim: make Makefile more robust (?)
923 o pkg/obcs:
924 * fix treatment of obcs_read_pickup for TAF
925 o pkg/shelfice:
926 * add missing initialisation of num_shifwflx
927 * new adjoint verification exp. for isomip
928 * change Prandtl and Schmidt numbers from generic formulations
929 (in terms of model diffus. and visc.) to separate runtime
930 parameters, with Holland and Jenkins (1999) default values.
931 o pkg/exf (interpolation):
932 - extended input field (2 rows) near the N & S poles:
933 * fill in with the symetric value (when even Nb of data in longitude)
934 * add average value at the poles only for scalar quantities ; for vector
935 component interpolation, skip the averaging and keep duplicated values,
936 unless the 2 components have same location (uvInterp=T) in which case
937 interpolate the 2 components together using S/R EXF_INTERP_UV.
938 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
939 together: this allows to account properly for local orientation when
940 averaging at N & S pole.
941 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
942 exf-interpolation near N & S poles. Undef by default.
943 - add debug check/print on 1rst iter if debugLevel >=2.
944 o pkg/exf:
945 - change masking flags definition (no longer "parameter"), put them in
946 common block and set them in S/R EXF_INIT_FIXED.
947 - change recognized masking flag from s,u,v to c,w,s since the mask
948 to use (maskC,W,S) depends on position on model grid and has little to
949 do with scalar/vector difference; fix masking if using P-coordinates.
950 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
951 and update results of exp. global_with_exf (x2).
952 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
953 o pkg/obcs
954 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
955 o pkg/exf (interpolation):
956 - assume periodicity in X only if input field cover full longitude range.
957 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
958 and should vectorise).
959 - fix input lat of the 2 added row (in case we provide N.pole data).
960
961 checkpoint63h (2011/12/30)
962 o pkg/seaice:
963 - change declaration of UVM from _RL to _RS in order to get B-grid
964 uIce,vIce monitor when _RS = real*4
965 o pkg/offline:
966 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
967 - compute vertical velocity if not read from file (switch on exactConserv
968 & staggerTimeStep);
969 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
970 o verification:
971 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
972 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
973 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
974 - update output of exp. global_ocean.cs32x15.viscA4 after changing
975 grid-file angles (used here for coriolis-3d);
976 - remove (or gzip) few files not needed to run fizhi-cs experiments.
977 o pkg/exf (vector interpolation):
978 - rotate vector component toward local grid-axis orientation using grid-angles
979 (stored in GRID.h) instead of locally computed rotation angle; keep old code
980 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
981 o pkg/seaice:
982 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
983 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
984 o pkg/PKG_OPTIONS.h files:
985 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
986 outside of the #ifdef ALLOW_THISPKG / #endif block.
987 - update verification/*/code/PKG_OPTIONS.h files.
988 o add a verification experiment (offline_exf_seaice/input.seaice) that test
989 the B-grid LSOR solver
990 o pkg/seaice: sort out emissivity and long wave radiation step 2:
991 - add emissivity for snow and ice as new run-time parameters
992 (unfortunately) that default to the corresponding exf values; this
993 changes results in most verification experiments so that for backward
994 compatibility these parameter have to be set explicitly to inconsistent
995 values (ugly);
996 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
997 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
998 until we agree how to handle this bug properly
999 o pkg/exf (interpolation):
1000 - add a set of run-time param ({inputfield}_interpMethod), one for
1001 each interpolated input field, to select the interpolation method
1002 with a value of zero switching off the interpolation;
1003 - print interpolation parameters to standard output;
1004 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
1005 (to use instead runoff_interpMethod=0 in data.exf).
1006 - simplify default setting of interpolation parameters (for all fields,
1007 set position to match model grid cell-center position, leading to trivial
1008 interpolation in case of regular Lat-Lon grid) and fix for the case of
1009 non-uniform delY.
1010 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
1011 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
1012 this factor is absolutely required, because the lw exitance (= out-going
1013 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
1014 where the reflectivity rho = 1-emissivity for conservation reasons. Once
1015 this is established, we can remove the CPP-Flag (if we want to).
1016 o pkg/seaice:
1017 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
1018 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
1019 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
1020 what the name implies (and not emissivity*BoltzmannConstant), this means
1021 the old default value of 5.5e-8 now means
1022 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
1023 S/R exf_readparms
1024 - FV-discretization of the B-grid LSOR solver, turn on with
1025 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
1026 of the calling routine dynsolver, so that B and C-grid code look a
1027 little more alike.
1028 - fix index bugs in ostres.F (B-grid code)
1029 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
1030 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
1031 default for SEAICE_emissivity, if useEXF; requires setting a wrong
1032 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
1033 backward compatiblity
1034 o model/src: use sigmaR in calc_ivdc
1035
1036 checkpoint63g (2011/12/16)
1037 o pkg/seaice/seaice_growth.F:
1038 fix heat conservation of the coupled ocean-seaice system.
1039 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
1040 solid vs liquid water treatment is resolved via QNET.
1041 o pkg/seaice/seaice_growth.F:
1042 add missing term for sublimation in saltFlux, which was breaking conservation.
1043 o pkg/seaice/seaice_model.F:
1044 Remove this patholigical case treatment in evolution branch,
1045 where it is un-necessary and breaks conservation.
1046 Update global_ocean.cs32x15/results accordingly for
1047 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
1048 o model/src:
1049 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
1050 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
1051 o pkg/obcs:
1052 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
1053 tendency for temperature and salinity that is then applied to update
1054 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
1055 horizontal advection and diffusion contributions on the boundary (in
1056 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
1057 removing the mask in S/R timestep_tracer. The advantage of this approach is
1058 that the updated tracer values include contributions from the surface
1059 forcing and vertical diffusion.
1060 This modification changes exp4.stevens because of vertical diffusion.
1061 o model/src:
1062 change non-curvilinear grid setting to also work with exch2 + blank tiles:
1063 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
1064 face dimensions.
1065 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
1066 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
1067 and INI_SPHERICAL_POLAR_GRID.
1068 change test-experiment global_ocean.90x40x15:
1069 - split the domain in many more tiles (9x4 tiles of 10x10 each);
1070 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
1071 - update results of both test (std & dwnslp).
1072 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
1073 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
1074 o model/src:
1075 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
1076 and fix initialisation when using sigma-coords.
1077 o model/src:
1078 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
1079 to their current value at the beginning of forward_step.F": add a new run-time
1080 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
1081 - set doResetHFactors=T in the following test exp:
1082 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
1083 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
1084 and tutorial_global_oce_in_p (nonLinFS in p)
1085 o pkg/ecco
1086 - added IES cost term
1087 o verification/advect_xz
1088 - scale down the depth by 1/100 (from 200 km to just 2.km)
1089 - add secondary test using divergent flow, r-star and implicit vertical advection.
1090 - add note (check_conserve_TS.txt) and matlab script to check global
1091 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
1092 o pkg/rbcs:
1093 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
1094 o pkg/obcs (Stevens BCs):
1095 - fix various problems in the phase speed computations of the Stevens
1096 boundary conditions:
1097 - sign error for western and southern boundaries,
1098 - time tendencies were underestimated by factor of dTracerLev and some just
1099 zero (for multidim advection schemes) -> now estimate time tendencies
1100 from difference between previous (n) time level and the one before (n-1);
1101 this requires storing a field per tracer per boundary, also in the pickup
1102 files.
1103 - replace deltaTmom in cflMer/Zon computation with dTracerLev
1104 - set default phase velocity to cflMer/Zon
1105 - update verification experiment exp4.stevens
1106 o pkg/generic_advdiff (implicit_r):
1107 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
1108 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
1109 - fix implicit vertical diffusion or advection with NonLin FreeSurf
1110 (was using current recip_hFacC instead of future recip_hFacC): set future
1111 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
1112 solver S/R ;
1113 - fill diagnostics of vertical advective fluxes (computed from tendency)
1114 when using implicit vert. advection;
1115 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
1116 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
1117 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
1118 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
1119 o pkg/diagnostics:
1120 - add diags for T & S tendency which goes through Adams-Bashforth.
1121
1122 checkpoint63f (2011/11/30)
1123 o pkg/obcs/obcs_calc_stevens.F:
1124 - join some loops to reduce number of if-statements
1125 - fix a bug in code for northern and southern boundaries.
1126 o pkg/seaice/seaice_init_varia.F
1127 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
1128 caused zero ice-velocities for the B-grid code
1129 o pkg/seaice/seaice_init_fixed.F
1130 - fix a bug in the initialisation of the second metric terms
1131 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
1132 - this affects all seaice configurations with useCurviLinearGrid = .true.
1133 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
1134 = .true. (default)
1135 - the only verification experiment affected is global_ocean.cs32x15:
1136 icedyn, seaice, and seaice_dynmix (AD)
1137 o pkg/thsice/thsice_diagnostics_state.F
1138 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
1139 not contain garbage that can lead to surprises in diagstats_calc.F
1140 o model/src:
1141 - move bi,bj loops inside INTEGR_CONTINUITY ;
1142 - call INTEGR_CONTINUITY directly from forward_step.F
1143 (previously called from momentum_correction_step.F)
1144 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
1145 forward_step.F and pkg/ecco/the_main_loop.F
1146 o model/src/do_oceanic_phys.F:
1147 - reset addMass to zero only if useICEFRONT ;
1148 - separated k-loop for rhoInSitu calculation ;
1149 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
1150 and at constant T,S (= WdRHOdP);
1151 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
1152 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
1153 transport of locally-referenced potential density);
1154 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
1155 o gluemnc:
1156 - replace ncrcat with ncks when adding variables to *.glob.nc
1157 - change the way variables without record dimensions are handled so that
1158 files that have variables with and without record variables can be glued:
1159 add a record dimension with a new unique name to be able to differentiate
1160 between variable with and without a-prior record dimensions. Remove
1161 this record dimension before adding the variable to the *.glob.nc file.
1162 This procedure automatically works also for grid.*.nc files that do not
1163 have any record dimension.
1164 o verification/cpl_aim+ocn:
1165 - generate new reference output on baudelaire (gfortran, mpich2) (previously
1166 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
1167 o pkg/obcs/obcs_calc_stevens.F:
1168 - add code for northern and southern boundaries.
1169 - reorder some loops to save some operations and so that drFBar can be scalar
1170 o model/src:
1171 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
1172 truncation) and add diagnostics for Adams-Bashforth tendency increment.
1173 - update test-exp. AD output:
1174 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
1175 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
1176 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
1177 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
1178 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
1179 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
1180 tutorial_plume_on_slope.
1181 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
1182 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
1183 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
1184 does not even come with an F77 compiler anymore, this should not be
1185 a limitation
1186
1187 checkpoint63e (2011/11/06)
1188 o pkg/seaice adjoint of LSR:
1189 - substantially rework STORE dirs.
1190 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
1191 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
1192 and only perform SOLV_MAX_FIXED adjoint iters.
1193 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
1194 always goes to same record, meaning that the last forward field will be
1195 the one used in the adjoint - an approximation.
1196 - now produces non-zero LSR-related gradients, and acceptable gradients for
1197 An's zonal (x-z) test case (to be checked in)
1198 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
1199 (but these are screwed up by the thermodynamics in the first place);
1200 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
1201 output_adm.txt also reflects changes to seaice_lsr
1202 - global_ocean.cs32x15:
1203 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
1204 (output_adm.seaice.txt was updated)
1205 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
1206 (output_adm.seaice_dynmix.txt)
1207 o test-exp. exp4+stevens:
1208 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
1209 o pkg/seaice (lsr solver):
1210 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
1211 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
1212 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
1213 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
1214 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
1215 - compute (with new S/R) and print initial (+ free-driff sol. if available)
1216 and final residual of linearised system.
1217 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
1218 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
1219 o pkg/obcs: Stevens BCs (still only for east and west)
1220 - fix Stevens BCs by using intermediate velocities of previous
1221 time step as "baroclinic" contribution rather velocity of one grid cell
1222 inside the boundaries; more consistent but makes the entire treatment
1223 more complicated, requires new pickup files and two new S/Rs:
1224 obcs_copy_uv_n and obcs_save_uv_n
1225 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
1226 (undefined by default)
1227 - silently move computation of some grid factors into separate loops to
1228 save some recomputations
1229 - add a hack for non-linear free surface
1230 - add a verification experiment to exp4 that tests this code
1231 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
1232
1233 checkpoint63d (2011/10/25)
1234 o pkg/obcs + seaice-dynamics:
1235 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
1236 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
1237 values (consistent with an implicit method).
1238 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
1239 return to older implementation (same results as before); note that none of
1240 the "experimental" OBCS_SEAICE options are implemented in the new version.
1241 - switch test exp. seaice_obcs to use new version (update output).
1242 o pkg/seaice:
1243 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
1244 - add parenthesis in Water-Ice drag calculations (evp & lsr);
1245 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
1246 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
1247 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
1248 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
1249 o pkg/layers:
1250 - Include potential density as new coordinate (Thanks to David Munday)
1251 o pkg/dic:
1252 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
1253 carbonate computation/output to CALC_PCO2_APPROX
1254 o pkg/generic_advdiff
1255 - make TAF generate code that vectorizes:
1256 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
1257 o model/src:
1258 - improve vectorization also for adjoint code of
1259 solve_tridiagonal and solve_pentadiagonal. As this requires up to
1260 5 new 3D-fields, this code is only turned on for the combination of
1261 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
1262 for singular matrix check (only for TARGET_NEC_SX).
1263 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
1264 ALLOW_AUTODIFF. This flag now needs to be set outside of
1265 solve_tri/pentadiagonal.F
1266 o pkg/exf:
1267 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
1268 optional namelist EXF_NML_OBCS).
1269 - add many debug-print (to trace down where pkg/cal error msg comes from)
1270 o pkg/mom_vecinv/mom_vi_hdissip.F
1271 - rearrange loops so that vectorization is improved and in particular
1272 the adjoint routine vectorizes. The code is a little longer now, but I
1273 think easier to read.
1274 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
1275 o pkg/seaice:
1276 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
1277 o pkg/exch2:
1278 - alternative code (without tile x tile matrix) for cumulated (global) sum;
1279 used as default; keep using matrix version in adjustment.cs-32x32x1.
1280 o tools/build_options:
1281 - after merging some MPI and/or multi-threads specific optfiles so that
1282 the modified default optfile support both built (using genmake2 -mpi
1283 for the MPI built, using genmake2 -omp for OpenMP built),
1284 move now obsolete optfiles to tools/build_options/unsupported/
1285 (add copy of email sent to support list in doc/optfiles_changes.txt)
1286
1287 checkpoint63c (2011/09/28)
1288 o pkg/ebm:
1289 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
1290 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
1291 o pkg/seaice (SItracer pickup)
1292 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
1293 To be done:
1294 - thorough testing of missing fields in S/R seaice_read_pickup
1295 - thorough matching between generic tracers and specific fields used
1296 (e.g. volume-weighted age, area-weighted age, salinity, ...)
1297 o pkg/grdchk:
1298 - all procs calculate and print finite-difference gradient (for testreport)
1299 - change description output used by testreport;
1300 - AD testing: also compare and report Finite-difference gradient;
1301 => update all output_adm*.txt
1302 o test exp. global_ocean_ebm:
1303 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
1304 and turn on exactConserve; update (fwd) output.
1305 o pkg/seaice (LSR):
1306 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
1307 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
1308 * identical results with non-CS topology (but save up to half of EXCH calls)
1309 * no much changes in cs-32 verification tests since no ice at face edges
1310 (differences due to convergence criteria, since nb of iterations changed)
1311 * expect some differences on lat-lon-cap grid.
1312 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
1313 o pkg/exch2:
1314 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
1315 many tiles); until alternative coding is added, just add a stop.
1316 o pkg/kpp:
1317 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
1318 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
1319 o optfiles:
1320 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
1321 into corresponding standard one, which now support different build:
1322 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
1323 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
1324 o pkg/obcs (seaice):
1325 - add missing EXCH for uIce,vIce after applying OBCS;
1326 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
1327 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
1328 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
1329 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
1330 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
1331 and eedata.mth for MPI and mutlti-threaded testing.
1332 o pkg/flt:
1333 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
1334 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
1335 - fix pickup and trajectories + profiles output with multi-threads;
1336 - add parameter to select group of fields to write along trajectory and
1337 profile (default unchanged);
1338 - only call PORT_RAND* function when flt_noise <> 0;
1339 - add multi-threaded test for verification exp. flt_example.
1340 o eesupp/src:
1341 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
1342 - USE_OMP_THREADING: check that number of threads (from eedata) matches
1343 actual number (from env.var. setting).
1344 o pkg/ebm:
1345 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
1346 - add multi-threaded test for verification exp. global_ocean_ebm
1347
1348 checkpoint63b (2011/08/29)
1349 o pkg/ebm:
1350 - fix sign of runoff;
1351 - update directly forcing fields (Qnet,EmPmR) to use standard
1352 external_forcing_surf.F (remove ebm_forcing_surf.F);
1353 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
1354 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
1355 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
1356 - update global_ocean_ebm parameters file data and update output (fwd+ad).
1357 o verification/matrix_example:
1358 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
1359 MPI and mutlti-threaded testing.
1360 o pkg/matrix:
1361 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
1362 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
1363 - fix for multi-threaded (remove DATA statement);
1364 - use standard DIFFERENT_MULTIPLE function;
1365 - add MATRIX_OPTIONS.h
1366 o verification/matrix_example:
1367 To allow to split the domain in several tiles, change the domain size
1368 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
1369 Western side) of land points.
1370 o (*_)write_pickup:
1371 - fix few bugs in mypackage_read/write_pickup.F
1372 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
1373 array of length 1 (was caught by compiler syntax-check).
1374 o pkg/diagnostics (velocity potential solver):
1375 - fix initialisation of main diagonal matrix (for overlap values)
1376 o tools/build_options:
1377 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
1378 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
1379 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
1380 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
1381 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
1382 and use "-devel" testreport option for standard testing on baudelaire.
1383 o pkg/grdchk:
1384 - Assume that all gradient-check position are within the same tile
1385 corresponding to global indices (iGloTile,jGloTile) and that
1386 positions (i,j indices or nbeg) are local to this tile;
1387 - set tile local-indices and proc. number according to tile global-indices;
1388 - remove grdchkwhichproc from namelist (retired param);
1389 - send adjoint gradient to all procs so that all procs print it to STDOUT;
1390 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
1391 o adding package bbl (Bottom Boundary Layer)
1392 description in MITgcm/pkg/bbl/bbl_description.tex
1393 example/test experiment in MITgcm_contrib/bbl
1394 o adjoint verifications
1395 - changed 5 experiments to multi-tiles
1396 * global_ocean.90x40x15
1397 * obcs_ctrl
1398 * offline_exf_seaice
1399 * tutorial_dic_adjoffline
1400 * tutorial_tracer_adjsens
1401 changed reference output for those that crossed tile boundaries
1402 (changed choices of gradient check positions)
1403 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
1404 - temporary bug fix in grdchk_loc.F for obcs
1405 o genmake2 & testreport
1406 - add target "obj" (just for OBJFILES files) to Makefile;
1407 - add option to specify FEXTRAFLAGS on command line.
1408 o pkg/mypackage:
1409 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
1410
1411 checkpoint63a (2011/08/02)
1412 o pkg/diagnostics (velocity potential):
1413 - fix velocity-potential calculation when using OBCS: balance net inflow
1414 at each level (new S/R OBCS_DIAG_BALANCE).
1415 - fix some of the problems with OBCS in stream-function calculation.
1416 o pkg/exf/exf_readparms.F
1417 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
1418 EXF_NML_OBCS) more consistent, so that you need not have these lists
1419 in data.exf when they are not used.
1420 o optim/optim_readdata.F:
1421 - add some output about obcs variables that might help debugging
1422 - add a check about nvarlength
1423 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
1424 o pkg/diagnostics (velocity potential):
1425 - fix mask for OBCS (still problems in stream-function with OBCS);
1426 - add specific parameter (default = main code CG2D params) for solver;
1427 - in case of poor convergence, use solution corresponding to lowest residual.
1428 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
1429 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
1430 and should be avoided where possible.
1431 o model/src (rStar):
1432 - include r* effect on reference-state (PhiRef) in totPhiHyd
1433 (so that it's really the potential anomaly at the cell center);
1434 affect solution only if z* with full pressure in EOS.
1435 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
1436 update output (because of z* in totPhiHyd and viscA4 changes);
1437 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
1438 @ constant r) until interpolation at constant r is implemented.
1439 o pkg/diagnostics
1440 - fix RCENTER diagnostics in case cell center is not at interface middle
1441 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
1442 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
1443 that THETA and SALT are "conservative temperature" and "absolute
1444 salinity"
1445 o pkg/ctrl
1446 - fix computation of endrec in s/r ctrl_init_rec
1447 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
1448 o pkg/seaice/seaice_growth.F
1449 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
1450 remove then obsolete STORE directives
1451 - fix STORE directives for tice and tices, so that only the
1452 appropriate part of the fields are stored (and not the entire
1453 field); update global_ocean.cs32x15.seaice AD output.
1454 - cosmetic changes: adjust CPP flags and indentation for better
1455 legibilty
1456 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
1457 Chris Wilson)
1458 o pkg/gmredi:
1459 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
1460 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
1461
1462 checkpoint63 (2011/07/11)
1463 o pkg/exch2:
1464 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
1465 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
1466 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
1467 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
1468 o pkg/diagnostics:
1469 - deal with pairs of post-processed diags which are computed together; in
1470 particular, re-order list of diags within 1 file to save 2nd computation.
1471 - add S/R to compute velocity stream-function (called after velocity-potential
1472 calculation) from divergence free transport -> new diagnostics "PsiVEL".
1473 - add parameter to select grid-point location where PsiVEL == 0.
1474 o eesupp/src:
1475 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
1476 (specific S/R needed with exch2 topology - for now, just print an error msg)
1477 o pkg/shelfice
1478 - Implement friction velocity-dependent transfer coefficients following
1479 Holland and Jenkins, JPO, 1999
1480 Original code by M. Losch with small modifs.
1481 Enable with CPP option SHI_ALLOW_GAMMAFRICT
1482 and runtime flag SHELFICEuseGammaFrict
1483 o verification lab_sea & global_ocean.cs32x15:
1484 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
1485 does not miss some dependencies (but is slower) and also works with many files
1486 (default makedepend limitation for AD built).
1487 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
1488 o pkg/diagnostics:
1489 - add run-time parameter "useMissingValue" (def=False) to fill land-point
1490 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
1491 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
1492 - Extend the use of "missing_value" setting from data.diagnostics for the case
1493 of counter-diagnostics (where fraction-weight is zero). This applies both to
1494 MNC and MDS output files.
1495 o pkg/seaice/seaice_growth.F:
1496 - add 'a priori' cap of latent heat flux based on actual mass considerations
1497 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
1498 non-legacy seaice_solve4temp.
1499 - add diagnostic of the residual sublimation freshwater flux (the freshwater
1500 flux taken from the ocean if the total actual latent heat fluxes exceed
1501 the maximum)
1502 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
1503 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
1504 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
1505 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
1506 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
1507 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
1508 o verification 1D_ocean_ice_column:
1509 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
1510 update results
1511 o pkg/diagnostics:
1512 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
1513 which are not filled-up but computed from other diags ; In this case, the mate
1514 diag points to the primary (filled-up) diag to used for post processing.
1515 - Update Velocity-potential computation using post-processed diag framework.
1516 ==> Change the ordering of fields and time-periods in MDS output file
1517 when using periodic averaging: now writes one time record with the full set
1518 of fields for this time period, then the next time reccord (it used to be
1519 one field with the full set of time records then the next field).
1520 Note: this is now similar to NetCDF (MNC) output file. <==
1521
1522 checkpoint62z (2011/06/21)
1523 o adjoint monitor:
1524 - Add adjoint monitor output for packages exf, seaice
1525 and update relevant testreport output
1526 o pkg/seaice:
1527 - re-order diags inits so that they appear in order in available_diagnostics.log
1528 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
1529 area/heff/hsnow preceeding thermodynamic growth/melt.
1530 - modified diag: SIdA; output actual effect, as the description states.
1531 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
1532 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
1533 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
1534 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
1535 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
1536 - added diagnostics for seaice generic tracers (SItr*).
1537 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
1538 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
1539 I. Fenty: 18-Jun-2011:
1540 Minor changes to seaice package:
1541 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
1542 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
1543 - Differentiated "regularization variables" from "floor variables"
1544 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
1545 * hiceMin became SEAICE_hice_reg (old hiceMin)
1546 (with _reg meaning regularization variable)
1547 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
1548 so as to ensure energy conservation when going between phases
1549 - A22 was not used anywhere
1550 2) Changed regularization procedure for heffActual and hsnowActual to ensure
1551 well-boundedness and smooth adjoint in seaice_growth.F
1552 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
1553 because the old regularization always set heffActual >= 0.05 cm
1554 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
1555 on AREA when HEFF > 0.
1556 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
1557 requiring that DISABLE_AREA_FLOOR *not* be defined
1558 Affected verifications:
1559 - 1D_ocean_ice_column (output.txt output_adm.txt)
1560 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
1561 o pkg/diagnostics:
1562 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
1563 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
1564 (was _RL, now integer) with option = 0 to retrieve all levels.
1565 - add pieces of code to compute velocity potential at each level (new diagnostics
1566 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
1567 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
1568 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
1569 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
1570 and in diagnostics_fract_fill.F (do not need a valid pointer for the
1571 diagnostics counter-mate); check that definition of counter-diagnostic
1572 includes a valid counter-mate (in diagnostics_set_levels.F).
1573 o model/src (rStar):
1574 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
1575 affect solution only if z* with full pressure in EOS;
1576 update output of test-exp global_ocean.90x40x15.
1577 o pkg/seaice:
1578 - introduce siEps=1e-5 parameter
1579 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
1580 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
1581 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
1582 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
1583 as well as ice cover age and ridging index (attached to AREA).
1584 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
1585 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
1586 Up to SItrMaxNum=3 tracers can be used simultaneously.
1587 o pkg/salt_plume:
1588 -introduce SPsalFRAC run time parameter that sets the fraction of the
1589 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
1590 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
1591 o model debug options:
1592 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
1593 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
1594 - Refine debug-msg printing selection (3 new levels):
1595 debugMode : controls printing of debug messages (sequence of S/R calls).
1596 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
1597 debLevZero = 0 ; /* level of disabled aux. msg printing */
1598 debLevA = 1 ; /* level of minimum aux. msg printing */
1599 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
1600 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
1601 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
1602 debLevE = 5 ; /* level of extensive debug printing */
1603 New debugLevel default: with default debugMode value (=F),
1604 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
1605 and if debugMode=T, default debugLevel = 4 (debLevD).
1606 Relation with previous settings:
1607 debLevB (=2) corresponds to former debLevA (=1)
1608 debLevD (=4) corresponds to former debLevB (=2)
1609 Note:
1610 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
1611 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
1612 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
1613 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
1614 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
1615 o pkg/obcs:
1616 - change OBCSfixTopo default from True to False (should not change the results);
1617 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
1618 o pkg/thsice:
1619 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
1620 2nd layer seaice sublimation (unlikely to happen)
1621 - use Interior mask for OBCS in thsice_advection.F (similar to what is
1622 done in gad_advection & seaice_advection).
1623 o adjoint:
1624 bug fix spotted by Gael Forget:
1625 seaice_advection and thsice_advection still had
1626 legacy CPP options to avoid CS corner updates for adjoint
1627 o pkg/seaice:
1628 => Change some of the defaults (2011/05/29):
1629 - change SEAICEuseFluxForm default (from False to True)
1630 - change DIFF1 default (from 0.004 m/s to 0. m/s)
1631 And print warnings if DIFF1 is not set in data.seaice and centered
1632 avection scheme is used without any diffusion.
1633 also:
1634 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
1635 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
1636 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
1637 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
1638 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
1639 update results of test exp.:
1640 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
1641 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
1642 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
1643 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
1644 seaice_obcs: output (SEAICEuseFluxForm=T)
1645 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
1646 for standard fwd & AD lab_sea tests (to keep the same output).
1647 o pkg/seaice/seaice_growth.F:
1648 - use Ian Fenty's capping formulas for actual ice
1649 thickness thoughout EVOLUTION branch.
1650 - put treatment pathological case #2) in CPP brackets
1651 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
1652 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
1653 o pkg/seaice:
1654 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
1655 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
1656 also pass fac as a param, which can be 1. (to update the tendency
1657 field) or the time step (to update the field itself).
1658 - seaice_advdiff.F: for multidim, call seaice_diffusion with
1659 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
1660 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
1661 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
1662 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
1663 o pkg/seaice:
1664 diffusion with centered advection scheme (diffus.F & advect.F):
1665 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
1666 to just compute the laplacian of input-field.
1667 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
1668 - fix flux-form version in diffus.F to conserve tracer.
1669 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
1670 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
1671
1672 checkpoint62y (2011/05/26)
1673 o pkg/seaice:
1674 - seaice_growth.F : in EVOLUTION branch, always include
1675 a_QSWbyATM_cover in qnet (as it should be).
1676 - verification/global_ocean.cs32x15 : update results accordingly
1677 (output.seaice.txt output_adm.seaice.txt).
1678 o pkg/seaice + obcs:
1679 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
1680 equivalent of assuming no tracer gradient outside the OB region.
1681 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
1682 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
1683 after changes above);
1684 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
1685 only at OB location (instead of over a band of OLx width).
1686 o pkg/seaice:
1687 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
1688 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
1689 o pkg/obcs:
1690 - split header file "OBCS.h" into 4 separated files:
1691 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
1692 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
1693 (contain no conditional statement which depends on OBCS options).
1694 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
1695 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
1696 o ctrl, cost, grdchk & autodiff pkgs:
1697 - make options file more standard (like other {PKG}_OPTIONS.h file but
1698 with AD_CONFIG.h); clean-up some of the included header files.
1699 o pkg/obcs:
1700 - do not mask tracer when applying OB (tracer == 0 could generate problems)
1701 - apply tracer OB values to tracer field only at OB location (instead of
1702 over a band of OLx width)
1703 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
1704 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
1705 obcs_apply_tloc.F & obcs_apply_sloc.F
1706 o obcs in model/src:
1707 - call OBCS_APPLY_W only if NonHydrostatic.
1708 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
1709 - reset dEtaHdt and wVel to zero outside OB interior region ;
1710 - leave tracer unchanged outside OB interior region: This has no effect
1711 on the solution but just to prevent unrealistic tracer value outside OB.
1712 - zero out velocity outside OB interior region: This has no effect on
1713 the solution but just to prevent unrealistic velocity outside OB.
1714 o obcs and non-lin free-surf:
1715 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
1716 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
1717 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
1718 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
1719 update results of test-exp. exp4(nlfs).
1720 o exp4 (nlfs) test-exp:
1721 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
1722 with NonLin-FreeSurf); update output.nlfs.txt
1723 o obcs and 2d/3d solver norm:
1724 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
1725 and outside OB interior region (will allow to place OB further inside the
1726 domain). Depending on the domain, can affects cg2d-Norm (previous
1727 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
1728 and cg3d-Norm (previous Norm was computed before canceling OB terms),
1729 e.g. in tutorial_plume_on_slope.
1730 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
1731 o pkg rbcs:
1732 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
1733 - add capability to apply relaxation to horizontal velocity uVel & vVel.
1734 o pkg/grdchk: add gradient check for control variable xx_shifwflx
1735 o pkg/shelfice/shelfice_init_fixed.F
1736 fix CPP-flag combinations
1737 o pkg/seaice: Merge iceage code of Pierre Rampal
1738 * update/change/correct ice age calculations
1739 * add age updates for pathological cases
1740 Probably needs more testing...
1741
1742 checkpoint62x (2011/05/13)
1743 o pkg/mom_vecinv:
1744 high-order vorticity scheme: use interior masks (maskInW & S)
1745 to zero-out (outside OB) gradient of vorticity.
1746 o verification exp.:
1747 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
1748 hs94.128x64x5 and seaice_obcs ; update results.
1749 o pkg/obcs:
1750 fix bug in OBeta for YZ sections in obcs_exf_load.F
1751 o pkg/ctrl, pkg/shelfice, and optim:
1752 - add new control variable xx_shifwflx (fresh water flux underneath ice
1753 shelves). This is almost as tedious as obcs-ctrl, because the
1754 variables needs its own mask.
1755 - add a cost function term that penalizes the deviation of xx_shifwflx
1756 from the first guess (zero) in analogy to other control variables
1757 o pkg/shelfice:
1758 - start basic adjoint
1759 o pkg/ctrl:
1760 - remove extra 2D field "for good measure" when initializing in
1761 ctrl_set_globfld_[xy/xz/yz].F
1762 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1763 - improve error messages in ctrl_set_unpack_*
1764 o OBC implementation in momentum:
1765 use interior masks (maskInC,W & S) in momentum S/R:
1766 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1767 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1768 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1769 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1770 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1771 (and also with Leith/Smagorinsky harmonic-viscosity).
1772 Update output of experiment dome and exp4 (+nlfs).
1773 o exp4 test-exp:
1774 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1775 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1776 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1777 time-varying OB at Western-side for wVel (NonHyd); update output.
1778 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1779 and biharmonic-viscosity ; also use prescribed time varying OB.
1780 o pkg/obcs:
1781 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1782 o model/src:
1783 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1784 - initialise startTime & nIter0 with unlikely values: allows to set one
1785 from the other without ambiguity.
1786 o seaice_obcs test-exp.:
1787 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1788 o pkg/obcs:
1789 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1790 no longer needed with maskInC,W,S in pkg/generic_advdiff.
1791 o pkg/seaice:
1792 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
1793 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
1794 - fixed bug in the initialization of sea ice salinity variable HSALT
1795 in seaice_init_varia.F (removed dependence on ICE2WATR)
1796 o fizhi-cs test exp.:
1797 switch reference output convention for these 2 non-standard test-exp,
1798 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
1799 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
1800 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
1801 o model/inc:
1802 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
1803 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
1804 o pkg/seaice:
1805 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
1806 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
1807 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
1808 and initial HSALT
1809
1810 checkpoint62w (2011/04/26)
1811 o pkg/mom_fluxform:
1812 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
1813 - use parameter "sideDragFactor" in no-slip BC side-drag part.
1814 - update output of exp. global_ocean.90x40x15
1815 o pkg/mom_vecinv:
1816 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1817 o update seaice exp.:
1818 use more consistent parameter values (remove "backward compatability only":
1819 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
1820 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
1821 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
1822 o update test-exp global_ocean.90x40x15:
1823 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
1824 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
1825 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
1826 o turn on zStar & viscA4 in standard set-up (dir input/)
1827 and update output files: output.txt & output.dwnslp.txt
1828 o new AD-test experiment: obcs_ctrl
1829 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
1830 o pkg/dic:
1831 fix two bugs in handling water vapour pressure in carbonate chemistry
1832 and air-sea fluxes. Found by Val Bennington and Galen McKinley
1833 (add DIC Option = WATERVAP_BUG to recover old results)
1834 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
1835 o adding allowInteriorFreezing option to check for water below freezing point
1836 at depth and bring the negative heat anomaly to the surface level
1837 o pkgs _fields_load:
1838 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1839 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1840 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1841 rbcs to get interpolation weights and time reccord number.
1842 - fix multi-threading in aim_fields_load.F
1843 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1844 o external_fields_load:
1845 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1846 interpolation weights) to use in a periodic time-series ; do not divide by
1847 time-step to convert to integer:
1848 - this fixes case where externForcingPeriod is not multiple of time-step
1849 (Thanks to Christopher L. Wolfe)
1850 - this fixes case where externForcingPeriod is an odd multiple of time-step
1851 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1852 store index of time-record which is currently loaded:
1853 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1854 - needed for the adjoint but not yet used because of extensive recomputations;
1855 (to be fixed soon)
1856
1857 checkpoint62v (2011/04/02)
1858 o verification/1D_ocean_ice_column added to test Ian Fenty's
1859 pkg/seaice_growth.F modifications for improving sea ice code differentiability
1860 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1861 (new velocity statistics after changing maskInW & maskInS definition)
1862 o pkg/generic_advdiff with OBCS:
1863 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1864 equivalent to assumption of no tracer gradient outside the OB region.
1865 This will affect the results if using obcs+biharmonic diffusion.
1866 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1867 o pkg/obcs:
1868 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1869 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1870 in Interior region. No impact on solution but affects Velocity monitor stats.
1871 o pkg/ptracers (adjoint)
1872 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1873 tape file for each tracer
1874 o model/inc/src and pkg/autodiff: add parameters that allow to turn
1875 of parts of the adjoint code at run time. For now, there are only
1876 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1877 parameters are set in data.pkg.
1878 This is the lazy coward's version of doing this, but still useful for
1879 debugging. In order to do it right, everything needs to be moved to
1880 pkg/autodiff.
1881 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1882 the end; this fixes the adjoint balancing code for open boundaries.
1883 o pkg/ctrl:
1884 - change behavior of xx_${varname}period to be analogous to exf-conventions:
1885 xx_${varname}period = 0., means time-independent control part
1886 xx_${varname}period = -12., means one-year-periodic monthly control part
1887 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1888 clean up ctrl_init a little, remove unused variables
1889 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1890 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1891
1892 checkpoint62u (2011/03/15)
1893 o model/src:
1894 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1895 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
1896 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
1897 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
1898 o pkg/ctrl/obcs/ecco:
1899 - remove obsolete, unused, and partially broken code:
1900 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
1901 ALLOW_CTRL_OBCS_BALANCE
1902 - put a stop statement into ecco/cost_obcsvol.F, but also add
1903 cost_obcsvol to ecco_ad_diff.list
1904 o pkg/ecco: fix counting cost function contributions for obcs (code
1905 by Matt M.) and diffkr for diagnostics
1906 o pkg/ecco, pkg/ctrl, pkg/grdchk:
1907 add cost penalty terms for initial uvel, vvel, eta controls
1908 and I/O for prior error files
1909 o pkg/mdsio:
1910 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
1911 (new argument) to check for tiled file in mdsioLocalDir : this fix the
1912 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
1913 o pkg/ctrl:
1914 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
1915 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
1916 unused and superfluous variables
1917 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
1918 o pkg/ecco
1919 - enable adjoint of Stevens OB
1920 o pkg/ctrl/ecco/grdchk:
1921 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
1922 Fortunately, we do not have any tests for the numerous cpp-flagged
1923 option of "obcs as control parameters" so we will never know
1924 if this is an improvement (but at least now things compile).
1925 - remove an obsolete initialization from ecco_cost_init_barfiles.F
1926 - fix some problems within never used ifdefs to make the code compile
1927 o pkg/obcs:
1928 - Refine Interior mask definition to work with more complex OB (e.g.
1929 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
1930 read in Interior mask from file. Check if Interior mask is consistent
1931 with OB list of indices.
1932 o pkg/seaice
1933 - beginning code for a seaice tracer package,
1934 but currently only used for seaice age: SEAICE_AGE
1935 SEAICE_num = 4
1936 iTracer = 1: area-weighted ice age
1937 = 2: volume-weighted ice age
1938 = 3, 4: template for one-year vs. multi-year ice
1939 data.seaice has new namelist SEAICE_PARM03 for arrays related to
1940 SEAICE_num
1941
1942 checkpoint62t (2011/03/05)
1943 o pkg/obcs:
1944 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
1945 then normal component. This ensures that the normal component is set
1946 correctly even when it conficts with tangential setting from an other OB.
1947 Affects results of test-experiment seaice_obcs: update the output.txt
1948 o pkg/obcs:
1949 - add code to monitor statistics of dynamical fields at OB.
1950 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
1951 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
1952 - change default: balance the Net inflow through all OB (instead of balancing
1953 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
1954 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
1955 to match Nortern OB inflow (OBCS_balanceFacN=0).
1956 o pkg/seaice:
1957 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
1958 o pkg/seaice (seaice_growth v 1.113):
1959 - reverting seaice_growth to v 1.111 in order to have code with exact bit
1960 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
1961 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
1962 runtime flag SEAICEareaFormula is kept but is inactive
1963 o model/src:
1964 - add new param to scale curvilinear grid distance and area when using
1965 a different sphere radius from the grid-files.
1966 - test/check multi-threads EXCH applied to local variable (cg2d_x)
1967 o adjoint:
1968 - enable adjoint of Stevens OB
1969 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
1970 (a bit delicate because of potentially modified adj. common block structure;
1971 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
1972
1973 checkpoint62s (2011/02/15)
1974 o pkg/seaice (seaice_growth v 1.112):
1975 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
1976 computing the ice cover tendency from effective thickness tendencies. Include
1977 Ian Fenty's formula.
1978 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
1979 SEAICEareaFormula.
1980 - simplify notations for the various d_HEFF/d_AREA terms.
1981 o pkg/gmredi:
1982 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
1983 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
1984 add a verification test-run (front_relax.bvp) to test GM_useBVP.
1985 o pkg/seaice (seaice_growth v 1.111):
1986 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
1987 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
1988 also melt ice.
1989 o pkg/seaice:
1990 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
1991 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
1992 o pkg/cheapaml:
1993 - from Nico Wienders: New version of this package.
1994 o pkg/flt:
1995 - add CPP options to prevent floats to re-enter the opposite side of
1996 a periodic domain (default: keep periodicity)
1997 o pkg/gmredi:
1998 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
1999 (needed for multi-dim advection).
2000 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
2001 o model/src:
2002 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
2003 o tutorial_tracer_adjsens
2004 - extend to NLFS and replace maskC by hFacC
2005 (change reference output accordingly)
2006
2007 checkpoint62r (2011/01/24)
2008 o testreport:
2009 - add option -deloutp (-do) to remove output file after successful run
2010 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
2011 extract exact list of procs from this file ; adjust COMMAND by
2012 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
2013 o pkg/ecco: replace old ineffective way of penalizing deviations from
2014 first guess (of obcs) with code by Matt Mazloff
2015 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
2016 exf/cal
2017 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
2018 and handle case of obcs?period == 0
2019 Not affected by these changes: There is still an inconsistency in
2020 the computation of start/endrec for the obcs variables for ALLOW_CAL
2021 defined (see comment by Menemenlis, 7-Mar-2003)
2022 - make S/R ctrl_get_gen_rec return something meaningful even if
2023 ALLOW_CAL is not defined
2024 - ctrl_getobcs?: simplify code so that it does not need to use
2025 S/R exf_swapfields
2026 o testreport:
2027 allow to test MPI with different number of processors for each experiment:
2028 create file "SIZE.h.mpi" in each build dir.
2029 Note: update of "-command" argument not yet implemented.
2030 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
2031 alleviate the need for additional 3D tapes when using
2032 the non-inear free surface in the adjoint. This is done
2033 by adding an 'update' of hfacc etc. to their current
2034 value at the beginning of forward_step.F.
2035 o pkg/seaice
2036 seaice_lsr: move stress-divergence computations out of outer pseudo-
2037 timestepping loop
2038 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
2039 up, so that the calls of the ctrl_* subroutines are really at the end
2040 of the routine.
2041 o pkg/gmredi:
2042 allow to specify a 2-D horizontal map and a 1-D vertical profil
2043 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
2044 o pkg/seaice:
2045 move lsr iterations from seaice_dynsolver to seaice_lsr.
2046 o pkg/seaice:
2047 reduce memory footprint of seaice mutldim advection tapes,
2048 by using a 2D tape independent of the generic_advdiff ones,
2049 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
2050
2051 checkpoint62q (2010/12/29)
2052 o model/src:
2053 - check horizontal grid-spacing for unset or zero/negative values.
2054 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
2055 o pkg/flt:
2056 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
2057 - precision of input and output files set according to readBinaryPrec
2058 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
2059 - initial float position from tiled file was not converted to index space
2060 (looks like a bug): fixed to make it similar to initial pos. global file.
2061 o global_ocean.cs32x15:
2062 change SIZE.h of AD set-up to get same tiling as with MPI.
2063 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
2064 o model/src:
2065 add flag to control printing of domain fields (bathymetry, hFac ...) in
2066 ini_mask_etc (call to plot_fieds_xy*).
2067 o pkg/thsice:
2068 if useEXF, some forcing fields are not valid in overlap: fixed by computing
2069 over the interior only + apply EXCH at the end (like with SEAICE advection).
2070 o pkg/mdsio:
2071 - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
2072 to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
2073 - change barrier call for safe multi-threads access to 3-D shared buffer.
2074 - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
2075 - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
2076 remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
2077 o pkg/flt:
2078 - add fourth-order Runge-Kutta integration
2079 - add basic exch2 support (only 1 facet supported so far!)
2080 o pkg/mdsio+rw:
2081 new S/R to read local (or tile independent) vector (read counterpart of
2082 mds_writevec_loc, and front-end write_glvec_rl/rs).
2083 o global_ocean.cs32x15: additional input_ad.seaice experiment
2084 that uses pkg/seaice rather than pkg/thsice.
2085 (using multidim advection for seaice)
2086 o towards more F95 syntax for array specification in namelist:
2087 - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
2088 of all verification experiments.
2089 e.g.: line: fields(1,3)='ETAN ','ETANSQ ',
2090 was changed to: fields(1:2,3)='ETAN ','ETANSQ ',
2091 - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
2092 o global_ocean.cs32x15: additional input.seaice experiment
2093 that uses pkg/seaice rather than pkg/thsice.
2094
2095 checkpoint62p (2010/12/17)
2096 o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
2097 to THSICE_SIZE.h to avoid conflict with pkg/seaice.
2098 o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
2099 allow for use of multim. advection in seaice adjoint.
2100 o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
2101 - first attempt to close budgets by taking into account the freshwater
2102 flux implied by the sublimation of snow and ice. So far only the
2103 volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
2104 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
2105 o eesupp/src:
2106 new S/R with new option (NML_EXTENDED_F77) to change array specification
2107 from F95 standard to commonly accepted extended F77 form.
2108 This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
2109 and to revert back to the original syntax (with -DNML_EXTENDED_F77)
2110 for less tolerant f77 compiler (e.g., pgf77, g77).
2111 o globalFiles:
2112 commented out in parameter file "data" since it's not safe with MPI
2113 (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
2114 in this case); no longer commented out in restart test (tst_2+2).
2115 o add adTapeDir to specify a special directory where adjoint tapes are
2116 written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
2117 and cannot be used together with mdsioLocalDir.
2118 o nesting pkgs:
2119 - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
2120 - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2121 - add parameter files + utils dir + output from short run on beagle.
2122 o pkg/seaice:
2123 fix seaice_growth.F store directives; update results of exp. lab_sea.ad
2124 o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
2125 unnecessary copying in adjoint code, requires new parameter NMAX_ITER
2126
2127 checkpoint62o (2010/11/25)
2128 o pkg/exf:
2129 - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
2130 o pkg/seaice:
2131 - seaice_ocean_stress: split a loop for better vectorization of the
2132 adjoint code
2133 - seaice_growth.F: fix bug in conservation of freshwater connected to
2134 capping of heff, put contribution into d_HEFFbyNEG
2135 - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
2136 by something more sensible (parameters that are what their name implies)
2137 - change some defaults, so that by default exf-parameters are used for
2138 things like rhoAir, cpAir,latent/sensible heat parameters, in order
2139 to reproduce the old results, many data.seaice now contain funny values
2140 for cpAir and latent heat of sublimation
2141 o packages_readparms.F: move exf_readparms up in line so that
2142 exf-parameters are visible for other packages (e.g. seaice)
2143 o debugMode & debugLevel=2:
2144 - differentiate between debugMode & debugLevel=2:
2145 debugMode: controls printing of debug messages (sequence of S/R calls).
2146 debugLevel: controls printing of algorithm intermediate results and stats.
2147 - remove "if debugLevel=2 => debugMode" but keep "debugMode => debugLevel=2";
2148 => allows to print debug-stats without all sequence of call messages.
2149 - switch control of debug print from debugLevel to debugMode in many S/R.
2150 o pkg/obcs (obcs-sponge):
2151 fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
2152 call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
2153 o pkg/generic_advdiff:
2154 - record overlap minimum size for each advection scheme;
2155 - refine criteria on overlap minimum size;
2156 - check and stop (in gad_check) if overlap size is too small.
2157 o pkg/obcs:
2158 - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
2159 once, in ptracers_implicit.F)
2160 - with seaice: remove test on empty file name in obcs_apply_seaice (always
2161 apply OB values when tile has OB)
2162 o model/src, coriolis setting:
2163 - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
2164 useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
2165 files (selectCoriMap=3) with any grid.
2166 - add parameter "fPrime" for constant second Coriolis coeff (default=0).
2167 o pkg/seaice/seaice_growth.F:
2168 a few cosmetic changes that reduce the number of lines of code
2169 o pkg/obcs: add boundary conditions following Stevens (1990)
2170 - the code follows old MOM/NAOSIM code
2171 - so far it is only implemented for the eastern and western boundaries
2172 and NOT for pTracers
2173 o pkg/rbcs:
2174 - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
2175 beginning of the first rbcs forcing period.
2176 - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
2177 offline package, i.e., one file per time, labeled by iteration number;
2178 deltaTrbcs sets the timestep with which the data was generated;
2179 rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
2180 - rbcsForcingCycle=0 makes forcing non-cyclic.
2181 - make arithmetic safe for negative times and odd forcing periods.
2182
2183 checkpoint62n (2010/11/09)
2184 o pkg/seaice:
2185 fix masking in free-drift S/R ; update results of exp. lab_sea.fd
2186 o pkg/obcs:
2187 New S/R to copy tracer value from the OB location to narrow band region
2188 (width = same as overlap) beyond the OB: preserve OB value (needed for
2189 high-order scheme) which were overwritten by EXCH call if in overlap
2190 region. Applied to theta, salt, ptracer and advected seaice variables.
2191 With seaice: use maskInC in similar way as in gad_advection.F,
2192 in seaice_advection.F and advect.F.
2193 Update output of experiment seaice_obcs and change exp4 to test OBCS with
2194 4th order Adv.Scheme. for pasive salt and ptracer.
2195 o tools/genmake2:
2196 - when looking for an optfile (not specified), only search for Fortran compiler
2197 (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
2198 - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
2199 (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
2200 - set default for CPP to "cpp -traditional -P" (was the case without specifying
2201 an optfile, but otherwise default was just "cpp".
2202 - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
2203 - when "CC" is not set in the optfile, look for possible C compiler
2204 (instead of just setting CC=cc)
2205 - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
2206 => add a ".F" to ".o" rule for source files with no "#include" (such as
2207 port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
2208 - move gfortran before g77 in list of possible Fortran compiler (consistent
2209 with reference compiler switch from g77 to gfortran)
2210 o pkg/seaice:
2211 o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
2212 seaice_check that stops the model, when the CPP flag is used.
2213 o seaice_growth.F: make capping of ice volume conserving by returning the
2214 capped ice as freshwater to EmPmR. This does not change the verification
2215 experiments but will change runs where the capping is acutally active
2216 o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
2217 (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
2218 global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
2219 lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
2220 o tools/genmake2:
2221 - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
2222 - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
2223 - clean previous genmake log files before anything else.
2224 - change Makefile to remove testreport log files (*.tr_log) and genmake log
2225 files only with "CLEAN" target (instead of "Clean");
2226 o pkg/generic_advdiff:
2227 Change OBCS in multiDim advection (gad_advection.F):
2228 Use maskInC to prevent intermediate update of tracer-field in OB regions,
2229 thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
2230 which were applying future time-step OB values.
2231 This way, all explicit calculations use current-time-step OB values
2232 (simpler and more consistent).
2233 Affects results when set-up uses time-varying OBC and multi-dim advection;
2234 update output of experiment seaice_obcs.
2235 o pkg/seaice:
2236 move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
2237 this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
2238 SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
2239 Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
2240 but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
2241 unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
2242 o pkg aim (2010/10/26):
2243 - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
2244 formulation with obliquity, eccentricity, ... as run-time parameters,
2245 - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
2246 upward shortwave radition at the surface (all-sky and clear-sky).
2247 o pkg/obcs:
2248 - writing sections with globalFiles=T does not work: switch to tiled-files
2249 when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
2250 - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
2251 - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
2252
2253 checkpoint62m (2010/10/21)
2254 o pkg/seaice: vectorize seaice_solve4temp.F
2255 - move iterations loops outside of i/j-loops
2256 - requires 2D arrays for TB and effConduct
2257 - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
2258 modified in this routine
2259 - a little bit of clean up, adjusting indentation, etc.
2260 - replaced a few TEN**a by exp(a*log(10.)) in new code for better
2261 performance and '**TWO' by '**2' (because TWO is a float),
2262 replaced ONE, ZERO
2263 o eesupp/src:
2264 fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
2265 o pkg/seaice/seaice_growth.F
2266 Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
2267 merging process. The merged routine has two branches, and one activates the 'evolution'
2268 branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
2269 In summary, here is what the '10/10 revision' did consist of
2270 part 1: seaice_growth.F revisions 1.71 to 1.75
2271 - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
2272 The emphasis here was on improving readability (e.g. by trying to use meaningful
2273 variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
2274 part 1.5:
2275 - revising the lab_sea experiment to make it a more useful (i.e. stable
2276 and representative of an actual model run). This was done by generating a
2277 (winter) pickup to start from, switching back the main experiment dynamic
2278 solver from evp to lsr, having one of the experiments use the free drift solution.
2279 part 2: seaice_growth.F revisions 1.76 to 1.85
2280 - Sorting out hard-coded constants that prevented heat and fresh water conservation.
2281 - Sorting out the various fields units and sign (set early on and reset at the end)
2282 to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
2283 fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
2284 - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
2285 and simplifying logical expressions to further improve readibility.
2286 part 3: seaice_growth.F revisions 1.86 to 1.89
2287 - Re-organize the blocks of code more logically.
2288 - Merging the '_if.F' pieces that add something new.
2289 o pkg/thsice:
2290 - vectorize thsice_solve4temp and thsice_get_exf.
2291 Problem: thsice_solve4temp has an unvectorizable statement that
2292 might also be problematic for TAF
2293 - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
2294 does not change the verifcation experiment, but will change all
2295 experiments that have this flag undefined (not tested in verification);
2296 a little reorganization to save a few 2D fields and recomputations
2297 - 1st step of revisiting thsice adjoint (major recomp. sorted out)
2298 - 2nd step: fix some store dirs
2299 o seems to work somewhat, i.e. using ifort but not g77
2300 o likely cause are incomplete init. or recomputation
2301 o start verification/global_ocean.cs32x15/input_ad.thsice
2302 o pkg/obcs: add support for exch2
2303 - the position of the boundary and prescribed values are specified using
2304 a global domain with exch2 facets stacked
2305 - in x for N,S boundaries (like W2_mapIO=-1)
2306 - in y for E,W boundaries (so E,W boundaries do not overlap)
2307 o pkg/mdsio: add support for writing global sections with exch2
2308 file layout is as for obcs described above:
2309 - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
2310 - for y-z sections, facets are stacked in y
2311 o pkg/thsice:
2312 - change a few routines for better vectorization: thsice_albedo.F,
2313 thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
2314 not affected, but in particular the latter routine has changed
2315 dramatically (not necessarily easier to read now).
2316 - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
2317 iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
2318 o verification/lab_sea:
2319 - overhaul of the forward model experiments. The main motivation
2320 for this revision is that lab_sea has proven quite fragile (when
2321 changing the sea-ice code, and switching platforms) to a point
2322 when failures were very hard to attribute to specific code problems.
2323 - the suspected reason for this fragility is noise amplification by evp so,
2324 to start with, we decided to replace evp with lsr in the main experiment.
2325 - the input.lsr experiment thus became obsolete and was removed.
2326 - it was replaced with the input.fd experiment that uses an
2327 analytical "free drift" solution as the ice velocity field.
2328 - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
2329 will hopefully allow us to discriminate problems due to dynamic solvers
2330 from problems due to the thermodynamic code. input.salt_plume (lsr) allows
2331 us to test additional options, along with the salt plume package.
2332 - Finally a pickup was generated (at the end of a one year run) to
2333 make the tests more representative of an actual model run. Previously
2334 the tests starting point was a 1m thickness of ice everywhere.
2335 o pkg/seaice:
2336 - introducing S\R seaice_freedrift.F that compute the
2337 analytical solution to an approximate ice momentum
2338 equation (i.e. the simple stress/coriolis balance).
2339 - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
2340 of the free drift velocity field, and enable its use.
2341 To actually use the free drift solution as the model ice
2342 velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
2343 o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
2344
2345 checkpoint62l (2010/10/04)
2346 o pkg/seaice:
2347 -fix the USE_ORIGINAL_SBI version (for variable freezing point);
2348 -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
2349 version (with USE_ORIGINAL_SBI undef);
2350 o add hooks for new packages OASIS, the package will follow
2351 (hooks exclude the seaice pkg for now)
2352 o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
2353 Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
2354 rather than mdsio_readvector.F/mdsio_writevector.F, within
2355 adread_adwrite.F to read/write adjoint-related tapes to disk.
2356 o eesupp and pkg/mdsio: ALLOW_WHIO
2357 Option to write/read 2D fields to files including tiles halos.
2358 The main purpose is for adjoint related "tape I/O".
2359 The secondary purpose is for debugging phases.
2360 A word on those rather specifically intended purposes.
2361 The code was meant to be stripped down to the bare minimum.
2362 Typically, there is a unique and basic mapping to the global
2363 buffer (tile by tile, then proc by proc, then level by level), and
2364 byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
2365 meant to generate user friendly outputs of various shapes and forms.
2366 Rather it is intended, for the knowledgeabale developers,
2367 to be largely independent of the many mdsio options, to allow
2368 outputs of tiles+halos in debugging phases and in adjoint runs,
2369 and to allow some flexibility in tuning (adoint) I/O depending on each
2370 file system behavior. With regard to tuning, most of the potential knobs
2371 (to leave files open, to allocate the I/O indep. of usesinglecpuio,
2372 to specify directories, to specify the typical size of I/O calls, etc.)
2373 are not yet included, and will be added if they prove useful.
2374 o pkg/seaice:
2375 fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
2376 o pkg/seaice:
2377 new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
2378 code (seaice_budget_ice_if.F) which enable to recover old standard
2379 code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
2380 temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
2381 o model/src (rStar):
2382 use simple average (not area weighted) of rStarFac at U,V point when using
2383 vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
2384 update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
2385
2386 checkpoint62k (2010/09/17)
2387 o adjoint
2388 * changed verification/global_ocean.cs32x15 ; adjoint now tests
2389 Adams-Bashforth 3 + NLFS + RSTAR
2390 * some more modifs required for ECCO-GODAE v4
2391 o pkg/seaice
2392 add SEAICE_AGE_VOL option to use volume instead of area for
2393 integrating SEAICE_AGE
2394 o model/src:
2395 first check-in of sigma & hybrid-sigma coordinate code ; also includes
2396 non-linear free-surface parts ; but pressure-gradient not yet coded.
2397 o pkg/ptracers:
2398 option for ptracer to convert Salt Relax into additional EmP.
2399 tested in exp. global_ocean.90x40x15.dwnslp (update output)
2400
2401 checkpoint62j (2010/08/25)
2402 o pkg/ggl90:
2403 other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
2404 o pkg/dic: car_flux.F, phos_flux.F
2405 - reduce number of exp-calls in order to improve performance
2406 - clean up a little (replace fields by their macros, etc., fix
2407 typo in CPP-flag)
2408 o pkg/ggl90: minor changes
2409 - GGL90diffKrS was removed --> always use GGL90diffKr
2410 - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
2411 - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
2412 (commented out for now)
2413 - change in max/min operations to ensure that smoothing is ok
2414 - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
2415 - always use diffKrNrT as background profile (i.e. never use diffKr field)
2416 o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
2417 o pkg/dic:
2418 - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
2419 vectorization
2420 - small bug fix in insol for the unlikely case of a cartesian grid
2421 - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
2422 + now vectorize, which also removes adjoint recomputations;
2423 + replace integer maksp1 by _RL maskp1
2424 + replace a**x by exp(x*log(a)) in phos_flux.F for speed
2425
2426 checkpoint62i (2010/07/21)
2427 o pkg/flt:
2428 - with OBCS: stop floats which enter the OB region
2429 o model/src:
2430 - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
2431 for implicit vertical advection.
2432 o pkg/seaice:
2433 - account for melting in seaice age evolution.
2434 - remove double counting of seaice ridging effect on seaice age.
2435
2436 checkpoint62h (2010/06/18)
2437 o pkg/exch2:
2438 - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
2439 o tools/genmake2
2440 - remove "-pdefault" option: redundant with the use of "packages.conf";
2441 - remove file pkg/pkg_default : set the default as a pkg group
2442 ("default_pkg_list") defined in pkg/pkg_groups;
2443 - fix for case pkg/pkg_depend is missing (was hanging before);
2444 - add option "-pgroups" to specify a different pkg_groups than the default.
2445 o verification/adjustment.cs-32x32x1:
2446 add a "minimal" set-up test (code_min & input_min) which only compiles
2447 eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
2448 o tools/genmake2
2449 - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
2450 - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
2451 o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
2452 files are nearly the same anyway.
2453 Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
2454 - redefinition of tau(i,i) (by a factor of ustar)
2455 - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
2456 - replace rhonil by rhoConstFresh in computation of evap (bug fix)
2457 - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
2458 - replace
2459 rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
2460 shn = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
2461 by
2462 shn = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
2463 (changes results)
2464 -> exf_bulkformulae v1.22,
2465 update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
2466 (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
2467 output.txt 1.63
2468 offline_exf_seaice: output.seaicetd.txt 1.7
2469 seaice_obcs: output.txt 1.10)
2470 Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
2471 -> exf_bulkformulae v1.23,
2472 unfortunately requires updating lab_sea.salt_plume (6 matching digits),
2473 and global_ocean.cs32x15.icedyn (only 11 matching digits)
2474 Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
2475 o adjoint of exch-1:
2476 - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
2477 (note: was already like this when using EXCH-2) and remove flow dir
2478 and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
2479 - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
2480 - update pkg/exch2 diff list.
2481
2482 checkpoint62g (2010/05/19)
2483 o eesupp/src (exch-1):
2484 - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
2485 and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
2486 (renamed to exch1_*rx_cube.F).
2487 - change accordingly exch_*_rx.template and AD version in pkg/autodiff
2488 to call new exch1 S/R ; update Makefile and .cvsignore.
2489 - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
2490 exch2_xy_rx later)
2491 Note: after updating your code, need to run "make clean" in eesupp/src
2492 o test experiment bottom_ctrl_5x5:
2493 new output_adm.txt with fewer grdchk & less monitor output.
2494 o model/src:
2495 remove the call to ini_cori in initialise_varia.F (just keep the usual one
2496 in initialise_fixed.F). More consistent with coriolis & horizontal grid
2497 beeing treated in the same way (ini_grid is not called a 2nd time).
2498 o pkg/exf:
2499 - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
2500 global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
2501 - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
2502 - cosmetic changes to exf_bulkformulae.F to make it look more like
2503 exf_bulk_largeyeager04.F
2504 o eesupp/src (exch-1):
2505 - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
2506 - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
2507 array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
2508 (even without using MPI).
2509 - Message mode: move RecvAck setting (indicator of buffer being ready)
2510 from send_put to recv_get S/R (was useless before, but not sure if
2511 it's much more useful now);
2512 - Switch the order of sync: MPI-proc 1rst and then threads;
2513 - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
2514 - fix AD code for communication mode ='get' (but not used).
2515 o model/src:
2516 initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
2517 not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
2518 o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
2519 o pkg/ctrl: require a specific set of control variables and exf-flags for
2520 adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
2521 o model/src:
2522 a) 1rst version of a new driver S/R to turn-off output freq and flags after the
2523 1rst forward sweep, to avoid over-writing output files during recomputations
2524 recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
2525 b) 2nd version:
2526 - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
2527 - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
2528 writePickupAtEnd) + seaice & ptracers output;
2529 - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
2530 o model/src:
2531 - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
2532 o pkg/exch2:
2533 - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
2534 - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
2535 o pkg/autodiff & exch2:
2536 process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
2537 (for now, only if ALLOW_EXCH2 is defined).
2538 o pkg/autodiff:
2539 - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
2540 (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
2541 + clean-up comments (_RS is not always real*4)
2542 - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
2543 - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
2544 was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
2545 o testreport (AD-tests):
2546 no longer link files from dir "../input" (1rst link files from
2547 "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
2548
2549 checkpoint62f (2010/04/29)
2550 o model/src/the_main_loop.F:
2551 adjust store directives for seaice evp and multicategory according to
2552 pkg/ecco/the_main_loop.F
2553 o adjoint:
2554 global_sum_ad was incomplete (noted many times by many people ;)
2555 nice description by Jean U. as follows:
2556 * allreduce(var) in global_sum.F can be interpreted as
2557 reduce(sum) followed by broadcast of sum.
2558 * The adjoint of that is
2559 sum(adjoint) followed by broadcast(summed adjoint value)
2560 or in other words, allreduce(sum, adjoint vars)
2561 We were missing the sum(adjoint)!
2562 Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
2563 (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
2564 The fix should produce 16-digit accuracy between
2565 single-CPU multi-tile (e.g. nSx=2, nPx=1) and
2566 multi-CPU single-tile (e.g. nSx=1, nPx-2)
2567 We'll probably change this yet again shortly
2568 o eesupp/src:
2569 - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
2570 o pkg/icefront
2571 - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
2572 specification of addmass array based on a 2D field, which is added
2573 at bottommost wet level at each horizontal location.
2574 o model/src:
2575 horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
2576 layout; (not always compatible with delX,delY setting; commented out for now).
2577 o pkg/exch2:
2578 change tile to processor setting (case nSy*nPy > 1): allows default model mapping
2579 (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
2580
2581 checkpoint62e (2010/04/15)
2582 o pkg/obcs:
2583 - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
2584 o pkg/dic:
2585 -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
2586 (note: not presently tested in any forward verification exp.)
2587 update tutorial_global_oce_biogeo AD output file.
2588 o pkg/exf:
2589 - account for the variation of albedo as a function of zenith angle
2590 by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
2591 o build_options:
2592 - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
2593 o pkg/dic:
2594 change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
2595 - use binary pickup file for restart;
2596 - initialise atmos-CO2 box from dic_pCO2 parameter;
2597 - fix multi-threaded.
2598 o pkg/rbcs:
2599 - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
2600 change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
2601 - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
2602 and update output.txt
2603 o pkg/kpp:
2604 - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
2605 - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
2606 (= ratio of KPP non-local (salt) flux relative to surface-flux) when
2607 using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
2608 - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
2609 KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
2610 o pkg/offline:
2611 fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
2612 (bug was added in version 1.10 on 2007-08-23).
2613 o pkg/offline:
2614 - no need to specify periodicExternalForcing, etc ... to use offline pack
2615 - offline input files no longer just single prec --> parameter offlineLoadPrec
2616 o verification/lab_sea:
2617 change AD test to multi-tile setup and update all 4 AD output.
2618 NOTE: while cost function values remain very similar,
2619 gradients are very different, although gradient checks are self-consistent
2620 Should try to get to the bottom of this (cost function summation order?)
2621 o pkg/dic:
2622 in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
2623 a weakness of TAF that drops part of double precision in log10 derivative.
2624 <= changes removed since problem has been fixed in current TAF version 1.9.71
2625 update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
2626 o pkg/ecco:
2627 add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
2628 update all 4 lab_sea AD output.
2629
2630 checkpoint62d (2010/03/22)
2631 o build_options:
2632 remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
2633 o remove unbalanced quote (single or double) in commented line of source code
2634 (may cause some warning with some preprocessor/makedepend versions).
2635 o pkg/seaice:
2636 fix seaice_model.F for adjoint (gael) and update AD results of experiments
2637 lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
2638 o testreport:
2639 add option '-runonly' (short: '-ro') to just do the run part (without make).
2640 o eesupp: remove JAM communication code (obsolete).
2641 o add option to genmake2 & testreport to switch "_RS" type to "real*4"
2642 (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
2643 to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
2644 (update also the output).
2645
2646 checkpoint62c (2010/03/02)
2647 o tools/build_options :
2648 move (some) old optfiles from build_options/ to build_options/unsupported/
2649 o model/src and pkg/exf
2650 surface relaxation -- separating data and data.exf options
2651 The point is to ensure that we specify the surface relaxation
2652 either in data or in data.exf (but not half and half) and to
2653 avoid an accidental relaxation to 0 (which happened if a time
2654 scale was specified but the file name was left empty)
2655 o model/src model/inc and pkg/mom_common
2656 ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
2657 => addition to the viscosity field as computed by others schemes
2658 o tools/build_options:
2659 - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
2660 but keep the former optfile for few weeks for smooth transition
2661 o pkg/ecco
2662 - allow user defined cost function contributions
2663 CPP: ALLOW_USERCOST_CONTRIBUTION
2664 USAGE: compute contributions in cost_usercost_all.F
2665 - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
2666 the two options are complementary.
2667 o pkg/smooth
2668 - migration from contrib to the main repository
2669
2670 checkpoint62b (2010/01/26)
2671 o pkg/monitor:
2672 - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
2673 (in case someone forgot to update customized pieces of code)
2674 o nonHydrostatic:
2675 - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
2676 - add a simple 2-D experiment (short_surf_wave) to test it.
2677 o pkg/icefront:
2678 adding the shell of, and the hooks to, a new package that
2679 will model melting and freezing of vertical glacier ice fronts
2680 o momentum:
2681 add diagnostics of momentum tendency from Hydrostatic pressure gradient
2682 (without surf.pressure term: would need a 2nd filling since implicit term).
2683 o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
2684 two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
2685 cannot deal with the former
2686 o cleaning:
2687 - remove all (except OpenAD) old TLM output from results_ad dirs.
2688 - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
2689 - comment out maskH definition (replaced by maskInC)
2690 o pkg/monitor:
2691 - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
2692 & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
2693
2694 checkpoint62a (2010/01/15)
2695 o model/src:
2696 - bottom pressure diagnostic: correct for r* (when nonlinFreeSurf >= 4)
2697 o pkg/diagnostics:
2698 - add optional level number diagnostics (i.e., level number to be define
2699 explictly with S/R DIAGNOSTICS_SETKLEV) with parser-code(10)="X".
2700 - strictly check for valid parser-code(10) ;
2701 - check if adding diag to the list from the right place.
2702 o pkg/longstep:
2703 - change parameters and fix tracer conservation with rstar/nonlinear free surface
2704 o diagnostics:
2705 - in all pkgs, replace remaining calls to old S/R DIAGNOSTICS_ADD2LIST with newer
2706 S/R DIAGNOSTICS_ADDTOLIST ; fix seaice VICE diagnostics.
2707 o pkg/diagnostics:
2708 - Add option for writing vertical integral (sum of selected levels) of an output
2709 field instead of writing output field levels. Activate this option on a per
2710 output-file basis, by setting the 2nd character of fileflag to 'I'.
2711 - Add field-specific information relative to level integral in 3rd postion
2712 of parser diagnostics code (gdiag): " "=cumulate levels, "R"=integrate
2713 vertically (x level-thickness x hFac), "r"=same but without hFac.
2714 o do_the_model_io:
2715 - pass end-of-model-run flag as argument, from forward_step to diagnostics_write:
2716 in case useSIGREG, will write (averaged) diagnostics (if dumpAtLast) before
2717 writing pickups and stopping.
2718 o pkg/diagnostics (for now, only with mdsio):
2719 - write time information to meta file (and modify accordingly rdmds.m) :
2720 time-averaged diagnostics output: write starting and ending time of the
2721 time-averaging interval ; snap-shot diagnostics output remains unchanged;
2722 o pkg/timeave:
2723 - S/R TIMEAVE_NORMALIZ: change size of cumulated-time array (was previously
2724 always Nr), now assumed to be equal to number of levels of averaged field;
2725 only used for DIC_COST monthly mean arrays: this fixes dic_aver_final.F
2726 o pkg/sbo:
2727 - fix ocean bottom pressure global-average & 2-D time-ave output (was
2728 neither initialised nor filled).
2729 - add starting iteration in suffix of global-average output file
2730 (to avoid over-writing the file after a restart)
2731 - use standard MDSIO pkg S/R instead of SBO_WRITEVECTOR (fix byte-swap Pb).
2732 o time-average:
2733 - use simple cumulative-time array (no k index) in all pkgs: {PKG}_timeAve(bi,bj)
2734 (pkgs: aim_v23, bulk_force, dic, gmredi, kpp, land, ocn_compon_interf,
2735 ggl90, my82, opps, pp81, ptracers, sbo, seaice, shelfice, thsice)
2736 this fix DIC_COST cumulative-time array (previously: bi,bj,k)
2737 - fix 1rst call (nIter0) snap-shot output and accumulation (pkg/shelfice)
2738 - fix missing accumulation for pkg/opps.
2739 - cumulate fields only if doing time-ave output ({PKG}_taveFreq > 0)
2740 (pkgs: ptracers, kpp, ocn_compon_interf, ggl90, my82, pp81);
2741 - fix initialisation of time-ave vars and do only full time-step increment
2742 (i.e.: no first & last "half time-step") (pkgs: ggl90, my82, opps, pp81);
2743 o pkg/layers:
2744 - use standard RW pkg S/R to write the output
2745 and remove local write_fld version (which had a problem).
2746 - use simple cumulative-time array (no level index) to fix time-ave S/R calls.
2747 - fix LAYERS_CALC argument list.
2748 o pkg/timeave:
2749 - store cumulative-time in a simple tiled array (drop the level index)
2750 - add new S/R (TIMEAVE_NORMALIZE) which uses simple cumulative-time array.
2751 o pkg/ocn,aim_compon_interf
2752 - changes for multi-threaded coupled run. (tested with ifort-11 on danton)
2753
2754 checkpoint62 (2009/12/23)
2755 o switch on useOBCSbalance in tutorial_plume_on_slope exp. and update output.
2756 (was not previously tested in any other exp.)
2757 o pkg/monitor:
2758 - clean-up _RL/_RS version: add specific S/R for statistics with mask & volume:
2759 mon_writestats_rl/s,F mon_calc_stats_rl/s.F ; will keep the old one
2760 (mon_printstats_rl/s,F mon_stats_rl/s.F) just for bare statistics.
2761 - use hFac & 2-D mask (instead of 3-D mask + hFac in previous mon_stats_rl.F).
2762 - change del2 calculation.
2763 - use interior masks (instead of maskH, <- to be remove).
2764 - shorter monitor suffix for forcing stats ("forcing" instead of "extforcing").
2765 o mask & obcs:
2766 - define 2-D "interior" masks (i.e., zero beyond OB) at 3 locations (C, W & S).
2767 - move global area computation from ini_masks_etc.F to ini_linear_phisurf.F
2768 (called after packages_init_fixed)
2769 o pkg/obcs:
2770 - move bi,bj loops into obcs_calc, so obcs_prescribe_read is called only once.
2771 Fixes bug in obcs+exf with nSx*nSy.GT.1
2772 - fix multi-tile handling in obcs balance code
2773 o nonHydrostatic:
2774 - Implement AB-3 for non-hydrostatic vertical momentum ;
2775 (change ordering of var. stored in pickup file when using NH)
2776 - move NH code from solve_for_pressure.F to 2 new S/R: PRE_CG3D & POST_CG3D.
2777 - add 2-D field to store Hydrostatic Surface Pressure adjusment from cg3d_x
2778 (in prep. for new NH free surface form).
2779 o pkg/obcs:
2780 add files & OB-variables for wVel (Non-Hydrostatic) with useOBCSprescribe
2781 o model/src:
2782 fix 2-D solver initialisation for deep-atmosphere (p-coord) with topography
2783
2784 checkpoint61z (2009/12/01)
2785 o nonHydrostatic:
2786 Fix missing vertical flux of vert. momentum near surface (k=1). This fixes
2787 a spurious source of energy in simple baroclinic adjusment test case.
2788 Update all non-hydrostatic exp output.
2789 o model/src (3-d solver):
2790 Change again 3-D solver free-surface RHS term when exactConserv=T:
2791 simpler, consistent with exactConserv, and works with implicDiv2Dflow < 1
2792 (which was not the case with previous formulation).
2793 To recover previous version, just reset "oldFreeSurfTerm" to previous value.
2794 Affects results of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW.
2795 o nonHydrostatic:
2796 - compatible with implicDiv2Dflow < 1 ; + implement implicit factor
2797 for Non-Hydrostatic pressure gradient (similar to implicSurfPress).
2798 - change 3-D solver to work with r* (for now, only with linear free-surf.)
2799 - add few debug diagnostics (cg3d_x, residual)
2800 o model/src:
2801 fix missing EmPmR in 3-D solver RHS (was in cg2d_b but missing in cg3d_b).
2802 update output of exp. global_ocean.cs32x15.viscA4
2803 o update output of exp. global_ocean.cs32x15.icedyn after removing
2804 #define SEAICE_OLD_AND_BAD_DISCRETIZATION from SEAICE_OPTIONS.h
2805 o add entry points for Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
2806 o mnc: add horizontal grid coordinates (XC,YC) and (XG,YG) to netcdf output
2807 for complex grids, for now only to "state", "adstate", "adexf", "adseaice"
2808 o model: add Christopher Wolfe's implemetation of the single reduction cg2d
2809 (d'Azevedo, Eijkhout, and Romine, 1999) with CPP-flag ALLOW_SRCG and
2810 runtime flag useSRCGSolver. Modify verification experiment global_with_exf
2811 to test this code
2812 o pkg/cd_code:
2813 Change defaut D-grid time-stepping to get the same for D-grid momentum as for
2814 C-grid momentum. D-grid velocity used to be stepped forward in time with
2815 Adams-Bashforth only on surface pressure term. Tests show that using AB on
2816 D-grid coriolis term improves stability (as expected from CD-scheme paper).
2817 To reproduce old results, add 2 options (in CD_CODE_OPTIONS.h).
2818 Update results of exp: global_with_exf (x2), ideal_2D_oce, isomip (x2),
2819 lab_sea (3 Fwd +3 AD), natl_box (x2), tutorial_global_oce_biogeo (Fwd+AD),
2820 tutorial_global_oce_latlon, tutorial_global_oce_optim & tutorial_tracer_adjsens.
2821 Keep old results by adding CD_CODE_OPTIONS.h in exp: cfc_example, exp2,
2822 global_ocean.90x40x15(+AD), global_ocean_ebm(+AD) and OpenAD.
2823 o pkg/obcs:
2824 - fix bug in initialisation (broken since Oct 1rst modification)
2825 for useOBCSprescribe without useEXF.
2826
2827 checkpoint61y (2009/11/15)
2828 o pkg/seaice
2829 - change (once again) the discretization for the evp solver: rather than
2830 squaring the averages of strain rates, average the squares to give
2831 a better approximation to VP behavior (in simple test); this breaks
2832 verification experiments that use EVP (lab_sea and lab_sea.hb87)
2833 --> update outputs
2834 o add CPP-flag (in mom_calc_visc.F) and TAF directive (in gmredi_slope_limit)
2835 to improve vectorization of adjoint code on TARGET_NEC_SX
2836 o verification/vermix:
2837 - change vermix to a more "classical" 1d column with high vertical
2838 resolution, seasonal heat flux forcing and constant wind forcing
2839 --> update outputs
2840 o pkg/seaice
2841 - fix diagnostics of principal stress components for EVP
2842 - add optional diagnostics of non-linear convergence for LSOR solver
2843 - make maximum zeta a runtime parameter
2844 o model/src (3-d solver):
2845 Undo modif from Dec 12, 2005 (solve_for_pressure.F cvs version v.49),
2846 which consisted in removing the Surf. Non-Hydrostatic pressure from the
2847 whole column and adding it to Eta (inspired from Casualli, 1999):
2848 Only affects 3-D solver initial guess and only if using ExactConserv,
2849 but tests did show a degradation of solver convergence. For this reason,
2850 decide to disable this piece of code.
2851 to recover previous version, just set zeroPsNH = exactConserv (line 78).
2852 Update output of exp. global_ocean.cs32x15.viscA4 & hs94.cs-32x32x5.impIGW
2853 o pkg/ggl90:
2854 - fix previous modif (unfortunatly has not been documented here).
2855 o pkg/seaice/autodiff:
2856 - add CPP flag to include clipping of zeta in EVP code;
2857 although clipping of zeta is not necessary for EVP and not recommended
2858 it was done by default, now clipping is disabled by default
2859 - modify computation and store zetaC/Z in seaice_evp for TAF
2860 - add CPP-flag SEAICE_ALLOW_CLIPVELS (undefined by default)
2861 - change seaice_calc_viscosities/strainrates for better
2862 vectorization after AD by TAF
2863 - rearrange common blocks in SEAICE.h once again for easier dumps of
2864 adjoint output, adjust adcommon.h and g_common.h
2865 - change flux form of default advection scheme for better vectorization
2866 of adjoint code
2867 - modify lab_sea/input.lsr to test the flux form of default advection
2868 scheme
2869 o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
2870 transition in checkpoint61r)
2871
2872 checkpoint61x (2009/10/19)
2873 o adjoint: adding two new verification experiments
2874 * tutorial_global_biogeo: an online dic sensitivity experiment
2875 (work with G. Forget)
2876 * tutorial_dic_adjoffline: an offline dic sensitivity experiment
2877 (an update of the Dutkiewicz et al., 2006 paper)
2878 Both use the same CO2FLUX cost function, but different controls
2879 Gradient checks look good, but some recomp. could still be traightened out
2880 Should add xx_dic control variable to test at some point
2881 o model/src:
2882 add run-time parameters to check and/or mask initial Temp & Salt
2883 o pkg/ptracers:
2884 apply zonal filter (if used) to all passive tracers
2885
2886 checkpoint61w (2009/10/12)
2887 o adjoint:
2888 * update and finish work on adjoint of dic package (G. Forget)
2889 * start adjoint of offline package
2890 * bug fix for cube-sphere TLM code (active_file_g.F)
2891 o tutorial_global_oce_optim:
2892 now tested with 4 tiles (change data.grdchk and update output_adm.txt)
2893 and add SIZE.h_mpi for MPI testing
2894 o pkg autodiff
2895 - fix bug in autodiff_restore
2896 - make genmake2 remove comments and empty lines from ad_input_code.f in
2897 order to reduce file size (new script file remove_comments_sed)
2898 o allows to specify vertical profile of vertical viscosity (viscArNr)
2899 o pkg autodiff
2900 autodiff_ini_model_io: comment out writing of grid information to netcdf
2901 files, because at this time the grid fields are a bunch of zeros
2902 (this is analogous to ini_mnc_vars.F)
2903 o pkg seaice/autodiff:
2904 left-over from removing the 3-time-level fields:
2905 - small rearrangement of common blocks (SEAICE.h)
2906 - fix field declaration in order to get meaningful output in
2907 adseaice.*.nc (adcommon.h)
2908 o pkg obcs:
2909 - go through NH code only if nonHydrostatic=T
2910 - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
2911 - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
2912 => Update output of experiment seaice_obcs
2913 - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
2914 - fix NH+Orlanski restart (add wvel OBC value in pickup file)
2915 - fix restart for useOBCSprescribe + useEXF
2916 o pkg ctrl
2917 - make obcs as control parameter work also with useSingleCPUio
2918 - replace a few sny and snx by Ny and Nx to be consistent with
2919 ctrl_set_globfld_x/yz.F
2920 o pkg seaice
2921 - re-introduce global field frWtrAtm for the case of
2922 ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
2923 - catch the case of an empty filename in seaice_cost_init_fixed.F
2924 o pkg ecco:
2925 - small bug fixes in the_main_loop
2926 . fix order of monitor arguments
2927 . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
2928 . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
2929 that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
2930 - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
2931 imbalance diagnostics for wmean_h/sflux = 0
2932 - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
2933 - catch the case of empty filenames in ecco_cost_init_fixed.F
2934 and ecco_readparms.F
2935 - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
2936 to make this statement meaningfull in ecco_cost_weights.F
2937 o pkg zonal_filt:
2938 - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
2939 - when using rStar, filter uVel*hFacW instead of uVel
2940 (tested without topography: fix a Pb of growing instability with NLFS)
2941 o pkg/aim/thsice:
2942 -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
2943 (works as SST restoring)
2944 o pkg/thsice:
2945 -add specific parameter for salt restoring in slab mixed-layer
2946 (by default equal to the temperature restoring)
2947
2948 checkpoint61v (2009/09/21)
2949 o pkg/kpp:
2950 -add double diffusive contributions as a hack, turned off by default
2951 for now, and the code can be excluded with a CPP-flag
2952 EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
2953 -add a verification experiments to "vermix" to test this code
2954 o pkg/mom_common:
2955 Move computation of length scales to mom_init_fixed.F (avoid recomputation
2956 at each time-steps*levels).
2957 o pkg/layers:
2958 Created a new package for computing volume fluxes in temperature or
2959 [not yet implemented] density layers, e.g. for calculating residual
2960 overturning circulations.
2961 o pkg/diagnostics:
2962 implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
2963 o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
2964 o pkg/mdsio (& pkg/rw): rework high level S/R interface:
2965 To avoid mixing type (RS/RL) of input/output array argument,
2966 replace single mixed-type array with a pair from each type (RS/RL).
2967 o setting pickupSuff force to start from a pickup (even if nIter0=0): this
2968 is now implemented for all pkgs (previously only done for the main pickup)
2969
2970 checkpoint61u (2009/08/25)
2971 o pkg/obcs:
2972 - change OB?eta from _RS to _RL and put them into a separate commen block
2973 - add code to read OB?eta from a file via obcs_prescribe_read: the code
2974 compiles and does not destroy any other experiments, the data is read
2975 properly, but the code is not tested in actual applications
2976 o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
2977 create a meaningful unit attribute for the time coordinate variable
2978 o pkg/ebm: add plenty of missing "_d 0" ;
2979 update results of experiment global_ocean_ebm (fwd + adjoint tests)
2980 Notes: several pieces of code only works for (very) specific set up
2981 (domain size, lat range, etc ...); should be documented & stop if one
2982 of those assumptions is not meet.
2983 o pkg/seaice: add missing "_d 0" in HSNOW initialisation
2984 update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
2985 and offline_exf_seaice (seaicetd + adjoint).
2986 o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
2987 update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
2988 seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
2989 o few changes to pass when compiling with strick checking of arguments
2990 across S/R (allow to find few bugs in S/R calls).
2991 o pkg/seaice:
2992 - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
2993 2d-fields, for slightly better performance
2994
2995 checkpoint61t (2009/07/22)
2996 o pkg/seaice:
2997 - remove unused variables in seaice_evp
2998 - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
2999 o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
3000 named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
3001 each processor opens a different file (a fix from Matt).
3002 o cg2d:
3003 use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
3004 this reduces number of EXCH calls by 2 when using exch2.
3005 For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
3006 directives and missing simple EXCH (exch_s3d_rx) adjoint code.
3007 o pkg/thsice:
3008 add code for Near Infra-Red albedo (from Jeff)
3009 (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
3010 o ini_model_io:
3011 move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
3012 MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
3013 to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
3014
3015 checkpoint61s (2009/06/30)
3016 o pkg/exch2 (exch2_rxN_cube*):
3017 remove last BARRIER (no need to synchronise after getting data from shared
3018 buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
3019 o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
3020 and generate new output (for the 2 tests) using default rotationPeriod.
3021 o pkg/exch2:
3022 - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
3023 (was already the case with AUTODIFF_EXCH2 defined)
3024 - add bj in exch2 arrays and S/R.
3025 - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
3026 MLAdjust to exch2 (identical results except with MPI -> truncation diff);
3027 o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
3028 - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
3029 GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
3030 - verification experiment natl_box.longstep
3031 o build_options: ifort+mpi_aces optfile (following Constantinos advise):
3032 allow different versions of ifort (8 or 9) and different versions
3033 of mpi (mpich or mpich2) to be used with the same optfile.
3034 requires to load a netcdf module and set MPI_INC_DIR (see comments inside
3035 optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
3036 o pkg/seaice:
3037 fix previous modif (3-level field removed) for old-pickup reading
3038
3039 checkpoint61r (2009/06/25)
3040 o pkg/seaice:
3041 - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
3042 1. introduce fields for time step (N-1)
3043 2. do not use levels 2 and 3 anymore (but keep them)
3044 3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
3045 includes changes to pkg/thsice/thsice_get_velocity.F,
3046 model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
3047 pkg/obcs/obcs_apply_uvice.F.
3048 - completely remove code for leap-frog time stepping for second order
3049 advection
3050 - adjusted adjoint accordingly;
3051 gradient checks have improved by an order of magnitude!
3052
3053 checkpoint61q (2009/06/22)
3054 o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
3055 - the boundary conditions along open boundaries are unclear, because the
3056 associated masks are set to zero and are thus treated as closed when
3057 applying the slip-boundary conditions.
3058 - move initialisation of grid variables from seaice_init_varia to _fixed
3059 o adding doc/diags_changes.txt
3060 o model/src:
3061 do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
3062 to avoid "_diags" naming if no relation to pkg/diagnostics.
3063 ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
3064 file and only call PLOT_FIELD_XYZ if debugMode=T.
3065 remove few PLOT_FIELD_XY calls outside initialisation.
3066 remove few unnecessary BARRIER.
3067 o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
3068 of salt_plume package in Southern Ocean
3069 o pkg/thsice:
3070 - fix hOceMxL in overlap (needed for sea-ice advection);
3071 update output of experiment global_ocean.cs32x15.icedyn.
3072 o pkg/seaice:
3073 - make the (placeholder-)tracer IceAge a little more meaningful
3074 by avoiding ridging of age due to convergent ice flow
3075 - add diagnostics for surface temperature, atmospheric and oceanic
3076 heat flux, and atmospheric and oceanic ice growth
3077
3078 checkpoint61p (2009/06/10)
3079 o eesupp (global_max & global_sum):
3080 - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
3081 - remove starting & endding barrier (no longer needed)
3082 o pkg/mdsio, writelocal:
3083 works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
3084 (remove the STOP): uses shared buffer IO to store data from all threads
3085 and then let master-thread write nThreads tiles.
3086 o pkg/mdsio (read/write field):
3087 - tiled IO done in 1 piece (all levels at a time);
3088 - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
3089 - multi-threaded: allow to read/write local (non-shared) array
3090 (was already working with singleCpuIO ; now works also without);
3091 => no longer needs barrier call after reading a file (added inside
3092 mds_read/write field).
3093 - move barrier calls outside gather/scatter_2d to mds_read/write_field
3094 o pkg/obcs/exf
3095 - exf_getffieldrec.F: add a few ". _d 0" and
3096 add code to catch the case fldperiod = 0.
3097 - obcs_precribe_read.F: change if statements so that they match
3098 the variable type (_RL)
3099 - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
3100 exf_iprec) as part of namelist EXF_NML_01
3101 o pkg/mdsio:
3102 - read/write tiled (local) files: read/write 1-level tile chunk at a time
3103 (instead of segment of length sNx); expected to speed up tiled IO.
3104 o pkg/exch2:
3105 - take buffer copy from/to array out of S/R exch2_send/recv into new
3106 S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
3107 (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
3108 - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
3109 - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
3110 (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
3111 including Topology header file (and common blocks).
3112 - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
3113 remove 2nd exch call in exch2_s3d_rx (no longer needed).
3114 - document S/R arg. list (+ update some comments)
3115 o pkg/seaice:
3116 - added SEAICE_CLIM_AIR code, which permits modulation of surface air
3117 temperature and humidity over sea ice based on climatological values.
3118 - clean up computation of Hibler+Bryan (1987) stress coupling for the case
3119 of LSR (this change is expected to change the results slightly because now
3120 it uses slightly difference moduli from the second last LSR solution, but
3121 that is more consistent with the stress computations; this part of the code
3122 is not tested in the verification experiments)
3123 - fix diagnostics for flux of ice in case of B-grid
3124 - turn strain rates eij and press into global fields within global
3125 common block in SEAICE.h for more straighforward diagnostics
3126 - fix diagnostics for principal stress components, press, zeta, eta
3127 to give something meaning full
3128 o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
3129 new output (all 4 tests) using default rotationPeriod.
3130 o pkg KPP:
3131 - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
3132 - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
3133 and normal grid from 1 to Nr)
3134 o Fix computations of L4rdt in mom_calc_visc.F
3135 o eesupp:
3136 new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
3137 should be called before a "stop" if we know that all process are going
3138 to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
3139
3140 checkpoint61o (2009/05/26)
3141 o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
3142 o model/src/ini_curvilinear_grid.F:
3143 compute angleSin/CosC when they are not read from a file
3144 o pkg/seaice:
3145 add pseudo time stepping for LSOR
3146 o pkg/exch2:
3147 temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
3148 o pkg/seaice:
3149 Adding separate sea ice albedo, drag coefficients, and HO in Southern
3150 Ocean from those in Arctic Ocean. See *_south in SEAICE_PARAMS.h
3151 o SingleCpuIO:
3152 fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
3153 o pkg/seaice:
3154 put exchanged variable in (local) common block for MPI+Multi-Threads
3155 to work (necessary with exch1, and for now with exch2 too).
3156 o verification: to get more experiments tested with mpi, mth and mpi+mth,
3157 change tiling of:
3158 aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
3159 hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
3160 update output of exp:
3161 exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
3162 tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
3163 + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
3164 (note: output.txt generated on faulks using only 1 tile)
3165 o eesupp & mdsio (SingleCpuIO):
3166 - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
3167 parameter "W2_useE2ioLayOut" (read from file "data.exch2").
3168 Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
3169 - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
3170 - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
3171 gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
3172 o pkg/exch2:
3173 - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
3174 read parameter file "data.exch2" if it exists; otherwise try default regular
3175 cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
3176 - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
3177 with new code (not to be used, just as a backup solution).
3178 - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
3179 in utils/exch2/input.
3180
3181 checkpoint61n (2009/05/12)
3182 o eesupp & mdsio (SingleCpuIO):
3183 - move mapping to global io-buffer inside gather_2d/scater_2d: this save
3184 memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
3185 receive real*4 array (instead of real*8) to read/write 32.bit files.
3186 (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
3187 and remove new mapping S/R)
3188 o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
3189 - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
3190 xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
3191 when using exch2. Add S/R to map global io-buffer to global model array.
3192 - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
3193
3194 checkpoint61m (2009/04/29)
3195 o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
3196 and add 3 other S/R for other types (R4,R8,RS).
3197 Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
3198 o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
3199 - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
3200 - reduce number of macro definitions (keep only those which are used);
3201 can always call directly the corrresponding S/R if needed.
3202 - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
3203 _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
3204 Fixed wrong type of arg in:
3205 atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
3206 ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
3207 To fix: global_sum of var in common block is wrong (multi-threaded) in:
3208 dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
3209 To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
3210 o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
3211 "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
3212 o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
3213 o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
3214 edges are closed (zero depth); might happen with "blank tiles";
3215 for now, disabled if using OBCS.
3216 o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
3217 link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
3218 o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
3219 to reduce length of 1.D array print in STDOUT.
3220 o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
3221 + use 48 tiles (16x8): this will allow to test "blank tiles".
3222 o start to test MPI + multi-threaded (change testreport to skip tests
3223 where number of tiles do not match).
3224 o genmake2: add option "-omp" to turn on Open-MP ;
3225 passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
3226 o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
3227 and keep the original tile numbering. Note: compatible with old
3228 W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
3229
3230 checkpoint61l (2009/04/07)
3231 o Overlaps had been forgotten in calculating ijk keys : fixed
3232 o fix cyrus makedepend for gcc 4.4
3233 o experiment fizhi-cs-aqualev20:
3234 switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
3235 and generate new output. Note: new output is much closer to the old
3236 one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
3237 the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
3238 o pkg/fizhi:
3239 - change to avoid indices going deliberately over array-bounds
3240 - remove unnecessary MPI stuff
3241 - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
3242 - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
3243 does not go over array-bounds and therefore returns reliable output.
3244 - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
3245 this S/R has 4 output arguments, which are used inside "get_alarm";
3246 when it is called with the same variable "ndum" in place of several
3247 output arguments, this produces weird side effect inside "get_alarm"
3248 (e.g., datein=dates(n) is overwritten by timein=times(n) since both
3249 datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
3250 address) and produces error.
3251 o tools/gemake2: (March 27-29 2009)
3252 with option "-mpi": link *_mpi files from "MODS" dir (this is what
3253 testreport does).
3254 o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
3255 o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
3256 update lab_sea.lsr & lab_sea.salt_plume results
3257 o pkg/seaice:
3258 Major overhaul of the LSOR solver: change discretization from original
3259 finite differences to finite volume. The old routine is still in the
3260 file seaice_lsr.F and can be turned on with the CPP-flag
3261 SEAICE_OLD_AND_BAD_DISCRETIZATION
3262 Along with this change, the discretization of the strain rates is changed.
3263 The same flag turns on the old discretization in seaice_calc_strainrates.F
3264 All verification experiments with seaice are affected (except for
3265 seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
3266 results by setting the above flag.
3267 Further changes involve changes in defaults:
3268 - ALLOW_FLOODING is defined and turned on by default
3269 - SEAICEadvSnow = .true. is now the default
3270 - SEAICEadvSalt = .true. is now the default
3271 - SEAICEadvAge = .true. is now the default
3272 - SEAICE_clipVelocities = .false. is now the default
3273 (as per J. Zhang's recommendation)
3274 - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
3275 is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
3276 - seaice_growth: replace computation of UG by a simple copy from wspeed
3277
3278 checkpoint61k (2009/03/18)
3279 o pkg/seaice: a few bug fixes mostly concerning the metric terms:
3280 seaice_lsr: fixed a few metric terms,
3281 affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
3282 add more debugging diagnostics
3283 seaice_evp: removed superfluous many metric terms of FV discretization
3284 of stress divergence
3285 affects lab_sea, lab_sea.hb87
3286 seaice_ocean_stress: removed superfluous many metric terms of FV discretization
3287 of stress divergence for non-evp solver
3288 (this part is not tested anywhere)
3289 seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
3290 they were effectively only half slip
3291 affects lab_sea.hb87
3292 updated all relevant verification experiments (except lab_sea//output_adm.txt
3293 which was left over, but fails at level 7 & 6)
3294
3295 checkpoint61j (2009/03/17)
3296 o pkg/seaice: turn a few hard wired parameters into run time parameters
3297 o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
3298 time in seconds as promised by the usints in seaice_monitor and exf_monitor
3299 o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
3300 that are not cubed-sphere grids
3301 o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
3302 o pkg/ctrl:
3303 fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
3304 o non-hydrostatic (calc_gw.F):
3305 fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
3306 update output of exp. global_ocean.cs32x15.viscA4
3307 o remove backward compatibility for thetaMin,phiMin
3308 (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
3309 o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
3310 interpolated wind field not only for curvilineargrid=.true., but also
3311 for a rotated grid (rotateGrid=.true.)
3312 o pkg/exf: add capability to bypass interpolation for runoff
3313 by setting yet another CPP-flag
3314 o eesupp/src, B-grid exchange:
3315 add simple (6 tiles, non MPI) CS exch + standard interface S/R.
3316 o autodiff
3317 new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
3318 allows to switch to single-prec common blocks;
3319 corresponding switch occurs in tamc.h, integer isbyte
3320 TAF store directivs "byte" and "kind" seem equivalent;
3321 Most tamc.h have been updated correspondingly.
3322
3323 checkpoint61i (2009/02/13)
3324 o autodiff:
3325 fix autodiff_sore/_restore indices for obcs
3326 (spotted by I. Hoteit, M. Mazloff)
3327 o pkg/autodiff, pkg/ctrl:
3328 Add flag to reduce all tapelev I/O to single-prec.
3329 In data.ctrl set
3330 doSinglePrecTapelev = .TRUE.
3331 o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
3332 check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
3333 o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
3334 real fresh water flux (not yet)
3335 o pkg/mdsio & rw:
3336 - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
3337 - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
3338 o pkg/flt:
3339 - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
3340 init_fixed & ini_varia.
3341 - clean-up & simplify linear interpolation S/R:
3342 move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
3343 - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
3344 - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
3345 - add vert. coordinate & horiz. indices to output files.
3346 - change vertical position in initial condition, from index to depth [m].
3347 - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
3348 (easier to get to a curvilinear grid) ; delX,delY no longer used.
3349 o pkg/ggl90: a few modifications:
3350 - fix bottom boundary condition, and interpolation of KappaE
3351 near top and bottom
3352 - use same set of viscosity/diffusivity for TKE/momnetum/tracer
3353 - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
3354 - add a few options for mixing-length upper limit (--> mxlMaxFlag)
3355 o rename thetaMin,phiMin -> xgOrigin,ygOrigin
3356 (maintain temporary backward compatibility, until next checkpoint)
3357
3358 checkpoint61h (2009/01/27)
3359 o pkg/diagnostics with "periodic averaging diagnostics":
3360 fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
3361 o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
3362 o pkg/obcs: fix loop ranges for balancing code
3363 o pkg/flt:
3364 - improve criteria for finding which tile owns a float.
3365 - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
3366 o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
3367 aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
3368 with ocean biogeo)
3369 o pkg/flt:
3370 - do some cleaning and fix the restart ;
3371 - add output.txt in flt_example/results to get this pkg tested.
3372 o genmake2: add an EXTENDED_SRC option and flag.
3373 for now, cannot be turned on on command line (only through genmake_local)
3374 o pkg/mdsio: read/write vector:
3375 - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
3376 - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
3377 & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
3378 - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
3379 (drop to 4 digits matching for grad). But this test does not look very
3380 reliable (was already failling on eddy, fc5, at 6.digits). Update output.
3381
3382 checkpoint61g (2008/12/29)
3383 o pkg/flt:
3384 - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
3385 + make OPTIONS file more standard.
3386 - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
3387 - fix _BYTESWAPIO CPP-Flag
3388 - standard reading of file-parameter "data.flt"
3389 - fix argument list of S/R FLT_RESTART
3390 still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
3391 o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
3392 o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
3393 a still unfixed compiler/optimization bug
3394
3395 checkpoint61f (2008/11/21)
3396 o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
3397 update results of global_ocean.cs32x15.icedyn test.
3398 o move getcon.F from model/src to pkg/fizhi.
3399 o pkg/exf: add parameter for extrapolation of temp up to the surface
3400 and option to prevent negative evap (in bulk_largeyeager04 only).
3401 o Prather Advection scheme: fix tracer conservation for divergent flow
3402 (e.g., when using NonLin Free-Surface).
3403 o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
3404 o gmredi (Visbeck-variable-K):
3405 - add more parameters to Visbeck-variable-K.
3406 - use a 5 points average for dSigmaR in Visbeck-K calculation
3407 (more "homogenous": same stencil and same weights as in dSigmaH)
3408 - update output of ideal_2D_oce experiment.
3409 o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
3410 (#undef REAL4_IS_SLOW)
3411 - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
3412 coordinate variable
3413 - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
3414 (surface forcing fields), removes some of the functionality
3415 - model/src/write_grid.F: write _RS variables as RS-netcdf variables
3416 - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
3417 probably not all: copy _RS surface flux fields to RL field before
3418 calling DIAGNOSTICS_FILL
3419 - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
3420 real*4 (CALL EXCH_*_RS) versions.
3421 - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
3422 (generate new output).
3423
3424 checkpoint61e (2008/10/23)
3425 o gmredi (Visbeck-variable-K):
3426 - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
3427 - change computation of Visbeck-K where Slope > Smax :
3428 now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
3429 previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
3430 o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
3431 to be the same as with Z-coord. (i.e., m/s & no-units respectively).
3432 o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
3433 o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
3434 does not become too large (to avoid precision problems in implicit-diffusion
3435 solver); update ideal_2D_oce output.
3436 o pkg ggl90:
3437 - in ggl90_cal.F: compute only one set of visc/diff, used to
3438 step forward TKE/T/S/momentum
3439 - default value of GGL90viscMax/GGL90diffMax larger and equal (to
3440 have Prandlt =1)
3441 o gmredi (fm07):
3442 - add lower limit on Transition layer thickness + lower limit on 1/lambda
3443 - allow to set few more params from data.gmredi
3444 o pkg ggl90:
3445 - add missing sqrt(2) factor in computation of mixing length
3446 scale in ggl90_calc.F
3447 (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
3448
3449 checkpoint61d (2008/09/25)
3450 o adjoint modifs
3451 - adapt to new field rhoInSitu
3452 - allow to revert from StoreDynVars2D, StoreDynVars3D
3453 to individual fields
3454 (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
3455 o store 3-D (in-situ) density in commom block (DYNVARS.h)
3456 - save 1 rho computation.
3457 - no longer modify T & S inland when using down_slope pkg.
3458 o gad_som : allow to switch to SOM advection for T & S without corresponding
3459 pickup files (using new S/R: MDS_CHECK4FILE).
3460 o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
3461 (for useSingleCpuIO to work in multi-threaded)
3462 o pkg/shelfice:
3463 - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
3464 with SHELFICEtopoFile in data.shelfice
3465 - move code for reading ice shelf topography and modifying hFacC into separate
3466 subroutines of the shelfice package
3467 - separate initialisation of "fixed" and "variable" variables
3468 - kTopC is not (yet) replaced by kSurfC, although this is possible
3469 o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
3470 o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
3471 and rename:
3472 ini_phiref.F --> set_ref_state.F (+ set anelastic factors)
3473 ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
3474 o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
3475
3476 checkpoint61c (2008/08/30)
3477 o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
3478 to add mass source/sink of fluid in the interior (3-D generalisation
3479 of oceanic real-fresh water flux).
3480 o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
3481 o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
3482 o new pkg: down_slope
3483 density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
3484 - presently, modify T & S inland (dwnslp_calc_rho.F).
3485 can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
3486 - implementation for ocean in P-coords not tested.
3487 - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
3488 o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
3489 (to facilitate conversion of oceanic pkg to p-coordinate).
3490 o change FIND_RHO to FIND_RHO_2D :
3491 pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
3492 o new pkg: cheapaml
3493
3494 checkpoint61b (2008/08/05)
3495 o exch2:
3496 change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
3497 - no longer depend on the order sequence (N,S,E,W).
3498 - 3rd exchange no longer needed (tested with 24 tiles).
3499 - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
3500 - exch_UV_A-grid readily available (but not yet tested).
3501 comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
3502 (both are no longer needed) in exch_uv: no effect in forward run; but
3503 get truncation error differences with adjoint exch.
3504 o exch2:
3505 - change index-bounds storage (moved from target to local tile,
3506 more intuitive this way) ; rename/remove some variables.
3507 - change utils/exch2/matlab-topology-generator & code_mods accordingly.
3508
3509 checkpoint61a (2008/07/29)
3510 o exch2/matlab-topology-generator:
3511 fix bug in index bounds for N-S internal exchange (hard to tell if this
3512 had any effect on the solution).
3513 o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
3514 is exceeded
3515 o testreport: modify syntax of awk, so that it works also with
3516 awk, and not only with nawk and gawk
3517
3518 checkpoint61 (2008/06/24)
3519 o autodiff
3520 Change default for TAF usage by removing argument '-nonew_arg'
3521 This changes TAF subroutine argument list (ordering of active var.)
3522 Omission of this flag leads to incompatibility w.r.t. TAMC
3523 To restore TAMC-compatibility, need following modifs:
3524 * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
3525 * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
3526 Tested TAF version is 1.9.22
3527 N.B.: exch2 hand-written adjoint code currently not TAMC compatible
3528
3529 checkpoint60 (2008/06/19)
3530 --->>> This is the last checkpoint for which generating the adjoint
3531 --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
3532 --->>> by default.
3533 --->>> Future checkpoints will ommit this flag by default.
3534 o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
3535 o pkg/grdchk: Add gradient check to etan0 perturbations.
3536 o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
3537 o pkg/autodiff: more flexibility in zeroadj.
3538 model/src: modifying do_oceanic_phys.F accordingly.
3539 o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
3540 o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
3541 special setup of gmredi for which the adjoint is stable
3542 enough for parameter optimization.
3543 o bridging the gap between eddy stress and GM.
3544 -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
3545 along with a change in CPP option (now ALLOW_EDDYPSI).
3546 -> when using GM w/ GM_AdvForm:
3547 The total eddy streamfunction (Psi = eddyPsi + K x Slope)
3548 is applied either in the tracer Eq. or in momentum Eq.
3549 depending on data.gmredi (intro. GM_InMomAsStress).
3550 -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
3551 The key modifications are in model/src/taueddy_external_forcing.F
3552 pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
3553
3554 checkpoint59r (2008/05/29)
3555 o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
3556 from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
3557 fix option to read coriolis(@ cell-corner) from files with CS-grid.
3558 o pkg/mnc: add some attributes to standard 1D-coordinate variables
3559 o pkg/diagnostics: enforce missing_value attribute for scalar variables at
3560 mass points, when using mnc for output
3561 - add runtime parameter (missing_value, missing_value_int) to override
3562 default (which is the value of getcon('UNDEF'))
3563 o pkg/mnc: prepare mnc for the actual use of missing values with the
3564 diagnostics package: small fix in mnc_cw_readwrite.template and more
3565 initialisation of never used fields
3566 - replace mnc_common.h and mnc_id_header.h with corresponding upper case
3567 versions
3568 o pkg/thsice/thsice_ini_vars.F added default initial values so that
3569 thermodynamics sea ice solver does not blow up when some initial fields
3570 are missing.
3571 o move from external_forcing_surf.F to ini_forcing.F
3572 the p-coord. hack consisting in using pLoad to set phi0surf ;
3573 update output of tutorial_global_oce_in_p (affected @ truncation level).
3574 o Freshen up a bit hs94.1x64x5, notably:
3575 remove rotationPeriod and tRef=5*0. (adjoint only), and add
3576 exactConserv=.TRUE.
3577 o pkg/generic_advdiff:
3578 change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
3579 applies to files where Temperature & Salinity 2nd Order moments are used.
3580 o pkg/ptracers: add second-order moment advection schemes (80 and 81);
3581 this uses a dynamically allocated internal state data structure
3582 (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
3583 and requires a fortran 90 compiler
3584
3585 checkpoint59q (2008/05/06)
3586 o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
3587 (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
3588 o Refresh tutorial_global_oce_biogeo, notably:
3589 - change bathymetry (put back seamounts in ACC, use hFacs)
3590 - change EOS (POLY3 --> JMD95Z)
3591 - use Bryan-Lewis vertical diffusivity
3592 - use multidimensional advection
3593 - remove old virtual virtual in dic pkg, now done through ptracer pkg
3594 - change a couple of parameters in dic pkg
3595 o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
3596 o pkg/obcs: change default to OBCSfixTopo = .true.,
3597 - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
3598 - replace "debugMode" with "debugLevel .GE. debLevB"
3599 o implementation of TAF directives for gchem,cfc,dic
3600 o remove "exp5" (replaced by tutorial_deep_convection).
3601 o pkg/obcs: add code to fix topography gradients normal to open boundaries;
3602 this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
3603 the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
3604 --> changes results in exp4, seaice_obcs
3605 o tutorial_deep_convection :
3606 update the set-up and increase resolution and domain size ; start
3607 from pseudo initial conditions = output at t=120mn in order to see
3608 something happening when running testreport.
3609 o pkg/seaice: add os7mp as an advection scheme
3610 add check for advection schemes
3611 add a flag for restoring T and S underneath sea ice
3612 o pkg/my82: add netcdf-support and diagnostics
3613 o thsice pkg:
3614 - Now hsMax limits snow height by turning it into ice following
3615 flooding scheme (and now conserving energy)
3616 - Slight rewriting of the formula in thsice_calc_thick.F
3617 - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
3618 --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
3619
3620 checkpoint59p (2008/04/10)
3621 o gchem / dic / cfc :
3622 - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
3623 - add new parameter files: "data.dic" & "data.cfc" ;
3624 - various re-arrangement in initialisation & header file ;
3625 - fix tutorial_global_oce_biogeo for multi-threaded test.
3626 o pkg/dic: test for "pickup_dic" file when restarting ;
3627 if no pickup-file, can restart with a re-initialised pH (same as it did
3628 before) providing pickupStrictlyMatch is set to False.
3629 o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
3630 + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
3631 o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
3632 and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
3633 o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
3634 & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
3635 (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
3636 o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
3637 scheme to use for vorticty-term ;
3638 - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
3639 (with default selectVortScheme, return to original discretisation)
3640 - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
3641 o pkg/seaice: add a line to the summary to indicate grid type (B/C)
3642 o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
3643 bottom ; only used with variable horizontal viscosity and non-hydrostatic.
3644 also fix diagnostics VISCAHW & VISCA4W.
3645
3646 checkpoint59o (2008/03/07)
3647 o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
3648 o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
3649 move a few statemens out the main loop into separate loops
3650 o pkg/shelfice:
3651 - sort out freshwater flux; convert freshwater fluxes to mass fluxes
3652 (kg/m^2/s), does not break tests, because in verification/isomip,
3653 rhoConstFresh=rhoConst (by accident)
3654 - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
3655 - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
3656 new file model/src/seawater.F, so that they are available for all pkgs.
3657 - convert potential temperature into in-situ temperature. This changes the
3658 isomip tests => update tests
3659 o add a flag writePickupAtEnd (default=true) to be able to suppress
3660 writing a pickup at the last timestep
3661 o tools/mpack-1.6 :
3662 - disable automake (not working) and autoconf (not needed).
3663 - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
3664 also cleaner with much less compilation warnings.
3665 o pkg/profiles:
3666 rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
3667 (for "less than 32 characters name" compiler requirement)
3668 o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
3669 conditions that have a different sampling frequency than S/T/U/V obcs
3670 o pkg/diagnostics (stats-diags):
3671 - fix global Min/Max in case 1 processor get only empty tiles
3672 o genmake2: replace (4 times)
3673 make genmake_tc_1.o >> genmake_warnings 2>&1
3674 with
3675 COMM="$CC $CFLAGS -c genmake_tc_1.c"
3676 echo $COMM >> genmake_warnings
3677 $COMM >> genmake_warnings 2>&1
3678 to make genmake2 always see the value of CC as specified in the optfile.
3679 o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
3680 - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
3681 - modify verification advect_cs test to test SOM-advection on CS-grid.
3682 o pkg/ctrl:
3683 - Rewrite of ctrl_map_ini_ecco.F,
3684 introducing a generic routine (ctrl_map_ini_gen.F).
3685 - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
3686
3687 checkpoint59n (2008/02/09)
3688 o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
3689 number in dedicate array "hdiag":
3690 - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
3691 with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
3692 - many small changes (integer format) for large number of diagnostics
3693 - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
3694 a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
3695 o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
3696 usingSphericalGrid, this allows to define the rotated grid coordinates
3697 via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
3698 geographical coordinates according to the inverse of the rotation defined
3699 by the Euler angles, so that Coriolis parameter and online-interpolation by
3700 exf works with the geographical coordinates on XC/YC/XG/YG.
3701 Naturally, this feature does not work with all packages, so some
3702 combinations are prohibited in config_summary (flt, flt_zonal, ecco,
3703 profiles), because there the coordinates are assumed to be regular
3704 spherical grid coordinates.
3705 o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
3706 - introduce isopycnal diffusion coefficient control.
3707 o tools/adjoint_options:
3708 - additional control vector components.
3709 o pkg/mnc: have mnc create marginally meaning full coordinate variables
3710 (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
3711 o pkg/mypackage:
3712 - add example of read/write pickup for state-var ;
3713 - add entry points to the main code for state-vars diags & write-pickup.
3714 o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
3715 transitions for useExfYearlyFields
3716 - add new subroutine that determines the file to read from for
3717 use*YearlyFields = .TRUE. and .FALSE.
3718 - add a verification experiment to global_with_exf that tests
3719 useExfYearlyFields with USE_EXF_INTERPOLATION defined
3720 o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
3721 analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
3722 subroutines (which could be generated from a template, because they are
3723 almost identical), for now they are included in obcs_prescribe_read.F for
3724 simplicity
3725 o pkg/exf:
3726 - add a little more diagnostic to exf_interp_read (in analogy to
3727 mds_read_field, can be turned off with debugLevel < debugLevA=1)
3728 - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
3729 ugly but fast by unrolling short inner loops, inserting a unroll=8
3730 directive in routine lagran, and splitting a loop and making do while the
3731 outermost loop (the latter requires the intoduction of index arrays)
3732 o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
3733 o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
3734 http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
3735 o verification/seaice_obcs: updated for restart test and latest options
3736 o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
3737 ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
3738 for now this is only available for the C-grid code and also within
3739 #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
3740
3741 checkpoint59m (2008/01/14)
3742 o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
3743 and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
3744 o gad_som : fix flux output (& diagnostics) to have same units as other
3745 advection scheme fluxes (was previously multiplied by deltaT).
3746 o added verification/seaice_obcs both to test seaice open boundaries
3747 and to provide an example matlab scrpt for generating them
3748 o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
3749 o pkg/salt_plume: clean up salt_plume_frac.F to
3750 remove redundancy in PlumeMethod 1 and 4
3751 o pkg/kpp: added saltplume diagnostics
3752 o pkg/obcs and pkg/seaice:
3753 - do not set uice and vice to zero when OB*icefile are unspecified
3754 - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
3755 - moved seaice tracer obcs after call to seaice_growth
3756 o pkg/salt_plume: added various options for salt plume depth
3757 criterion and for vertical distribution of the salt
3758
3759 checkpoint59l (2007/12/18)
3760 o pkg/ptracers: new version of ptracers pickup:
3761 read meta file and write only fields which are needed to restart.
3762 ( same logic as main pickup file ; also using pickupStrictlyMatch )
3763 o pkg/seaice:
3764 - add timescale for melting due to warm mixed layer as a means of
3765 setting SEAICE_availHeatFrac more conveniently
3766 - add a CPP-flag/runtime parameter check for flooding algorithm
3767 - reformulated availHeat in seaice_growth.F to be independent of AREA
3768 o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
3769 unit changes
3770 o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
3771 o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
3772 SX vector computer.
3773 o pkg/seaice:
3774 - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
3775 seaice forcing fields can now be read only through pkg/exf
3776 - removed some unused halos
3777 o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
3778 o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
3779 or U/VICE from U/VWIND before computing U/VSTRESS
3780
3781 checkpoint59k (2007/11/30)
3782 o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
3783 dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
3784 o fix un-initialised variable problem (in mom_vecinv & shap_filt):
3785 all experiments pass when compile with un-initialised var. checking option.
3786 o added pkg/salt_plume
3787 o script to test restart (for now, in MITgcm_contrib/jmc_script)
3788 o pkg/seaice: new read/write pickup version.
3789 read meta file and write only fields which are needed to restart.
3790 ( same logic as main pickup file ; also using pickupStrictlyMatch )
3791 o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
3792 o lab_sea.hb87: modify the domain & update output.hb87.txt :
3793 lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
3794 at j=1 & j=Ny+1 : this case is not treated correctly in the restart
3795 process. Fixed here by closing the domain at the Northern boundary.
3796 o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
3797 o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
3798 a set of consecutive levels in/from a 3-D array.
3799 o pkg/ptracers:
3800 use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
3801 to-do: fix pkg/diagnostics when large number of diagnostics are defined.
3802
3803 checkpoint59j (2007/11/09)
3804 o in pkgs: dic, obcs, offline, rbcs:
3805 standard way to compute coeff. for time interpolation between 2 time reccords
3806 which retains full precision (& make results less dependent on compiler).
3807 update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
3808 o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
3809 packages instead of reading ice cover and wind speed separately
3810 o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
3811 (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
3812 to allow to compile customized code before the update)
3813 o cleaning-up:
3814 - fix CPP instruction syntax in pkg/obcs
3815 - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
3816 add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
3817 - fix some threads issue in IO parts.
3818 o pkg/dic:
3819 - add tons of "_d 0" (--> much better testreports !)
3820 and then update outputs of tutorial_global_oce_biogeo
3821 o pkg/mom_fluxform:
3822 add a special version of momentum advection intended to conserve momentum
3823 next to a bathymetry step or a coastline edge. (default = off = #undef)
3824 o new read/write pickup version:
3825 - for now, only implemented for main (mdsio) pickup file.
3826 - write out only what is needed to restart; merge pickup_nh , pickup_ph
3827 and main pickup together.
3828 - read meta file; read only what is needed to restart; stop if a field
3829 is missing (if pickupStrictlyMatch=T, = the default) or try to restart
3830 if it make sense (even if the restart is not perfect).
3831 - if no meta file, assume that pickup to read corresponds exactly to
3832 a pickup that would currently be written.
3833 - read pickup written in the old format (until checkpoint59i) if it
3834 recognizes an old meta file (no field-list).
3835 - add a meta file in exp. which starts from a pickup: 2 cases:
3836 a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
3837 e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
3838 b) a meta file describing the content of the associated pickup file
3839 e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
3840 o pkg/mdsio & pkg/rw:
3841 - new routine to read a meta file ; new set of routine to read
3842 Multiple-fields file (with meta file).
3843 o added open boundary conditions capability for seaice
3844 HSNOW, HSALT, UICE, and VICE
3845
3846 checkpoint59i (2007/10/21)
3847 o adjoint:
3848 * fix multiDimAdvection adjoint
3849 (partial recomputation problem by TAF for fVerT(:,:,kDown)
3850 and comlev1 size definition (maxpass vs. max. number of tracers)
3851 * verification/global_ocean.90x45x15 adjoint now tests
3852 NLFS and multiDimAdvection using DST3 (=30)
3853 * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
3854 o pkg/kpp: add "_d 0" to real constant (if missing);
3855 update output of exp: natl_box (10.digits); vermix (std, 7.digits)
3856 and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
3857 o prepare for "clever pickup" implementation: add new header file "RESTART.h"
3858 for internal parameters related to restart process (formerly from PARAMS.h)
3859 and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
3860 o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
3861 as argument. (only atm2d & obcs write_pickup have not yet been updated)
3862 o pkg/monitor:
3863 - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
3864 - fix mon_stats_rs (statistics over the full domain, even where field is zero)
3865 - account for deep Atmosphere factor and density factor (anelastic)
3866 o added open boundary conditions capability for seaice HEFF and AREA
3867 o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
3868 thermodynamics
3869 - requires a little reorganization, which affects the testreport results
3870 of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
3871 so that now the conservative form is tested
3872 - add a few comments
3873 o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
3874 o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
3875 o add new diagnostics to seaice: advective, diffusive fluxes (only for
3876 multidim-advection, for scheme 2 they are not filled) and transports,
3877 thermodynamic growth rates
3878 o change units of EmPmR (inside the code, + within coupling interface)
3879 from m/s to kg/m2/s (mass flux) but leave input file unchanged.
3880 Affects results @ truncation level (cg2d match) and update output of
3881 experiments: lab_sea(6), global_ocean.90x40x15(10),
3882 global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
3883 + adjoint results: global_ocean_ebm(11) and lab_sea (12).
3884 Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
3885 Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
3886
3887 checkpoint59h (2007/09/29)
3888 o pkg/exf:
3889 - improve vectorization by moving if-statement out of loops in
3890 exf_mapfields, exf_radiation
3891 - exf_bulkformulae.F: introduce 2D fields and vectorize code
3892 o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
3893 o testreport:
3894 - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
3895 monitor & update offline_exf_seaice exp. output.
3896 - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
3897 o pkg/seaice:
3898 - bug fix in the evp solver: boundary conditions were affected be
3899 masking of zMax/zMin (changes results)
3900 - minor bug fix in boundary conditions in seaice_calc_strainrates
3901 (changes results for no_slip)
3902 - seaice_lsr.F: make interpolation of eta dependent on boundaries
3903 - replace hardcoded lower limit for zeta (zMin) by runtime parameter
3904 - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
3905 stress formulation and no-slip boundary conditions
3906 o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
3907 in gad_calc_rhs.F ; add few safety stops in initialisation phase.
3908 o pkg/seaice: a first HSALT time stepping equation has been checked in
3909 o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
3910 in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
3911 without requiring DO-IF statements
3912 o pkg/thsice:
3913 use continuous power-law function for partition of energy between lateral
3914 melting/freezing and thinning/thickening ; old code using step function
3915 still available with #undef THSICE_FRACEN_POWERLAW
3916 update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
3917 o testreport: change AD testing : check against results/output_adm.txt
3918 using same scripts as for forward test.
3919
3920 checkpoint59g (2007/09/17)
3921 o adjoint testing: in preparation for changing testreport:
3922 - output format: cost and grad written on separated lines
3923 - ad output results in directory "results" (instead of "results_ad")
3924 o pkg/seaice: adding ice salinity HSALT as a prognostic variable
3925 o pkg/seaice: changes for using pkg/seaice with pkg/obcs
3926 o pkg/ecco: allow user defined cost function contributions
3927 o testreport:
3928 Allow to choose (per experiment) the list of tested output variables
3929 and the main variable (used to issue a pass/FAIL ) ;
3930 - for now, done by adding the specific list in file: [exp]/input/tr_checklist
3931 - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
3932 Also modify printing of summary:
3933 a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
3934 b) echo the list of tested variables in the individual summary.txt of
3935 each experiment.
3936 o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
3937 threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
3938 (but still depend on the tile decompostion of the domain).
3939 o pkg/seaice: change a discretization detail to make the B-grid code
3940 "more symmetric". This change is likely to remove all "ridges/leads" that
3941 where quasi-aligned with the grid in B-grid solutions. It may also be
3942 the solution to the stress coupling issues with the B-grid.
3943 o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
3944 remove .cvsignore from input dir. (since testreport no longer run here).
3945 o pkg/thsice:
3946 - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
3947 - fix reshaping of sea-ice just after advection:
3948 melt all the ice only if ice-volume is too small.
3949 - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
3950 prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
3951 and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
3952 o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
3953 tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
3954 o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
3955 forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
3956 (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
3957 and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
3958 of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
3959 -> update output.txt
3960 o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
3961 this affects truncation error: -> update output.txt of exp:
3962 global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
3963 ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
3964
3965 checkpoint59f (2007/08/21)
3966 o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
3967 o pkg/ctrl: ctrl_bound forces parameter corrections to stay in
3968 a bounded range (in forward mode)
3969 o pkg/ecco, ctrl, autodiff and mom_common:
3970 internal parameter controls, completements of implementations
3971 o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
3972 o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
3973 (not seem any difference in testing results).
3974 o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
3975 at face corners.
3976 o pkg/generic_advdiff:
3977 - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
3978 loop range indices for computing vertical advection tendency
3979 and do the calculation in the interior only (no overlap) ;
3980 for now, only implemented for SOM advection (to save CPU time).
3981 - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
3982 o exch2 adjoint
3983 First set of changes:
3984 - add exch2 hand-written adjoint templates
3985 - exch2 hand-written no longer use TAF-flag 'nownew_arg'
3986 This will require cleanup in pkg/autodiff/*.F
3987 (changed routines currently kept separate in verif. code/)
3988 - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
3989 that used to hide exch2 or cubed-sphere specific code
3990 (commented via 'cph-exch2')
3991 o pkg/seaice
3992 - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
3993 o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
3994 output of global_ocean.cs32x15.thsice .
3995
3996 checkpoint59e (2007/07/26)
3997 o exch2: new S/R that only use the cube-tracer (center-position) exchange:
3998 for B-grid vector (not yet tested) and C-grid vector (<- only used
3999 when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
4000 o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
4001 (#ifdef ALLOW_SALT_PLUME)
4002 o gather_2d/scatter_2d: removed halo regions
4003 o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
4004 scheme and the corresponding test case (under front_relax dir). For now,
4005 only available with Skew-flux form and not yet tested in realistic set-up.
4006 adjoint: store directives updated, but gradient checks deteriorated,
4007 so maybe GM/Redi adjoint is now broken.
4008 o seaice adjoint
4009 * add AREA, HEFF, HSNOW as control variable
4010 (should not change lab_sea results)
4011 * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
4012 o pkg/seaice:
4013 * added computation of saltFlux in seaice_growth;
4014 For time being, sea ice salinity is assumed constant
4015 contribution of snow flooding to freshening of sea ice is neglected.
4016 SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
4017 defaults to 0.0 in order to maintain backward compatibility.
4018 Typical values for SEAICE_salinity are 4 to 10 g/kg.
4019 * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
4020 * added SEAICE_availHeatFrac, which specifies fraction of surface level
4021 heat content used to melt or grow ice
4022 * commented out cap of HICE: it helps keep ice thinner
4023 * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
4024 * applied OBCS T/S mask to HEFFM sea ice mask
4025
4026 checkpoint59d (2007/06/21)
4027 o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
4028 for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
4029 (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
4030 o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
4031 and change default value of parameter "GM_Small_Number";
4032 update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
4033 global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,
4034 tutorial_global_oce_biogeo, tutorial_global_oce_latlon
4035 o pkg/ecco: cost function when applying pkg/smooth to controls
4036 o pkg/ctrl: add forcingPrecond run time parameter
4037 o pkg/seaice:
4038 - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
4039 - fix bug in metric terms of u-equation in LSR solver (implicit part),
4040 changes verification/lab_sea
4041 - rearrange implicit part of u-equation in LSR solver to make it easier to
4042 read, understand, and debug. This causes changes at the truncation level.
4043 - fix (serious) bug in the boundary conditions (sign error in the implicit
4044 part) of the LSR solver. Changes all LSR results.
4045 - fixed problem with HSNOW initialization to avoid thick snow when AREA
4046 is initilized with small values - does not change lab_sea results.
4047 - added HsnowFile initialization capability
4048 o pkg/smooth: addition to model/src and pkg/ctrl so allow
4049 initialization of pkg/smooth and application to control vector
4050 o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
4051 o dependencies: pkg/profiles requires pkg/cal
4052 o pkg/profiles:
4053 - added option ALLOW_PROFILES_GENERICGRID
4054 -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
4055 that interpolation information (grid points and coefficients) is provided
4056 within the netcdf input files.
4057 -> sample matlab scripts can be found in MITgcm_contrib/gael
4058 that allow you to prepare netcdf input files.
4059 - also modified: cleaner include statements, cleaner error print statements,
4060 cleaner stops when error, and more tests of the netcdf input files consistency.
4061 o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
4062 o pkg/seaice:
4063 - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
4064 requires a new routine: seaice_diagnostics_fill.F
4065 - make sure that seaice does not move if not forced (pressure replacement
4066 method, Hibler and Ip, 1995), changes results
4067 - and new damping criterion for EVP solver according to Hunke, JCP, 2001
4068 - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
4069 It is turned off by default (=-1.), because it changes the results.
4070 - make it possible to read AREA from a file, too.
4071
4072 checkpoint59c (2007/06/04)
4073 o add S/R and diagnostics for oceanic mixed-layer depth
4074 o move GMRedi call after all vertical mixing schemes (including KPP)
4075 o pkg/thsice:
4076 - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
4077 (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
4078 o pkg/obcs:
4079 - bug fix for balance code
4080 o pkg/seaice:
4081 - allow values of SEAICE_elasticParm > 1
4082 - add new parameter SEAICE_evpTauRelax as an alternative
4083 to SEAICE_elasticParm
4084 - make lsr boundary conditions free slip (by default), changes result
4085 - add code for no slip boundary conditions for lsr
4086 - set minimum of zeta to zero (and not 4e8) (changes results)
4087 - add a cap on AREA after advecting AREA if seaice_growth is not called
4088 o change calculation of Visbeck K:
4089 - no longer depend on tapering scheme; instead, compute slope (limited
4090 by GM_maxSlope). this is equivalent to what was comuted before with
4091 clipping or linear tappering.
4092 - fix vertical averaging (wrong by 1/2 level)
4093 - leave the old version (but will not be maintained) within
4094 #ifdef OLD_VISBECK_CALC / #endif
4095 - update output of exp. ideal_2D_oce
4096 o change error catch in calc_r_star to improve vectorization
4097 o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
4098 add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
4099 o adjoint:
4100 Re-organized adjoint checkpointing according to Matt Mazloff
4101 (but with modifs/completions/cleanups)
4102 Storing is now bundled into large arrays to optimized I/O
4103 (and second step in cleanup of the_main_loop)
4104
4105 checkpoint59b (2007/05/16)
4106 o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
4107 - export/import (between ocean & coupler) fields needed for ocean DIC.
4108 o pkg/seaice:
4109 - get rid of three more exchanges seaice_calc_viscosities (required
4110 different loop boundaries in seaice_lsr and seaice_ocean_stress)
4111 - bug fix in seaice_ocean_stress (update of lab_sea required)
4112 - reduce loop boundaries to necessary minimum also in seaice_evp
4113 - go back to the old way of computing deltaC/Z as the adjoint likes that
4114 better
4115 o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
4116 passive tracer to an Age Tracer) + update output.txt
4117 o pkg/exf:
4118 - implement A-grid / C-grid selection for wind-stress input files.
4119 - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
4120 for now, in exf_bulk_largeyeager04.F only :
4121 - change implementation for case where windspeed + 2. components wind-stress
4122 are read-in. AND use rhoConstFresh to convert evap.
4123 o pkg/seaice:
4124 - use correct EXCH_UV for wind-forcing (on A-grid).
4125 - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
4126 SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
4127 o pkg/exf:
4128 - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
4129 EXF_INTERPOLATION:
4130 - merge global_with_exf/code version of exf_interp_read.F
4131 to the main code ;
4132 - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
4133 reading the file ; Important: This options needs to be defined to recover
4134 previous code.
4135 otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
4136 - no longer loose real*8 precision along the way when using exf_iprec=64.
4137 o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
4138 - change discretisation of evp-solver in order to avoid another exchange
4139 (changes lab_sea) and clean up a little
4140 - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
4141 help the adjoint (this also changes the results slightly)
4142 - add a few "_d 0" where they had been missing in seaice_evp.F
4143 - cleaning up: remove unused seaice_calc_rhs.F
4144 o pkg/exf: some cleaning-up:
4145 - change various "constants" into runtime parameters
4146 - cleaned-up Large&Yeager04 routine which should eventually
4147 replace exf_bulkformulae.F (changed names of S/R and CPP)
4148 and merged various ALLOW_ATM_WIND options
4149 only used with thsice pkg (in thsice_get_exf.F):
4150 - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
4151 which are used when useStabilityFct_overIce=TRUE (= the default)
4152 - change default values of ice & snow emissivity and scale downward LW
4153 by ice & snow emissivity.
4154 o pkg/thsice:
4155 fix few little problems, in thsice_calc_thickn.F:
4156 - growth vertically (and not laterally) if iceFrac == iceMaskMax
4157 - melt only laterally if hIce < hThinIce (as the comments say)
4158 and in thsice_extend.F:
4159 - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
4160 - start to form ice as soon as the minimum ice-volume is reachable.
4161 update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
4162 and cpl_aim+ocn
4163 o pkg/kpp
4164 - move computation of surface related input fields to KPP into a new
4165 subroutine kpp_forcing_surf.F
4166 - remove wrong (within bi,bj loops) EXCH calls.
4167 - little cleaning (add argument myThid in last position, cvs header ...)
4168 - for now, fix conservation problem by exchanging KPPviscAz (may not
4169 be the best fix)
4170 o pkg/seaice
4171 - check for inconsistent evp parameter/cpp-flag combination
4172 - remove leftover errIO flat for obsolete name list error handling
4173 o OpenAD
4174 - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
4175
4176 checkpoint59a (2007/05/01)
4177 o pkg/seaice: some parameter clarifications and a little bit of clean up
4178 o pkg/thsice: rename run-time parameters:
4179 himin -> hIceMin
4180 himin0 -> hThinIce
4181 hihig -> hThickIce
4182 i0 -> i0swFrac
4183 transCoef -> bMeltCoef
4184 frac_energy -> fracMelting
4185 add new parameters: hNewIceMax, fracFreezing, dhSnowLin
4186 with default values (for now) that do not change the results.
4187 remove old version of thsice vars advection in pkg/seaice.
4188 o in FFIELDS.h:
4189 - replace #ifndef ALLOW_EXF by #ifndef EXCLUDE_FFIELDS_LOAD
4190 - make pLoad & sIceLoad always available (but still only used if
4191 ATMOSPHERIC_LOADING is #define).
4192 o pkg/kpp: replaced _KPP_RL with _RL
4193 o bug fixes for vertical diffusivity computations when both KPP and
4194 3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
4195 are no longer updating the vertical diffusivity array
4196 (passed as argument) but are (re-) setting those arrays.
4197 o pkg/seaice: fix bug in evp solver, while doing that
4198 - change (improve?) discretization of stress computations for both
4199 cgrid-lsr and evp solver
4200 - add a new routine to compute strain rates
4201 - the above changes lab_sea results
4202 - add no slip conditions for evp solver (off by default), lsr-version
4203 may follow
4204 - fix exchange for shear at Z-points (does not change lab_sea)
4205 - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
4206 (to force the user to pick a time step since there is not "safe" way
4207 of choosing it)
4208 - add principal stress diagnostics
4209 - rearrange fields for evp a little to avoid having to call a: too many
4210 exchanges and b: exchanges for stress trensor components which we do
4211 not have.
4212 - modify Hibler+Bryan (1987) stress coupling so that it reuses information
4213 of evp, complete rewrite for lsr case (latter is does not yet work
4214 in all cases)
4215 o pkg/kpp: add code to have mixing in shelf ice caverns
4216 - add myThid to all kpp routines (long overdue)
4217
4218 checkpoint59 (2007/04/19)
4219 o pkg/exf:
4220 - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
4221 ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
4222 - move exf header files from lower_case.h to UPPER_CASE.h ;
4223 add missing cvs Header & Name
4224 - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
4225 - add namelist param. selectStressGridPosition, exf_monFreq
4226 - retire many _CLIM routines, and remove data.exf_clim
4227 + params moved to data.exf
4228 + climsst, climsss now handled by exf_set_gen, i.e.
4229 climss?period=0 refers to constant field,
4230 climss?period=-12 to monthly forcing
4231 - split up namelists in data.exf
4232 o pkg/seaice:
4233 - remove seaice_exch and seaice_exch_uv
4234 - remove superfluous exchange of theta
4235 - add myThid to seaice_budget_ocean/ice
4236 - add new interface for atmospheric wind forcing (C-grid only)
4237 + new routine
4238 + two new field (taux, tauy for stress over ice)
4239 + removed one global field (DAIRN) for C-grid case only
4240 o pkg/thsise
4241 - 2nd set of modifs for thsice adjoint in conjunction with exf
4242 o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
4243
4244 checkpoint58y_post (2007/04/15)
4245 o Added capability for latitudinal dependence of Bryan and Lewis, 1979
4246 vertical diffusivity, similar to that in MOM4; turned on using
4247 #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
4248 diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
4249 o Added capability for 3D specification of background vertical diffusion
4250 coefficient. This is done by (i) #define ALLOW_3D_DIFFKR
4251 in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
4252 "data" file that contains the 3D vertical diffusivity coefficients.
4253 o ice dynamics (pkg/seaice) with thsice thermodynamics:
4254 - add code within pkg thsice to advect & diffuse sea-ice fields
4255 similar to (and will replace) what has been added in seaice_advdiff.F,
4256 but: - conserving Mass, Heat & Salt.
4257 - better when using non-linear advection scheme (not yet fully tested)
4258 - can also be used in atmospheric set-up (for now, only the diffusion).
4259
4260 checkpoint58x_post (2007/04/04)
4261 o IO option for global-file compact format:
4262 - add options when generating topology (utils/exch2/matlab-topology-generator)
4263 - add I/O capability (pkg/mdsio).
4264 - adapt utils/matlab/rdmds.m to read this format.
4265 for now long-line format not yet supported by pkg/mdsio (& exch2).
4266 o shelfice: add a few diagnostics
4267
4268 checkpoint58w_post (2007/03/13)
4269 o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
4270 rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
4271 (and replace horiVertRatio in NH code).
4272 Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
4273 and tutorial_plume_on_slope (sensitive to truncation)
4274 o seaice: if ALLOW_ATM_WIND is undefined use wind stress
4275 directly to drive seaice model (C-grid only)
4276 o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
4277 - reintroduce computation of wind from stress,
4278 - compute tau (in exf_bulkformulae.F) from windstress averaged to
4279 mass points to avoid tau = 0
4280 - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
4281 o rdmnc.m: make it work with "global" files created with gluemnc
4282 o rdmnc.m : some improvements in dealing with singleton dimension
4283 (tested on all testreport mnc output files).
4284 o genmake2: disable pkg/profiles if netcdf test fails.
4285 o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
4286 o move call to cal_readparms up to make calendar parameters/variable available
4287 to all packages
4288
4289 checkpoint58v_post (2007/02/08)
4290 o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
4291 useDynP_inEos_Zc tested.
4292 o pkg/exf: changes to properly interpolate/mask/scale initial fields
4293 o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
4294 and portions thereof. See read_cs.txt for description and examples.
4295 o utils/matlab/cs_grid/bk_line: to compute transport through passages,
4296 add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
4297 following the great-circle arc between those 2 points.
4298 o trap un-initialized variable with pathscale compiler on weddell.mit.edu
4299 (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
4300 o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
4301 - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
4302 - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
4303 - still needs work (not working with some options ; efficiency to improve)
4304 and serious testing.
4305 - use this scheme for temperature & salinity in 2 advection test exp.:
4306 advect_xy & advect_xz, respectively.
4307
4308 checkpoint58u_post (2007/01/12)
4309 o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
4310 o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
4311 o testreport: add option "-skipdir" to skip some test.
4312 o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
4313 momentum calculation.
4314 o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
4315 o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
4316 remove checkpoint.F and the_correction_step.F (no longer used);
4317 do the k loop inside CYCLE_TRACER (supposed to be more efficient).
4318 o add option (linFSConserveTr) to correct for tracer source/sink due to
4319 Linear Free surface
4320 o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
4321 o pkg/thsice: fix reading mnc-pickups
4322
4323 checkpoint58t_post (2006/12/30)
4324 o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
4325 o pkg/mdsio:
4326 - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
4327 move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
4328 mdsio_write_field.F (S/R MDS_WRITE_FIELD);
4329 - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
4330 - collect old S/R in one file: mdsio_rw_field.F (now just a call to
4331 either MDS_READ_FIELD or MDS_WRITE_FIELD )
4332 - new S/R (to replace MDSWRITEMETA), which allows to write more
4333 informations (variable names, time ...) to meta files.
4334 - modify rdmds.m to give back the meta file content.
4335 o pkg/diagnostics: change vertical interpolation to be safer, and more
4336 flexible (define p-levels to interpolate to in data.diagnostics);
4337 add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
4338 diagnostic pointer.
4339 o pkg/seaice: more cleaning up of seaice_growth, added many comments
4340 o pkg/exf: put runoff0 and runoff1 into the appropriate common block
4341 o fix multi-category seaice:
4342 - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
4343 SEAICE_MULTICATEGORY
4344 - fix short wave heat flux
4345 o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
4346 and allow to use EVP solver. Change forward lab_sea: test both EVP
4347 solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
4348 o Initial check-in of lab_sea adjoint
4349 (very similar to natl_box_adjoint/code_seaice)
4350 * used C-grid and EVP solver
4351 * used KPP, GM/Redi
4352 * uses inAdExact=.TRUE.
4353 * gradient checks fail for both ADM and TLM
4354 due to sensitive snow melt code in seaice_grwoth (look for "JZ")
4355 f.d. gradients actually seem more problematic than ADM, TLM gradients;
4356 issue is related to forward mismatch between g77 an ifort
4357 o pkg/seaice: overhaul of thermodynamics
4358 - growth.F and groatb.F are replaced by new routine seaice_growth.F
4359 - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
4360 - move a few global fields out of SEAICE.h into seaice_growth.F and
4361 make them 2D (FICE/QNETO/ ...)
4362 - remove FO (it is the same as QNETO)
4363 - introduce a few local fields to avoid modifying external fields such
4364 as atemp, etc.
4365
4366 checkpoint58s_post (2006/12/11)
4367 o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
4368 changed exf_set_gen.F so that
4369 genperiod=0 means input file is one time-constant field and
4370 genperiod=-12 means input file contains 12 monthly means
4371 o CG2D: use pre-computed solver main-diagonal (stored in common block);
4372 this affects truncation error ; generate new output file for exp. which
4373 fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
4374 global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
4375 ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
4376 MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
4377 tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
4378 vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
4379 o start implementation of deep-atmosphere and anelastic formulation
4380 o verification: remove 2nd copy of input files and use script "prepare_run"
4381 to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
4382 o mom_common/vecinv/fluxform: fix a few initialisation isssues
4383 o profiles: fix for multithreaded case
4384
4385 o diagnostics: rename few diags:
4386 s/'PRESSURE'/'RCENTER '/g
4387 s/'TICE '/'oceFreez'/g
4388 s/'TAUX '/'oceTAUX '/g
4389 s/'TAUY '/'oceTAUY '/g
4390 s/'SWFLUX '/'oceQsw '/g
4391 s/DIFx/DFxE/g
4392 s/DIFy/DFyE/g
4393 and add few ocean-forcing diagnostics:
4394 atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
4395 o modifications to pkg/seaice/growth.F and budget.F, which change results of
4396 lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
4397 as actual snow thickness. It now refers everywhere to effective snow
4398 thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
4399
4400 checkpoint58r_post (2006/11/17)
4401 o modifications to pkg/seaice/growth.F, which change results of
4402 lab_sea experiment: fixes pertain to melting snow over open water, to
4403 masking EVAP under sea ice, and to using the correct AREA variable for
4404 computations of EVAP, PRECIP, HSNOW, and GHEFF
4405 o add ability to read bathy, salt, and theta using MNC (off by def)
4406 o add flooding algorithm and advection of HSNOW for pkg/seaice;
4407 both are turned off by default and do no change any results
4408 o seaice advection with pkg/thsice: a step toward the use of non-linear
4409 advection scheme, but #ifdef or commented out for now (requires more EXCH).
4410 o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
4411 (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
4412 in natl_box (affects results @ truncation level: update output.txt)
4413 o multi-threading and IO:
4414 - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
4415 - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
4416 (needed to work with SingleCpuIO): tested in all verif. exp.
4417 o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
4418 affects the results (but none of the verification test uses this scheme).
4419 o Adding some pkg/diagnostics capability to pkg/seaice
4420 (will certainly be subject to changes)
4421 o ctrl: adding new control variables:
4422 lwflux, lwdown, evap, snowprecip, apressure, runoff
4423
4424 checkpoint58q_post (2006/10/20)
4425 o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE. Speeds up
4426 1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
4427 high_res_cube configuration by 4% on Columbia.
4428 o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
4429 add (in global_with_exf/code) a version of EXF_INTERP_READ without
4430 dynamical allocation (seems to work in multi-threaded).
4431 o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
4432 single CPU io) so that TAF does not have to see EESUPPORT.h
4433 o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
4434
4435 checkpoint58p_post (2006/09/08)
4436 o obcs: stop if obcs is used with useCDscheme = .true.
4437 o shelfice:
4438 - fix a sign error so that no slip at shelfice interface works
4439 - remove stop for combination non-hydrostatic code and shelfice. That does
4440 not mean, that the results are correct, but at least they are numerically
4441 stable
4442 o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
4443 o added adjoint exch routined for all exch*3d* routines
4444 and updated flow directives
4445
4446 checkpoint58o_post (2006/08/28)
4447 o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
4448 remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
4449 o change controling S/R for writing pickup file (new S/R do_write_pickup)
4450 and clean-up reading/writing of pickup files.
4451 o fix local version of read/write pickup (NH part) in rotating_tank/code
4452 o simplify EXCH interface:
4453 - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
4454 - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
4455 o added the regrid package
4456 o shelfice:
4457 - add a simple boundary layer scheme to reduce noise
4458 - fix the indexing in shelfice_u/v_drag so that there will be actually drag
4459
4460 checkpoint58n_post (2006/08/14)
4461 o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
4462 local variable (not in common block).
4463 o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
4464 - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
4465 - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
4466 to work with SingleCpuIO.
4467 o add "_d 0" to real constant of pkg/cfc subroutines ;
4468 update exp. cfc_exemple & tutorial_cfc_offline output files.
4469 o multi-threading and IO:
4470 - all threads call READ_FLD S/R (needed if using SingleCpuIO):
4471 (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
4472 - barrier before and after reading.
4473 - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
4474 - avoid using MDS_WRITELOCAL for LAND pkg output.
4475 - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
4476 common-block variables ; Allows multi-threading with master-thread IO.
4477 o change default MAX_NO_THREADS from 32 to 4 ;
4478 and stop cleanly when MAX_NO_THREADS is too small.
4479 o add S/R BAR_CHECK to check multi-threaded barrier synchronization
4480
4481 checkpoint58m_post (2006/07/17)
4482 o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
4483 and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
4484 o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
4485 keep global_ocean.90x40x15 (for AD testing) with former secondary test
4486 (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
4487 o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
4488 add MITgcm_tutorials (= code + all the tutorials)
4489 o ecco, option to compute cost for total ssh (mean+anom)
4490 o consistent with addition of ptracer and ssh in pkg/profiles
4491 o profiles: adding ptracer and ssh
4492 o testreport: change multi-test output-file name
4493 (from output.txt.{name} to output.{name}.txt)
4494 o profiles: now ok for mutli-tiles case
4495 o seaice: add 4 parameters for different advection schemes for area,
4496 (effective) seaice thickness, enthalphy, and snow height. Their default
4497 is the standard parameter SEAICEadvScheme
4498 o calc_gw:
4499 - add cosFacU in zonal viscous flux (harmonic.visc.).
4500 - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
4501 of tutorial_plume_on_slope.
4502 o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
4503 o calc_gw: true flux-form, account for horizontal grid spacing.
4504 update rotating_tank results, but not plume_on_slope (affected at
4505 truncation level, 11 digits).
4506
4507 checkpoint58l_post (2006/07/12)
4508 o calc_gw:
4509 - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
4510 - remove side-drag for now (need to fix it); update plume_on_slope results.
4511 - fix for partial-cell & non-uniform dz; update plume_on_slope results.
4512 o commit code to make SST/SSS weights spatially variable
4513 (based on either variable in-situ or variable initial T/S weights)
4514 o pkg/ecco:
4515 * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
4516 now based on horizontally varying weights wthetaLev, wsaltLev
4517 * cost_averagesflags now returns year indices in addition to day, month
4518 * sflux balance is performed on annual basis
4519 (sflxumm, sfluxmm2, bal_sfluxmm)
4520 * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
4521 including separate counting and multipliers
4522 o pkg/rbcs
4523 * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
4524
4525 checkpoint58k_post (2006/07/06)
4526 o testreport:
4527 - always build in dir. "build" (if not there, mkdir build instead of building
4528 & running in input)
4529 - run in dir run (if it exists), in build otherwise.
4530 - call prepare_run (if input/prepare_run exists)
4531 - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
4532 o pkg/exf modifications to interpolation and rotation routines for more
4533 reasonable treatment of North Pole singularity: for tracers North Pole
4534 value is set to northernmost zonal-mean value, for zonal velocity it is
4535 set to zero, and for meridional velocity it is set to northernmost value.
4536 o pkg/exf/exf_check_range.F
4537 - add tile index to diagnostics and move stop statement to the very
4538 end of the routine.
4539 o pkg/diagnostics: (diagnostics_main_init.F)
4540 define title of isomorphic variables according to the current config.
4541 o pkg/thsice with pkg/seaice dynamics:
4542 - fix domain of computation (interior only, required for exf) and do exchanges
4543 - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
4544 o towards a standard way of dealing with multi-threading in MONITOR
4545 and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
4546 o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
4547 to W momentum equation in nonhydrostatic and quasihydrostatic runs.
4548 o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
4549 o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
4550 o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
4551 (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
4552 o tracer advection:
4553 - clean-up and simplify calc_common_factors.F
4554 - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
4555 advection subroutine (but still not used within DST advection S/R)
4556 o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
4557
4558 checkpoint58j_post (2006/06/15)
4559 o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
4560 from file (collects calls previously in FORWARD_STEP)
4561 o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
4562 o adjoint store dir. adjusted accordingly
4563 o genmake2
4564 replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
4565
4566 checkpoint58i_post (2006/06/14)
4567 o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
4568 on wind stress (SEAICEstressFactor defaults to 1.)
4569 o Total number of Timers is finite (<=40): comment out 2 non-essential one
4570 in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
4571 o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
4572 on CS-grid: no longer loosing mass.
4573 o exf & curvilinear-grid: no longer modify longitude xC & xG.
4574 o pkg/ggl90: fix sloppy output and fix a bug
4575 o pkg/seaice: added SEAICEuseEVPpickup parameter
4576 - Set to false in order to start EVP solver with
4577 non-EVP pickup files when using SEAICEuseEVP
4578 - fix sign error in diffusion in seaice_calc_rhs
4579
4580 checkpoint58h_post (2006/06/07)
4581 * Modifications for bottom topography control
4582 o replace hFacC by _hFacC at various places
4583 o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
4584 o add non-self-adjoint cg2d_nsa
4585 o update autodiff support routines
4586 o re-initialise hfac after ctrl_depth_ini
4587 o works for 5x5 box, doesnt work for global_ocean.90x40x15
4588 * Adding verification for 5x5 box (4-layer) bottom topography control
4589
4590 checkpoint58g_post (2006/06/07)
4591 o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
4592 used for mean seasonal cycle, mean diurnal cycle); add an example
4593 in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
4594 o pkg/ggl90:
4595 - add parameter (minimum surface kinetic energy)
4596 - fix bug (avoiding division by zero)
4597 o couple pkg/thsice to pkg/seaice:
4598 - modify advection in seaice to accomodate new scalar fields to be advected
4599 - only muliDimAdection scheme work with seaice/thsice
4600 - mapping of thsice-variables to seaice-variables, back and forth
4601 - does not break the verification experiments, but does not give the
4602 desired results either
4603 o pkg/seaice
4604 - make (default) second order advection a bit less confusing?
4605
4606 checkpoint58f_post (2006/06/05)
4607 o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
4608 to pkg/seaice):
4609 - new routines thsice_map_exf and thsice_get_exf provide the interface
4610 - add an additional formal parameter to thsice_solve4temp
4611 o pkg/exf:
4612 - add new fields wspeed, snowprecip (to be able to couple to thsice)
4613 - correct Stefan-Boltzmann constant
4614 - new parameter for longwave surface emittance
4615 - separate some stuff from exf_bulkformulae into new routines
4616 exf_radiation, exf_wind
4617 - add new parameters and constants: longwave emissivity for ocean, ice
4618 and snow, evaporation parameters over ice
4619 - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
4620 either wind from stress or stress from wind
4621 o pkg/thSIce:
4622 - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
4623 - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
4624 and THSICE_CALC_THICKN
4625 - for now, call to THSICE_GET_BULKF remains inside i,j loops.
4626 - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
4627 to make debugging easier.
4628 - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
4629 o pkg/bulk_force:
4630 - clean-up comments and parameters ;
4631 - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
4632 o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
4633 generate new output for test-experiment: aim.5l_cs.thSI
4634 o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
4635 testreport accordingly
4636
4637 checkpoint58e_post (2006/05/17)
4638 o SEAICE_CGRID adjoint done
4639 o R_STAR adjoint implemented.
4640 * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
4641 * need to sort out init. of h0facc, etc.
4642 o Make pkg/profile fully independent of ecco,cost, etc. stuff
4643 to be able to use it in pure forward.
4644
4645 checkpoint58d_post (2006/04/21)
4646 o upgrade simple test-experiment to tutorial example:
4647 step.1: duplicate the experiment and (step.2) will remove the old copy.
4648 tutorial_barotropic_gyre <- copy of exp0 (R1:barotropic_gyre_in_a_box)
4649 tutorial_baroclinic_gyre <- copy of exp1 (R1:baroclinic_gyre_on_a_sphere)
4650 tutorial_global_oce_latlon <- empty for now (R1:global_ocean_circulation)
4651 tutorial_global_oce_biogeo <- copy of dic_example
4652 tutorial_deep_convection <- almost like exp5 (R1:nonhydrostatic_deep_convection)
4653 tutorial_plume_on_slope <- copy of plume_on_slope
4654 tutorial_tracer_adjsens <- copy of carbon (R1:tracer_adjoint_sensitivity)
4655 tutorial_global_oce_optim <- empty for now (David ?)
4656 tutorial_global_oce_in_p <- copy of global_ocean_pressure
4657 some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
4658 o correct a sign problem in cost_scat.F
4659 o obcs and ptracers: fix boundary conditions for advections schemes
4660 with larger stencil
4661 o thsice adjoint: start
4662 o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
4663 completeness
4664 o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
4665 and COSINEMETH_III, add comments in default CPP_OPTIONS.h
4666 o ptracers adjoint:
4667 * avoid extensive recomputatations
4668 * fix missing re-init. of gptr (missed by TAF)
4669 o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
4670 me to turn off the excessive output to STDOUT that this package produces
4671 o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
4672 and add those terms in Vector-Invariant formulation.
4673 o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
4674 if the control period (xx_hfluxperiod etc) is 0
4675 o in profiles pkg, clean routines and fix details
4676 o in ecco pkg, reading ssh data:
4677 fix problem in case the model does not start at iter0=0
4678 o fix mnc-pickup/restart for ptracers
4679 o new package prifiles:
4680 code to compute profile-based cost by Gael Forget
4681 (modifs in ecco, ctrl, autodiff)
4682 o Benign bug fix in initialization (spotted by M. Mazloff) of
4683 ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
4684
4685 checkpoint58c_post (2006/03/23)
4686 o adjoint: finish NLFS adjoint and provide reference output in
4687 verification/global_ocean.90x40x15/results_ad_nlfs
4688 o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
4689 documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
4690 SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
4691 with SEAICE_CGRID defined.
4692 o move calendarDumps from "data" to "data.cal" and clean-up the code
4693 with a simple call to pkg/cal S/R: CAL_TIME2WRITE
4694 o add useEXF & useCAL flags (for now, set in hard-coded way)
4695 o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
4696 (were missing in NH mode, and wrong in quasihydrostatic mode).
4697 waiting for Chris updated version of calc_gw to add those CALLs.
4698 o fix bug in quasihydrostatic S/R ;
4699 add a test for this option: global_ocean.90x40x15.qshyd
4700 o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
4701 (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
4702 o add on/off flag useOffLine for package OFFLINE
4703 o seaice:
4704 - modify advection so that it works also on the C-grid
4705 - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
4706 problem in multi-tile runs with C-grid
4707 - add flags for clipping ice velocities and/or masking solver forcing
4708 - fix drag (ocean on ice) formulation and a bug that caused noise in the
4709 C-grid solver
4710 - added a few comments to seaice_diffusion.F
4711 - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
4712 are now exclusive)
4713 - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
4714 required re-ordering the code a little:
4715 + make DAIRN global variable (defined in SEAICE)
4716 + move computation of the viscosities eta and zeta into a new separate
4717 routine (because I need to recompute them in seaice_ocean_stress.F)
4718
4719 checkpoint58b_post (2006/03/13)
4720 o AIM+thSIce: fix sign of Short-Wave through the Ice ;
4721 update output.txt of exp. aim.5l_cs.thSI
4722 o various mnc cleanups and improvements:
4723 + shrink lookup tables by factor of ~4
4724 + better error reporting when running out of lookup space
4725 + able to handle longer path/file names (up to 500 chars)
4726 o adjoint:
4727 - Another overhaul of store dirs. for NLFS to eliminate "hidden" recomputations.
4728 - TBD: "hidden" mom_vecinv recomp. in dynamics
4729 o change forcing_In_AB to affects both T,S forcing and Momentum forcing
4730 (allow to differentiate between forcing components using new integer flags:
4731 momForcingOutAB=1/0 & tracForcingOutAB=1/0)
4732 and add new flag to put Dissipation tendency out of Adams-Bashforth.
4733 o ecco
4734 - enable trend removal from SSH anomaly obs.
4735 o adjoint
4736 - a fix for PmEpR when #undef EXACT_CONSERV
4737 - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
4738 - try to fix "hidden" recomp. in forward_step for NLFS
4739 (NLFS seems broken sometimes after I checked it in)
4740 o seaice:
4741 - add c-grid version of the dynamic solver:
4742 + three new routines that are the c-grid substitute lsr, dynsolver
4743 and ostres
4744 + put a few fields that were local to dynsolver into global common
4745 blocks, so that I can move the computation of stresses etc into
4746 seaice_lsr (saves coding but may break the adjoint).
4747 - replace more hardwired parameters by runtime parameters
4748 - add ice masks that mask the rhs of the implicit solvers where there
4749 is no ice (commented out in seaice_dynsolver, because i am not sure
4750 if this works properly), eventually this should replace the clipping
4751 of ice velocities in seaice_dynsolver to +/-40cm/s.
4752 o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
4753 include it only where its needed
4754 o move balancing of fluxes before the call of external_forcing_surf
4755 o seaice:
4756 - correct units of turning angles (now they are really in degrees)
4757 - move computation of GWATX/Y out of main routine into dynsolver
4758 - initialize GWATX/Y in seaice_init
4759 o Apply mask on Fresh-Water flux (needed for SSH forcing).
4760 update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
4761 o seaice: add runtime flags for turning angles (default to zero)
4762 o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
4763 and trend from exf forcing and ctrl control adjustments
4764 o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
4765 (since checkpoint57x_post)
4766 o change the default rotation period to 86164.s = the Earth rotation
4767 o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
4768 and based on a reference stratification. Tested within hs94.cs-32x32x5.
4769 o seaice advection: add code for choosing between the default (2nd order
4770 central differences) and multiDim advection schemes provided by
4771 pkg/generic_advdiff
4772 o seaice:
4773 - removed all references to SEAICE_GRID.h fields from
4774 dynsolver, advect, diffus, lsr, without changing the results of lab_sea
4775 (cubed-sphere configuration will change a little)
4776 - grid computations in seaice_init are obsolete now.
4777 - cleaned up code a little so that is easier to read (hopefully).
4778 - added new (better?) discretizations of default advection and diffusion
4779 (turn on with SEAICEuseFluxForm)
4780 - replace 1 in 3d global fields by kSurface in growth.F
4781
4782 checkpoint58a_post (2006/02/13)
4783 o seaice:
4784 - bug fix in advect.F
4785 o shelfice:
4786 - separate shelfice load anomaly from pload (breaks with time
4787 dependent forcing), => introduce constant field shelficeLoadAnomaly.
4788 Its default is 0., but it may be computed more cleverly from (unknown)
4789 t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
4790 done offline. A good approximation of the pressure load anomaly is
4791 necessary to avoid large initial adjustment processes underneath
4792 deep-reaching shelfice.
4793 - small fix in ISOMIP shelfice_thermodynamics
4794 - add more sophisticated thermodynamics of Hellmer (1989), this is
4795 now the default
4796 - give a few constants more intuitive names
4797 o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
4798 if bulk formulae are used in long integration (especially EmPmR). Turn
4799 on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
4800 if balancePrintMean, the imbalance that is substracted is printed to
4801 STDOUT.
4802 o fix bug (typo) in obcs_apply_eta.F
4803 o add a new package shelfice which enables us to model the circulation
4804 underneath shelf-ice with draughts of hundreds of meters.
4805 - works
4806 - to do: + include improved thermodynamics
4807 + check whether kSurfC (from model/inc/SURFACE.h) can be used
4808 instead of new field kTopC
4809 + can we use topoFile, Ro_surf and existing code in ini_depth.F
4810 instead of new field R_shelfIce and new code in ini_depth.F
4811 and ini_mask_etc.F?
4812 + adjust vertical mixing schemes?
4813 o seaice pkg:
4814 - add a cpp-flag to include a simple formula for a salinity dependent
4815 freezing point of sea water at the surface
4816 - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
4817 meridional stresses are now different (and hopefully correct)
4818 o AIM pkg: change threshold on large-scale condensation to conserve Heat.
4819 update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
4820 and change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
4821 o pkg/diagnostics: add options and parameters for regional-statistics
4822 diagnostics ; define regions by reading a region-mask from a file
4823 (might add other options later)
4824 o pkg/bulk_force:
4825 - add option and parameters to use AIM surface-flux formulae.
4826 - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
4827 others forcing fields (defined in PARM05, parameter file "data") are loaded
4828 from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
4829 - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
4830 - use the right EXCH call for uwind,vwind (to work on CS-grid).
4831 - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
4832 and parameters (note: calcWindStress replaces .NOT.readwindstress).
4833 - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
4834
4835 checkpoint58 (2006/01/12)
4836 o add "--embed-source" option to genmake2 which, when the supporting
4837 tools can be compiled (as determined by genmake2) will turn on the
4838 embed_files package which then embeds the entire MITgcm source code
4839 (*.[fFhc] + Makefile) used for the build within the executable
4840 - requested by CNH but off by default
4841 - adds a paltry <9MB to the mitgcmuv executable in most cases
4842 - only writes the output when useEMBEDSRC in eedata is true
4843 o clean up 3-dim. relaxation codes:
4844 * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
4845 * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
4846 * Thanks to Tom Haine for testing!
4847
4848 checkpoint57z_post (2005/12/31)
4849 o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
4850 affects output (@ truncation level) of exp. plume_on_slope ; updated.
4851 o fix the pickup behavior for obcs in combination with ptracers
4852 o fix a bug in ptracers_external_fields_load
4853 o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
4854 affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
4855 o transfered surface NH pressure to eta field (if exactConserv).
4856 o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
4857 and update lab_sea output.txt file.
4858 o completing 3-dim. relaxation code: additional term
4859 1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
4860 in S/R EXTERNAL_FORCING_T (file external_forcing.F)
4861 * At compile time, in "EXF_OPTIONS.h" set
4862 #define ALLOW_CLIMTEMP_RELAXATION
4863 #define ALLOW_CLIMSALT_RELAXATION
4864 * At runtime in "data", under &PARM03 set (e.g., units in seconds)
4865 tauThetaClimRelax3Dim = 15552000.0,
4866 tauSaltClimRelax3Dim = 15552000.0,
4867 * 3 cases:
4868 1) Use a constant-in-time 3-dim. field
4869 2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
4870 3) Real-time relax. to time-evolving prescribed field
4871 o Adding Laplacian-type smoothness constraint on
4872 initial and boundary (forcing) controls (ic, bc)
4873 * enable at compile-time via
4874 ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
4875 * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
4876 * Absolute scale somewhat unclear so far
4877 * no area weighting was included since no other cost term does so far
4878
4879 checkpoint57y_post (2005/12/08)
4880 First step for a NLFS adjoint
4881 o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
4882 o new init. routines for calc_r_star, calc_surf_dr
4883 o still need to deal with ini_masks_etc
4884 o testreport seemed happy
4885 checkpoint57y_pre (2005/12/08)
4886
4887 o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
4888 o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
4889 o add new offset feature to offline pkg (plus minor cleanup)
4890 o cfc fixes for final year of integration
4891 o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
4892 be in GCHEM_OPTIONS).
4893
4894 checkpoint57x_post (2005/12/04)
4895 o fix testreport Pb in multiple test experiment.
4896 o cleanup our namelist syntax in verification:
4897 - make it more F95 standards compliant (some work still needed)
4898 - allows the vast majority of our tests to work with gfortran
4899 o Non-Hydrostatic:
4900 - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
4901 - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
4902 o Allow to apply AB on T,S rather than on AB(gT,gS):
4903 - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
4904 - use the same arrays (gtNm,gsNm) to hold tracer field at previous
4905 time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
4906 - need a "clever" read_pickup to restart from the other AB formulation
4907 o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
4908 o remove some unused variables (reduces number of compiler warnings)
4909 o adjoint
4910 * Disable useVariableViscosity for adjoint for time being
4911 (there are a number of extensive recomputations)
4912 * Initialize certain variables needed for adjoint
4913
4914 checkpoint57w_post (2005/11/03)
4915 o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
4916 fix the singleCpuIO RS version of MDSWRITEFIELD
4917 and add a WARNING if using globalFiles=T with multi-processors.
4918 o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
4919 using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
4920 o tracer advection scheme:
4921 add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
4922 those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
4923 was not very convenient).
4924 add implicit version for DST-3 & DST3_Flux_Limit vertical advection;
4925 (further tests needed for the implicit DST & Flux-Limiter schemes).
4926 o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
4927 and sRef for convenience, handy, when you want to initialize
4928 ptracers in a large domain with a constant non-zero value. Also,
4929 untangle ptracers_init.F a little.
4930
4931 checkpoint57v_post (2005/10/13)
4932 o change dome exp. to use variable viscosity in side-drag terms.
4933 o remove all the files from the cfc_offline test since they are now
4934 incorporated into tutorial_cfc_offline which has been producing
4935 identical results for a few days of testing
4936 o add new parameter: sideDragFactor to enable half-slip-side BC
4937 and change side-drag S/R to use viscosity from mom_calc_visc
4938 (can switch back by setting sideDragFactor=0.); affects results at
4939 truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
4940 global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
4941 o vorticity & strain are now computed without masking, to account for
4942 no-slip-side BC in variable viscosity calculation ; mask is applied
4943 anyway later on, before computing advection/coriolis terms.
4944 o modify exp4 to test new obcs support for reading from external files
4945 and for passive tracers
4946 o fix behavior of ptracers_monitor when monitor output is written to a
4947 netcdf-file; still not independent of monitor.F (writes in the same
4948 file).
4949 o change default value of tRef (put a uniform, meaningful value for ocean
4950 & atmos) and initialize sRef (was missing, as Martin mentioned).
4951 o Redefine viscC?Leith*. Change the coefficients of Leith viscosity
4952 to be proportional to enstrophy dissipation length. Thus,
4953 viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
4954 This is now consistent with Smagorinsky and with the manual.
4955
4956 checkpoint57u_post
4957 o OBCS and PTRACERS: add open boundary support for passive tracers
4958 - either use homogenous (pseudo) v.Neumann conditions or prescribe
4959 OB-values from file; this is not different from the way theta and salinity
4960 are treated
4961 - however, Orlanski-radiation conditions are not supported, and the model
4962 will stop if you use pTracers and Orlanski at the same time.
4963 - beefed up the rountine obcs_external_fields_load: now only those open
4964 boundary values are overwritten with values from files for which there
4965 are really files, otherwise the OB-fields remain untouched. This makes
4966 it possible to use different OBs at different ends of the domain (as
4967 with EXF)
4968 o reduce number of exch calls in shap_filt (s2).
4969 o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
4970 truncation level) 4/5 MLAdjust test results (11&12 digits match).
4971
4972 checkpoint57t_post (2005/10/03)
4973 o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
4974 o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
4975 same truncation, independent of the face number: affects affects several
4976 test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
4977 o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
4978 note that biharmonic viscosity + no-slip was not tested in any experiment.
4979 o fix bug in non-linear free-surf side-drag ; generate new output for
4980 global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
4981 o make mnc honor the writeBinaryPrec flag for most kinds of output
4982 o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
4983 o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
4984 error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
4985 o add brackets in multi-terms sum to get same truncation, independent of
4986 the face number (manage to get exactly same value of gU,gV at the cs-edge)
4987 affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
4988 o Clean, new version of mom_calc_visc. Adds a new feature, viscAhRemax
4989 and viscA4Remax, which allow one to limit the minimum viscosity by specifying
4990 a maximum grid-scale Reynolds number. Also, changes all length calculations
4991 in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
4992 Suggested values of viscosity parameters found in mom_calc_visc.
4993 Many new viscosity diagnostics available.
4994
4995 checkpoint57s_post (2005/09/20)
4996 o Add clearing-house for viscosity calculations, mom_calc_visc and
4997 correct numerous bugs in LeithD and Smagorinsky discretizations.
4998 mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
4999 used simultaneously, and to be used in mom_vecinv and mom_fluxform.
5000 Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
5001 and with Strain-Tension viscous term calculation (mom_hdissip.F).
5002 The Strain-Tension form is now called with useStrainTensonVisc=.true.
5003 ViscAhStrain and viscAhTension are now retired.
5004 o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
5005 o In response to JMC's bug report, genmake2 now ignores any soft-links
5006 that it finds in the *current* directory when searching for files.
5007 Soft-links found in any other source directories will still work as
5008 they did before.
5009 o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
5010 a C routine to unlimit the stack size
5011 o mnc-ify pkg/aim snapshot vars
5012 o mnc-ify pkg/land as requested by Daniel
5013 o various changes to mnc including:
5014 - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
5015 - output can now be grouped so that all files within a group
5016 change the ITER portion of their names in lock-step together
5017 - can now read ("global") PER-FACE (in addition to PER-TILE) files
5018 and works with both EXCH1 and EXCH2 (but needs more testing)
5019 - writing works for all verification test cases w/ g77 on Linux
5020
5021 checkpoint57r_post (2005/09/07)
5022 o make MNC variable initialization happen earlier
5023 o add diagnostics for (almost) each term of the momentum Eq.
5024 o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
5025 o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
5026 o remove MINIMAL_TAVE_OUTPUT option ;
5027 add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
5028 o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
5029 allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
5030 o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
5031 o add time-dependent SST, SSS control
5032 o cost terms in ecco/ modularized (new cost_generic.F)
5033 o cost_averages routines are modularized (new cost_averagesgeneric.F)
5034 o new infrastructure for seaice model vs. obs misfits in seaice/
5035 * driver from the_main_loop.F is seaice_cost_driver.F
5036 * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
5037 * gradient check in Exp. 6a of natl_box_adjoint/
5038 o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
5039 (see README file)
5040
5041 checkpoint57q_post (2005/08/19)
5042 o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
5043 o fix annoying months-old bug in mnc/mdsio output for seaice pkg
5044 - bug was reported by Jean-Michel and Ian Fenty
5045 o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
5046 update exp. cpl_aim+ocn output.
5047 o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
5048 Needed for high-res. runs with large global files
5049 to be able to limit tapelev size
5050 o Changed some tests for adjoint:
5051 * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
5052 * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
5053 * global_ocean.90x40x15/ back to default 3-level checkpointing
5054 o Modifications to enable scripted COMMON to MODULE conversion
5055 * verification/OpenAD/code/ has necessary scripts and description;
5056 * converts, compiles and runs successfully;
5057
5058 checkpoint57p_post (2005/08/01)
5059 o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
5060 o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
5061 (already the case for some pkgs, including recent MNC_init, e.g. thsice)
5062 o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
5063 o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
5064 (was already the case for dissipation with mom_vecinv,
5065 and also the case for grad.PhiHyd when staggered-timeStep)
5066 This will allow to put dissipation out-off the AB time-stepping.
5067 Unfortunately, affects truncation error. Update output of exp. that "fails"
5068 (cg2d matching number) and leave the others for later: front_relax(10),
5069 global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
5070 matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
5071
5072 checkpoint57o_post (2005/07/30)
5073 o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
5074 (2) its ready to be documented during the 20050801 DocFest
5075 o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
5076 for ideal_2D_oce and lab_sea on linux_ia32_g77
5077 o set to #undef CTRL_SET_OLD_MAXCVARS_30
5078 in global1x1_tot/code_seaice_adj to access indices 32, 33
5079 (worth another tag)
5080
5081 checkpoint57n_post (2005/07/29)
5082 o adding precip control xx_precip 32
5083 o adding swflux control xx_swflux 33
5084 o Replacing 10 forcing penalty cost routines by 1 generic.
5085 o Implementing partitioning in time-mean and variable adjustment
5086 for atmos. state.
5087 o Time-mean constant error is now read in data.ecco (instead of hard-coded)
5088 o in natl_box_adjoint:
5089 * updated exp 1 to 10
5090 (but does not have time-mean vs. variable split results yet)
5091 o updated global1x1/*_seaice_adj/
5092 to incorporate latest changes
5093 o enable useSingleCpuIO for mdsio vector routines
5094 (applies in particular to tapelev I/O)
5095 o removed inefficient K-loop in all active_file*control*.F
5096
5097 checkpoint57m_post (2005/07/28)
5098 o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
5099 and advect_cs (use EXCH-2 and standard cs-32 grid files).
5100 o pkg/exch2: filling of face-corner halo regions is optional
5101 (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
5102
5103 checkpoint57l_post (2005/07/14)
5104 tag before updating tutorials (pre-release-2)
5105 o add cos & sin of grid-direction orientation angle (curvilinear grid only,
5106 for output and interpolation of input fields onto model grid)
5107 o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
5108 Affects results of exp. rotating_tank ; update output.txt.
5109 o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
5110 and taking the square quantity and/or using a fraction-weight field.
5111 o fix aim_diagnostics_init.F mate numbers.
5112 o add mnc output capability to diagnostics/diagstat and update
5113 our cvsignore files for the ACSII output generated
5114
5115 checkpoint57k_post (2005/07/02)
5116 o lab_sea now uses diagnostics package and provides a suite of
5117 new EXF diagnostics output.
5118
5119 checkpoint57j_post (2005/06/30)
5120 o exf
5121 * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
5122 Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
5123 terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
5124 * extended diagnostics output
5125 - now includes all EXF variables
5126 - hs, hl moved to common block
5127 - separate S/R for diagnostics, called after ctrl vector is added
5128 - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
5129 - EXFqnet contains true Qnet (i.e. includes qsw)
5130 * updated verif. lab_sea, global_with_exf
5131 * Rearranging hflux (exf_mapfields -> exf_getforcing)
5132 to ensure that diagnostics sees a true EXFqnet
5133 o add matlab scripts for CS-grid vectors (in utils/cs_grid)
5134 o diagnostics pkg: change pointers so that 1 diagnostic can be used
5135 several times with different frequencies.
5136 o mnc-ify the thsice package as requested by Daniel Enderton
5137 - the monitor--MNC output needs work
5138 - many attributes need to be added (most are currently blank)
5139 o mnc-ify theaim_v23 package as requested by Daniel Enderton
5140 - many attributes need to be added (most are currently blank)
5141 o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
5142 o add Sadourny like discretization to the 4th.O vorticity advection scheme
5143 o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
5144 update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
5145 fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
5146 o fix few little things to avoid floating error with -ftrapuv (ifort v9)
5147 (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
5148
5149 checkpoint57i_post (2005/06/19)
5150 o Diagnostics package was changed: diagnostic allocation is now deactivated
5151 by setting an empty file name in the namelist (used to be by setting 0 frequency)
5152 o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
5153 add 1rst Order upwind vertical Shear.
5154 o add a quick fix for A/B checkpointing in OFFLINE mode
5155 o add IGNORE_TIME define and -ignore_time option to genmake2 as an
5156 end-run around the C/Fortran linking horror in eesup/src/timers.F
5157 o added pkg/runclock: allows user to terminate run based on wall clock
5158 o added non-hydrostatic scaling parameter: nh_am2
5159 o pkg/my82: futile attempt to make results compiler-independent by adding
5160 some "_d 0", etc. no effect.
5161 o for mnc output, fill the 'T' coordinate var with myTime and create a
5162 separate 'iter' variable for iteration count
5163 o pkg/diagnostics:
5164 add new capability: output of Global/Regional & per-level statistics ;
5165 tested against monitor output (including land & thSIce) on various exp.
5166 o make seaice-pkg I/O type flags (MNC/MDS) more standard.
5167
5168 checkpoint57h_done (2005/05/19)
5169 tag after changing user customized files (DIAGNOSTICS_SIZE.h,
5170 data.diagnostics, data.gchem, data.ptracers) is done.
5171
5172 o pkg/diagnostics: prepare for Global/Regional statistics.
5173 add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
5174 o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
5175 and rename it: DIFFERENT_MULTIPLE
5176
5177 checkpoint57h_post (2005/05/14)
5178 o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
5179 o pkg/diagnostics: change output frequency, now in seconds (instead
5180 of Nb of iterations). This requires to change data.diagnostics.
5181 checkpoint57h_pre (2005/05/12)
5182
5183 o in mnc, let the user create the output dir if both mnc_outdir_date
5184 and mnc_outdir_num are false
5185 o add fflags() to pkg/diagnostics which allows one to specify, on a
5186 per-file basis, the file precision [default behavior is unchanged]
5187 o added diagnostics to pkg/kpp, including computation of mixed layer
5188 depth based on a temperature/density criterion
5189 o updated verification/natl_box to test the new pkg/kpp diagnostics
5190 o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
5191 o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
5192 o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
5193 not mnc -- this mistake was found by JMC and is now corrected
5194
5195 checkpoint57g_post (2005/04/15)
5196 o add Adams-Bashforth 3rd Order time stepping:
5197 - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
5198 - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
5199 checkpoint57g_pre (2005/04/15)
5200
5201 o make lambda[Theta,Salt]ClimRelax spatially varying
5202 (default remains spatially uniform constant based on tau)
5203 o added new control variables
5204 * init. uVel, vVel, etanN
5205 * lambda[Theta,Salt]ClimRelax
5206 o separate masks used for ctrl_pack/unpack 'from write_grid' output
5207 (suggested by G. Forget)
5208
5209 checkpoint57f_post (2005/04/06)
5210 o add parameter "baseTime" = model base time = time at iteration zero
5211 new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
5212 account for baseTime shift
5213 o move Coriolis arrays from PARAMS.h to GRID.h
5214 checkpoint57f_pre (2005/04/06)
5215
5216 o mnc-ifying the seaice package
5217 o introduced an alternative length scale calculation for use in the limiting
5218 maximum viscosity (off by default, see mom_vi_hdissip.F for details)
5219 o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
5220 o added modified Leith scheme with viscosity proportional to grad(Hdiv)
5221 as well as grad(vort3). Made it compatible with both approximate form
5222 for the cubed sphere and full form of these gradients. Added flag
5223 useFullLeith to select between approximate and full form.
5224 o add "d0" in getcon.F to reduce differences between compilers/platforms
5225 update output.txt of exp. fizhi-gridalt-hs
5226 o change port_rand funtion to allow to set the seed.
5227 o fix obscure MNC bug involving conversion between reals and integers
5228 - it caused no problems with certain (eg. gcc, ifc) compilers but the
5229 new version is now more standards-compliant
5230 o adjoint-related modifications
5231 * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
5232 * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
5233 * mom_vi_hdissip: to be able to use Leith scheme in adjoint
5234
5235 checkpoint57e_post (2005/02/28)
5236 o Adding eddy stress controls a la Ferreira et al.
5237 checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
5238
5239 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
5240 update output.txt of exp. fizhi-gridalt-hs
5241 o add more "Z" dimensions and associated coordinate vars to MNC
5242 o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
5243 o parameter calendarDumps: when set, approximate months (30-31 days) and years
5244 (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
5245 KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
5246 months and years. Requires pkg/cal.
5247 o diagnostics: add pickup functionality
5248 - off by default for backwards compatibility
5249 - current version only uses MDSIO -- MNC will be added
5250 o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
5251 o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
5252
5253 checkpoint57d_post (2005/02/11)
5254 o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
5255 o modify verification/ideal_2D_oce so that it tests the creation of mnc
5256 output from the diagnostics package
5257 o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
5258 o make genmake2 more portable by using ".$FS" instead of ".f" for more
5259 of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
5260 o add coordinate variables to the MNC output from the diagnostics package
5261 o change MNC-flags default value: true when useMNC=TRUE
5262 o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
5263 the ability (off by default) to read the grid information using MNC
5264 o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
5265 o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
5266 o do snap-shot diagnostics at the middle of the time-interval (instead of
5267 at the end).
5268 o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
5269 new test for AIM with thSIce + slab-ocean
5270 o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
5271 o move state variable diagnostics to the beginning of the time step ;
5272 (note: still needs some work specially for snap-shot diagnostics)
5273 duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
5274
5275 checkpoint57c_post (2005/01/27)
5276 o Change testing option (-ieee) to get closer agreement between g77 & ifort
5277 o generate new output.txt files on faulks with g77 & the new -ieee option
5278 checkpoint57c_pre (2005/01/27)
5279
5280 o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
5281 update output.txt of exp. global_ocean.90x40x15
5282 o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
5283 results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
5284 o add saltFlux(+File) forcing capability with periodicExternalForcing
5285 o allow to use pkg diagnostics for GM-Redi & ThSIce output
5286 o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
5287 o improvements for the MNC output from DIAGNOSTICS:
5288 - correct handling of the unlimitied dimension
5289 - all dims now have associated coordinate variables
5290 - variables located at U, V, and Corner ("Z") points are now written
5291 with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
5292 *all* data points are output
5293 o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
5294 o added pkg/seaice/seaice_monitor.F
5295 o mdsio_readfield.F can now read files visible only to master MPI process.
5296 o pkg/seaice: some test code for ice-modified ocean stress
5297 o exf_getffields interpolation defaults to bilinear for all scalar forcing
5298 fields (remains bicubic for wind velocity and stress). This avoids, e.g.,
5299 spurious negative numbers for precipitation and humidity. Will cause
5300 some small numerical differences for integrations using pkg/exf/exf_interp.F.
5301 o pkg/ctrl/
5302 * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
5303 May be enabled via doPackDiag
5304 * introduce z-scaling of
5305 + gradient (doZscalePack) and
5306 + control (doZscaleUnpack)
5307 o pkg/mdsio/
5308 * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
5309 * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
5310
5311 checkpoint57b_post (2004/12/20)
5312 o simplify options in diagnostics_fill arguments (remove weird combinations)
5313 o fix MNC coordinate variables so that they now contain per-face index
5314 values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
5315 general, EXCH2 grids are only aligned to a "local" coordinate system
5316 o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
5317 o Implement instantaneous output within pkg diagnostics:
5318 setting a negative frequency in data.diagnostics produces
5319 "snap-shot" output (as opposed to time-average if freq > 0)
5320 o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
5321 NOTE: change ptracer diagnostics name: use 2 characters to work with
5322 more than 9 tracers. Add also diagnostics of advect & diffus flux.
5323 o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
5324 becomes the coordinate variable for the 'T' dimension
5325 o add CF-style coordinate variables to MNC
5326 - just a first cut: numbers are meaningless on the cubesphere and
5327 missing along the T axis but otherwise it works!
5328 o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
5329 o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
5330 o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
5331 this is based directly on what the model compute, so that the content of
5332 each diagnostics might be affected by switching options (e.g., implicitDiffusion)
5333 o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
5334 o clean up build options files for SunOS, in particular
5335 - remove -traditional from xmakedepend
5336 - change -xarch=v9 to -xarch=native for f77
5337 - restore use of make (not gmake)
5338 - add CC=gcc if using g77
5339 o changes per discussion of AM, JMC, & EH3 today:
5340 - move redundant "grid" variables out of "state" -- in preparation of
5341 creating proper CF-style coordinate variables and in recognition
5342 that any/all grid variables can be easily copied (eg. w/NCO) from
5343 the grid files into any of the other NetCDF files
5344 - *always* output grid variables with MDSIO (this will eventually be
5345 changed)
5346 - output MNC grid file if useMNC is true
5347 o every instance of _END_MASTER() has been found and replaced with
5348 _END_MASTER( myThid ) in order to satisfy certain picky Sun
5349 preprocessors
5350 o re-arrange diagnostics pkg initialisation:
5351 - allow each package to extend the available diagnostics list
5352 - add some checking and fix small problems (multi-threaded, ...)
5353 - new S/R diagnostics_fill (replace fill_diagnostics):
5354 look through the short list of active diag. (instead of the long list)
5355 create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
5356
5357 checkpoint57a_post (2004/12/10)
5358 o this set of changes restores TAMC compatibility
5359 tested for global_ocean.90x40x15 adjoint on trough
5360 (what a pain)
5361
5362 checkpoint57a_pre (2004/12/10)
5363 o some modifs in tools/build_options for sunos
5364 o call ctrl_pack for ctrl at end for optimcycle=0
5365
5366 checkpoint57 (2004/12/09)
5367 o add horizontal bi-harmonic viscosity for vertical velocity
5368 - new parameter viscA4W (defaults to viscA4)
5369 - affects only non-hydrostatic code
5370 - to be done: no-slip lateral boundary conditions
5371 o switch back to "sflux = sflux - runoff" in exf_getforcing.F
5372 o implement Implicit Vertical advection for pTracers
5373 o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
5374 (implemented also for implicit vertical diffusion & advection)
5375 o OBCS: extend application of tracer open boundary conditions
5376 to a strip beyond the boundary of width Olx/Oly
5377 o add call monitor to TAF set of required calls (flow directives)
5378 and include in natl_box_adjoint
5379 o untangle a few ifdefs related to cost, ctrl, autodiff
5380 untangel a few ALLOW_ECCO_OPTIMIZATION
5381 o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
5382 (theta2, salt2 in ecco_cost_weights)
5383
5384 checkpoint56c_post (2004/12/03)
5385 o OBCS as control variables
5386 - update ctrl_ad_diff.list, obcs_ad_diff.list
5387 - remove balance of obcs controls from default
5388 - fix index bug nobcs in ctrl_init
5389 - fix dummy fields filen in ctrl_pack
5390 - add dummy weights for obcs
5391 o lsopt: comment out fort.94 output
5392 o optim:
5393 - remove unnecessary header files
5394 - adjusted namelists
5395 - add xerbla.F to Makefile
5396 o exf:
5397 - multiple modifications of exf_check_range
5398 - unit change in exf_init_runoff from [m/year] to [m/s]
5399 o mdsio:
5400 - i/o-vector change debugLevel from debLevA to debLevB
5401
5402 checkpoint56b_post (2004/12/01)
5403 o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
5404 is called from DO_THE_MODEL_IO
5405 - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
5406 - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
5407 - clean up PTRACERS_WRITE_TIMEAVE a little
5408 o add another verification experiment that tests both the cfc-pkg and
5409 the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
5410 reactive tendencies treated inline with regular timestepping
5411 o testreport previously did a lousy job of comparing small numbers, so
5412 we (Ed and Martin) changed the way the cut-off of 1.e-12 is
5413 implemented in the little c-progam tmp_cmpnum.c which is embedded in
5414 testreport.
5415 o ptracers_monitor: bug fix for MPI
5416
5417 checkpoint56a_post (2004/11/28)
5418 o GCHEM: finish reorganizating the package
5419 - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
5420 (introduces another 3D-array for each passive tracer, but only if
5421 GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
5422 gchemTendency is not needed because the timestep is done separately)
5423 - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
5424 - GCHEM is now---more or less cleanly---separate from PTRACERS
5425 - to bo done: handling of surfaceForcingPtr that is needed for KPP not
5426 so clear to me how that should be done in a general way.
5427 o CFC: improve formatting of output in CFC_ATMOS
5428 o PTRACERS:
5429 - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
5430 that ALL experiments with ptracers enable can be checked. This makes
5431 GCHEM_MONITOR obsolete.
5432 - include a runtime parameter PTRACERS_monitorFreq that defaults to
5433 monitorFreq
5434 - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
5435 o add PTRACERS (PTR0[1-5]) to testreport output
5436 o exf_check_range:
5437 * default changed to .TRUE.
5438 * will check values for niter0 if debLevA, every timestep if debLevB
5439 * STOP in exf_check_range if 'out of range'
5440 * range chosen generous to allow for potential extema
5441 TBD: a version with stricter range
5442 permitted range would be runtime parameters
5443 o GMredi:
5444 - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
5445 - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
5446 - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
5447 o GCHEM:
5448 - move call to GCHEM_FORCING_SEP, so that it is now called before
5449 the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
5450 - introduced a useGCHEM runtime flag and applied it everywhere.
5451 - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
5452 this flag is now only visible within GCHEM-pkg routines.
5453 - moved gchem_forcing_int temporarily into ptracers_forcing, this will
5454 be replaced by a 3D array that is computed before thermodynamics; for
5455 this, the tracer ID iTracer had to be included into the parameter list
5456 of ptracers_forcing
5457 - set up forward_step to call gchem_forcing, that will replace
5458 gchem_forcing_int in ptracers_forcing
5459 - cleaning up
5460 o small cleaning of exch2: remove files that are also in eesupp/src
5461
5462 checkpoint56 (2004/11/17)
5463 o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
5464 o mnc: cleanup "full" files--fixes out-of-memory problem
5465 o ECCO-GODAE
5466 * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
5467 * fully merged and updated from SIO code
5468 windstress sign change affects
5469 - exf_inscal_[u/v]stress
5470 - sign of xx_tau[u/v] adjustments
5471 - signs in cost_scat
5472 * ctrl_get_gen: avoid update of tau[u/v] for first few days
5473 * natl_box_adjoint updated and compressed
5474 * 2-level checkpoint switch added
5475 (tested in EXP. 1 of natl_box_adjoint)
5476 * new switch doInitXX to avoid init. of xx_... in optimcycle=0
5477 o SVD
5478 * first complete, non-hacked version for SVD calculations
5479 * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
5480 performed via direct access files admtlm_vector.it????
5481 (via ctrl_[un]pack)
5482 * optimcycle is used for ARPACK iteration counter
5483 (note: adxx_... is iterated, rather than xx_...; latter is constant!)
5484 * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
5485 and add linear transforms where necessary
5486 * controls are initial/final SST, SSS (can be extended; need to check
5487 ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
5488 o mdsio: filename info to both stderr, stdout
5489 o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
5490 from sign change
5491
5492 checkpoint55j_post (2004/11/10)
5493 o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
5494 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
5495 o add consistent build directories and .cvsignore files to verification
5496 o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
5497 o make all subroutines 30 or less characters in length for certain older
5498 compilers to work (a thorough search only turns up two routines in
5499 pkg/ptracers)
5500 o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
5501 affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
5502
5503 checkpoint55i_post (2004/10/28)
5504 o change arrays for total vertical diffusivity (2.D if explicit,
5505 3.D if implicit) ; each ptracer uses its own background value.
5506 o added mnc/NetCDF output capability to ocn_compon_interf
5507 - added bits to verification/cpl_aim+ocn so that it can run on
5508 ITRDA and other clusters without the mpirun "-wd" option
5509 o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
5510 configuration
5511 o give MNC the ability to create additional files rather than
5512 exceeding a specified file size limit "MNC_MAX_FILESIZE"
5513 - the default is just less than 2GB which is a practical limit
5514 on many systems
5515 o Compute the non-local term using either KPP vertical diffusivity (=default)
5516 or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
5517
5518 checkpoint55h_post (2004/10/20)
5519 o add verification test "vermix"
5520 o remove all the *_ioinc flags and replace with the single global
5521 outputTypesInclusive flag
5522 o allow to set a vertical profile of vertical diffusivity for T & S
5523 o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
5524 o useMNC moved from data.mnc to data.pkg
5525
5526 checkpoint55g_post (2004/10/14)
5527 o Renaming carbon AD experiments to comply with testreport conventions
5528 o Updating adjoint of Held-Suarez hs94.1x64x5
5529 o Fixing directives for non-ECCO forward_step, after ECCO directives
5530 have been fixed to avoid recomp. of do_oceanic_phys
5531 Works well for global_ocean.90x40x15,
5532 but recomp. issue remains for carbon
5533 o Updating adjoint output for natl_box_adjoint after
5534 pkg/ecco has been modified (see taga c55d_post)
5535
5536 checkpoint55f_post (2004/10/13)
5537 o rename to timeave_init_fixed
5538
5539 checkpoint55e_post (2004/10/13)
5540 o some delicate re-shuffle of store directives to avoid one
5541 extra call of do_oceanic_physics
5542 affects ecco_the_main_loop.F, do_oceanic_physics.F
5543 checkpoint_lev1_directives.h
5544 o NB: this may break global_ocean adjoint temporarily,
5545 but it is clear how to fix it. Will do later, need this now.
5546
5547 checkpoint55d_post (2004/10/11)
5548 o ECCO specific cost function terms (up-to-date with 1x1 runs)
5549 o ecco_cost_weights is modified to 1x1 runs
5550 o modifs to allow observations to be read in as
5551 single file or yearly files
5552 o enable to read exf forcing fields as either
5553 single file or yearly files (flag useExfYearlyFields)
5554 checkpoint55d_pre (2004/10/08)
5555
5556 o switch between 2-level and 3-level checkpointing
5557 o add ability of MNC to write local and "partial" (eg. 2D slices where
5558 the full 3D field is never actually stored) arrays to NetCDF files
5559 with the correct (that is, the complete multi-dimensional) set of
5560 array indicies
5561 - used in mom_vecinv() to write the diagFreq output
5562 - tested (demonstrated) in verification/aim.5l_cs
5563 o further mnc-ification
5564 - add verification/lab_sea to the list with mnc setups
5565 - fix undefined mnc v-names in cd_code
5566 - add kpp to mnc output (both snapshot and timeave)
5567 o non-hydrostatic code
5568 - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
5569 in calc_gw.F
5570 - defaults to viscAh
5571 - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
5572 friction or Leith) in non-hydrostatic mode, as long as there is
5573 no biharmonic friction and/or Leigth or equivalent for vertical velocity.
5574 o pkg/cost
5575 extend simple cost functions to treat time mean quantities
5576 (T,U,V) via cost_accumulate_state from cost_tile
5577 o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
5578 be 2 times larger than the minimum size the advection scheme requires.
5579 now get a perfect conservation of salt in advect_cs test-exp (updated)
5580 o GGL90 (Gaspar's TKE mixed layer)
5581 - add horizontal diffusion of TKE, requires exchanges in
5582 do_fields_blocking_exchanges, horizontal diffusivity is zero by
5583 default. In OPA there is no horizontal diffusion of TKE but the
5584 mixing coefficients are computed from a horizontal average of TKE of
5585 6 points or so. I think that diffusion has a little more physical
5586 justification.
5587 - clean up ggl90_calc in the hope of reducing memory usage (this hope
5588 was in vain)
5589 - mask tke-variable in ggl90_init
5590 o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
5591 o fix biharmonic diffusion on CS-grid.
5592 o more obcs stuff
5593 - added obcs_external_fields_load as an alternative to the EXF-pkg option
5594 for reading boundary values. This routine is called from
5595 obcs_prescribe_read
5596 - updated obcs_check
5597 - changed sponge layer relaxation parameter units for days to seconds
5598 - turned off sponge layer by default
5599 - changed argument list of OBCS_CALC to myTime+deltaTclock
5600 - fixed about 35 bugs in obcs_external_fields_load
5601
5602 checkpoint55c_post (2004/09/23)
5603 o obcs stuff
5604 - new runtime flags useOBCSprescribe, useOBCSbalance
5605 - re-arranged obcs_calc
5606 - moved exf_getobcs to obcs_prescibe_read
5607 obcs_prescibe_read is called after ORLANSKI stuff
5608 and independent of it (executable can contain all).
5609 - updated obcs_check
5610 - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
5611 These may be necessary only if tangential velocities are
5612 prescribed at OB, not sure, needs testing.
5613 o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
5614 which simplifies the calls and passes the ifc check-bounds test
5615
5616 checkpoint55b_post (2004/09/22)
5617 o add a 2D scalar, Z location, exchange_2 routine.
5618 o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
5619 to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
5620 affects advect_cs results (for the wrong reason): update output.txt
5621 o use a more standard discretization for biharmonic viscosity ;
5622 (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
5623 affects results of dome set-up: update output.txt
5624 o fix gad_advection.F (CubedSphere part), back to version 1.23
5625 o fix bug in mom_vi_del2uv.F (CubedSphere part).
5626
5627 checkpoint55a_post (2004/09/20)
5628 o merged code to
5629 * prescribe/read time-dependent open boundaries
5630 (works in conjunction with exf, cal)
5631 * sponge layer code for open boundaries
5632 * each boundary N/S/E/W now has its own CPP option
5633 (healthy for the adjoint)
5634
5635 checkpoint55 (2004/09/17)
5636 o up-to-date adjoint of previous breaks
5637 - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
5638 - global_ocean_ebm: adjoint still needs fix (TLM ok)
5639 - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
5640 - carbon: * remove tr1-related adjoint verification
5641 * add ptracer as control variable
5642 o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
5643 (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
5644
5645 checkpoint54f_post (2004/09/16)
5646 o in verification/carbin/ remove experiment related to
5647 ALLOW_PASSIVE_TRACER (array tr1 etc)
5648 code_ad/ input_ad/ results_ad
5649
5650 o add two new packages
5651 - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
5652 + subject to optimization (memory)
5653 - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
5654 + subject to reordering (many GOTOs in the original code)
5655 + so far opps is called for every (i,j) point, and then operates in
5656 the vertical; one may want to reorder the scheme in order operate in
5657 horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
5658 fields)
5659 o overhaul of IO so that we now have flags for MDSIO and/or MNC
5660 - all verification tests compile and run with linux_ia32_g77
5661 - defaults are compatible with current input files--nothing
5662 should change if you were not previously using MNC
5663 - MNC output has been added in numerous places (eg. timeave)
5664 but there are still a few writes not yet do-able with MNC
5665 (this is in progress)
5666 - flags now allow for either/or/both use of MDSIO and MNC and
5667 documentation will soon follow
5668 - numerous small formatting cleanups for ProTeX
5669 o add version info (via BUILD_INFO.h) to MNC and stdout
5670
5671 checkpoint54e_post (2004/09/02)
5672 o add two new packages
5673 - pp81 (Packanowski and Philander, 1981), Richardson number and
5674 stratification dependent mixing
5675 - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
5676 - these scheme operate in a similar manner as KPP (without ghat, of
5677 course), however there is only one diffusivity that is used for both
5678 temperature and salinity (and passive tracers)
5679 o add offline package
5680 o add "verification/dic_example" which contains a dic-gchem-ptracer setup
5681 provided by Stephanie Dutkiewicz
5682 o genmake2: add ability to search for C compilers and cleanup test output
5683 - fixes recent SX-6 problems and should help with others (eg. HP-UX)
5684
5685 checkpoint54d_post (2004/07/27)
5686 o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
5687 o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
5688 leading to additional shift by 5 days each year of integration
5689 (i.e. leading to considerable offset over the years)
5690 o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
5691 o start with no AB and no initial filtering (staggerTimeStep):
5692 change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
5693 o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
5694 (external loading & cpl import/export stay in forward_step.F)
5695 o update coupling interface to work with new staggerTimeStep
5696 o change MDSIO ptracers_pickup.
5697 o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
5698 o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
5699 o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
5700
5701 checkpoint54c_post (2004/07/18)
5702 o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
5703 this affects (truncation error) output.txt of test-exp:
5704 global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
5705 o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
5706 o change Qnet to always be the net heat flux, (+upward).
5707 affects (truncation error) output of natl_box exp.: updated
5708 o define the max number of passive tracers in PTRACERS_SIZE.h
5709 o start to test mnc routinely in exp0
5710 o add sea-ice loading (sIceLoad) as a new forcing field.
5711
5712 checkpoint54b_post (2004/07/08)
5713 o add testreport "-j JOBS" option for parallel builds (tested and pretty
5714 impressive on Altix and Opteron systems)
5715 o diagnostics can now write NetCDF files through the mnc package
5716 o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
5717 o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
5718 o staggerTimeStep & NLFS: rescale T & S surface tendencies.
5719 affects (truncation error) output of lab_sea & natl_box exp.: updated
5720 o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
5721
5722 checkpoint54a_post (2004/07/06)
5723 o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
5724 o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
5725 o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
5726 o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
5727 + internal_wave (shift in writing cg2d_ini_res)
5728 checkpoint54a_pre (2004/07/05)
5729
5730 o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
5731 - modified verification/lab_sea and natl_box_adjoint accordingly
5732
5733 checkpoint54 (2004/07/02)
5734 checkpoint53g_post (2004/07/02)
5735 o prepare splitting of thermodynamics: store convect.counter in common block
5736 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
5737 output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
5738 o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
5739 o new parameter "nShapS": allow to treat differently S from T (nShapT)
5740 o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
5741 o restore adjointability
5742
5743 checkpoint53f_post (2004/06/25)
5744 o modifications that affect AIM experiment results (update output.txt):
5745 - no advection of S at top interface Nr (pkg/generic_advdiff)
5746 - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
5747 o AIM pkg:
5748 - include stability function into surf.Flux derivative relative to Tsurf
5749 - calculate clear-sky radiation & surface temp. change (for diagnostics)
5750
5751 checkpoint53e_post
5752 o merged cylindrical coord configuration
5753 o added rotating_tank experiment
5754 checkpoint53e_pre
5755
5756 checkpoint53d_post (2004/06/14)
5757 o faulks upgraded: re-generate output.txt that have changed:
5758 global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
5759 o Added Bryan and Lewis, 1979, vertical diffusivity profile
5760 o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
5761 o added Sadourny discretization of Coriolis
5762 - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
5763 - re-enabled use of omega3 (useAbsVorticity)
5764 o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
5765 vector-invariant equations
5766 - note: does *NOT* yet use same variable visc. for no-slip BC's.
5767 o recoded the lateral boundary conditions for non-hydrostatic w, this time
5768 hopefully without new bugs
5769 - still to do: biharmonic friction for non-hydrostatic w
5770 o bug fix for mom_*_sidedrag: rA -> rAs,rAw
5771 o regenerated output for global_ocean_ebm (using -ieee)
5772 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
5773 of mom_common/
5774 - simple re-arrangement of instructions within computing loop
5775 checkpoint53d_pre (2004/05/21)
5776
5777 checkpoint53c_post (2004/05/21)
5778 o new version of coupler for AIM+thSIce and Ocean models
5779 - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
5780 - land: change Evaporation of snow
5781 - aim with thSIce: fix bug in snow-precip.
5782 o changes to calc_gw.F
5783 - bug fix for w^2 term near the bottom boundary
5784 - (hopefully) improve the lateral slip boundary condtions for use with
5785 partial/looped cells
5786 - because the bug fix changes two verification experiments anyway (exp5
5787 and plume on slope), change the lateral boundary condition from half slip
5788 to the value of no_slip_sides
5789 o ebm package wasnt quite up to the parallel task. Fixed that.
5790 o Adjoint of EBM package + verification
5791 * TLM OK
5792 * ADM not sufficient accuracy yet (needs further testing)
5793
5794 checkpoint53b_post (2004/05/14)
5795 o Commiting new energy balance model to repository
5796 * package is pkg/ebm
5797 * verif. is verification/global_ocean_ebm
5798 * references are in ebm_driver.F
5799 C * X. Wang, P. Stone and J. Marotzke, 1999:
5800 C Global thermohaline circulation. Part I:
5801 C Sensitivity to atmospheric moisture transport.
5802 C J. Climate 12(1), 71-82
5803 C * X. Wang, P. Stone and J. Marotzke, 1999:
5804 C Global thermohaline circulation. Part II:
5805 C Sensitivity with interactive transport.
5806 C J. Climate 12(1), 83-91
5807 C * M. Nakamura, P. Stone and J. Marotzke, 1994:
5808 C Destabilization of the thermohaline circulation
5809 C by atmospheric eddy transports.
5810 C J. Climate 7(12), 1870-1882
5811 o Will need long integration testing.
5812 checkpoint53b_pre (2004/05/14)
5813
5814 o created pkg/mom_common in preparation for variable viscosity code
5815 o renamed and split ini_mnc_io
5816 o pkg/land: only liquid water can diffuse or run-off
5817 o AIM using land: soil wetness availability account for snow
5818 o added printMapIncludesZeros to EEPARMS namelist
5819
5820 checkpoint53a_post (2004/05/11)
5821 o restore TAMC compatiility for exf_constants.h
5822 (no usage of _d in .h)
5823 o Additional storing in KPP in an attempt to fix
5824 TAMC problem with adjoint of KPP code.
5825 (no success...)
5826 Identical code works fine with TAF.
5827 o Fixed verification/natl_box_adjoint experiments.
5828 Initial conditions for Experiments 4 and 5 are now
5829 set to "SEAICE_initialHEFF=0", which is more reasonable,
5830 and hence gives results closer to that of Experiment 2.
5831 Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
5832
5833 checkpoint53 (2004/05/06)
5834 o stable checkpoint with up to date adjoint
5835 TLM tests only run for 1st grdchk at the moment. Its unclear if
5836 this is a code problem or a problem with resetting code for g_
5837 variables that is being autogenerated wrong.
5838 Otherwise:
5839 o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
5840 o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
5841 are both still in chaos following their security messes.
5842
5843 checkpoint52n_post (2004/05/06)
5844 o various build (mostly genmake2) changes including:
5845 - ability to build/run more easily within Cygwin and MacOS X
5846 - more complicated Makefiles with a stronger dependence on Gnu Make
5847 o pkg/seaice modifications
5848 - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
5849 of pkg/seaice. For time being, SEAICE_deltaTtherm = deltaTtracer
5850 and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
5851 - changed proxy for geostrophic velocity and updated
5852 verification/lab_sea/results/* accordingly
5853 - removed ADI dynamic solver from pkg/seaice
5854 - replaced all occurrences of 1/CSTICE or 1/CSUICE
5855 they caused a segmentation fault under certain circumstances
5856 - removed unused field WATR
5857 o bug fix in exf-package:
5858 - u/vwind are defined at tracer/pressure points. The values of u/vwindmask
5859 now reflect that.
5860 o small fixes in the cal-package:
5861 - set reference date to first of January for the 'model'-calendar
5862 - failing of cal_CheckDate in cal_FullDate now actually results in a
5863 warning
5864 o small modifications in exf-package to increase flexibility:
5865 - change climtempfreeze from a constant to a runtime parameter that
5866 is specified in data.exf_clim (default = -1.9)
5867 - introduce runtime parameter windstressmax (default = 2.0) that is
5868 specified in data.exf
5869 o fix in pkg/thsice:
5870 - update Evap (Tsf changes) to be consistent with Latent heat flux
5871 - maintain snow precipitation unchanged (even if Tsf >=0).
5872 both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
5873
5874 checkpoint52m_post (2004/04/18)
5875 o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
5876 this does not change any of the results, because myIter=0 in swfrac always
5877 lead to jwtype=2 (the default anyway), but the call makes little sense
5878 as a default
5879 o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
5880 o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
5881 atmospheric model (AIM) to use it ; add a "slab ocean" component.
5882 o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
5883 o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
5884 o extending useSingleCpuIO option to work with new exch2 I/O format
5885 - old-style, missing-tile I/O is still accessible by defining CPP
5886 option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
5887 o monitor package can write to NetCDF files and/or STDOUT
5888 o fix re-definition bug in MNC_GRID_INIT_ALL()
5889 o doc/api_reference added
5890 - a framework for building an API Reference Manual using all
5891 the "protex" comments embedded in the code
5892 - see pkg/generic_advdiff, pkg/mnc for examples
5893 o MNC:
5894 - make myThid the last argument for all subroutines
5895 - new default for the grid files: NO halos
5896 - add useMNC and other run-time flags
5897 - separate per-file-group handling of the unlimited dimension
5898 - early initialization of MNC w/ flags read at the eeboot stage
5899 and lookup tables set in initialize_fixed
5900 - write all MNC output to a freshly-created directory
5901 o thermodynamics sea-ice (thsice) is now tested with testreport.
5902 o test exp. advect_cs: use the standard cs32 grid ; update output.
5903 o Added functionality to grdchk:
5904 pick global i,j,k position (or nearest wet) where to perform check.
5905
5906 checkpoint52l_post (2004/03/11)
5907 o new land formulation:
5908 a) use ground enthalpy as prognostic variable to ensure exact
5909 energy conservation.
5910 b) account for water temperature and for latent heat of freezing
5911 in all processes (rain, run-off, ground storage)
5912 c) compute surface and ground temperature implicitly.
5913 o aim_v23 modification for new land model:
5914 a) Treat separately land / ocean / sea-ice surface fluxes
5915 to allow implicit computation of land & sea-ice surface temp.
5916 b) add snow precipitation.
5917 checkpoint52l_pre (2004/03/11)
5918
5919 o fix problem (when 1 tile is empty) in min/max monitor.
5920 o fix bug in timeAve (u,vZetatave in common block)
5921 o no restoring terms under ice for pkg/seaice
5922 o moved SEAICE_DO_DIAGS to S/R do_the_model_io
5923 o bug fix for pkg/seaice pickups
5924 o change MNC call locations and add coordinate attributes
5925 o mask vorticity at the corner ; affects global_ocean.cs output
5926 o fix ini_curvilinear_grid ; test CS experiments with mpi
5927 o aim.5l_cs: modify sea-ice fraction input file ; update output
5928 o exf: Adding simple range check routine for exf fields after read
5929
5930 checkpoint52k_post (2004/02/23)
5931 o removed top-level directory "diags"
5932 - we migrated these functions to pkg/timeave a long time ago
5933 o fixed bug introduced in pkg/monitor
5934 o accuracy ctrlprec = 32 insuffient for gradient checks using
5935 averaged fields (I/O via cost_averages)
5936 -> use ctrl.h in active_file*.F to control I/O precision.
5937 o paramter list of CALL ADTHE_MAIN_LOOP
5938 o added initial do_the_model_io to ecco
5939 o set all ...Freq to zero after cost_final
5940 taveFreq, dumpFreq, pChkptFreq
5941 o MAIN and ECCO differentiability restored
5942
5943 checkpoint52j_post (2004/02/18)
5944 o fix nchklev in tamc.h for global_ocean...
5945 o Bringing flow and store directives up-to-date
5946 o Really weird thing!
5947 call do_the_model_io from the_main_loop with parameters
5948 starttime, niter0, instead of mytime, myiter, screws up the adjoint:
5949 TAF places a faulty re-call of initialise_varia
5950 after cost_final call which should not be there!
5951 checkpoint52j_pre (2004/02/03)
5952
5953 o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
5954 error messages
5955 o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
5956 o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
5957 debug output
5958 o modfied mdsio_writefield.F to handle non-global files under exch2
5959 o update AIM Cubed-Sphere exp (aim.5l_cs):
5960 use land, p*, and Franco.M forcing fields with fractional land-sea mask.
5961 o update AIM Equatorial Channel exp:
5962 use standard aim_v23 pkg and change the SST fields to be more realistic.
5963 o globalFile now works with exch2
5964 o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
5965 mon_vort3.F to make exch2 friendly with >1 tile per cube face
5966 o limit timeave output for hi-res integrations
5967
5968 checkpoint52i_post (2004/01/21)
5969 o removed CPP_EEOPTIONS.h from verification/*/code
5970 o updated the tiling for global_ocean_pressure
5971 checkpoint52i_pre (2004/01/20)
5972
5973 o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
5974 the old pkg/aim).
5975
5976 checkpoint52h_pre (2004/01/20)
5977 o shortened offending lines in exch2_send_rx?.template
5978 o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
5979 o genmake2: add build & execute test for NetCDF code
5980 o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
5981 old grid files, moved CPP_EEMACROS.h to pkg/exch2
5982 o added useSingleCPUIO flag to monitor.F and mon_out.F
5983 o added temporary hack for sea-ice dynamics on the cube:
5984 metric terms are ignored and it is assumed that
5985 there is no sea-ice on cube faces 1, 2, 4, and 5.
5986
5987 checkpoint52f_post (2004/01/09)
5988 o added exch2 cube routines to pkg/exch2
5989 o modified hs94.cs-32x32x5 to use it
5990 o added new grid files to hs94.cs-32x32x5
5991 checkpoint52f_pre (2004/01/07)
5992
5993 checkpoint52e_post (2004/01/07)
5994 o first attempt to solve vertical advection (momemtum & T,S) Implicitly
5995 for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
5996 o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
5997 to work with implicit vertical advection and AB ;
5998 o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
5999 o update output (gad_calc_rhs.F changes affect truncation error) of exp:
6000 front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
6001 checkpoint52e_pre (2004/01/02)
6002
6003 o fix bug in impldiff when Nr=1 or Nr=2.
6004 o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
6005 o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
6006 o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
6007 ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
6008 o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
6009 o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
6010 o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
6011
6012 checkpoint52d_post (2003/12/16)
6013 o re-tiled many expts to allow comparison in multi-processor mode
6014 - updated output accordingly
6015 - changed hs94.128x64x5 to use intial T from file rather than use the
6016 random number generator
6017 o add infrastructure in model routines for fizhi and gridalt packages
6018 o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
6019 o changes to permit hi-res, cubed-sphere, configuration
6020 - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
6021 - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
6022 - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
6023 of surface winds for the cube
6024 (A verification experiment, based on global_ocean.cs32x15, but with
6025 pkg/seaice turned on and with on-the-fly interpolation from the NCEP
6026 Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
6027 complete with example surface forcing files and matlab scripts to look
6028 at the output and compare it with that of global_ocean.cs32x15.)
6029 o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
6030 but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
6031 to conform to the common rule.
6032 o check-in the first version of the coupler + interfaces for multi-components
6033 set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
6034 - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
6035 - atmosphere: use pkg aim_v23 ; no sea-ice for now.
6036 - ocean and atmos. share the same horizontal grid (no interpolation).
6037 - exchanges between component and coupler is done in forward_step
6038 o new verification experiment, cpl_aim+ocn:
6039 coupled ocean - AIM atmosphere on cs32 grid.
6040
6041 checkpoint52d_pre (2003/12/06)
6042 o surface flux time-av diagnostic modified for NLFS & RealFreshWater
6043 o add call to AIM pendant S/R in external_forcing & external_fields_load.F
6044
6045 checkpoint52c_post (2003/11/25)
6046 o Fixing OPTIONS files for use of exf:
6047 - ALLOW_ECCO not needed
6048 - ECCO_CPPOPTIONS.h should not be included from
6049 EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
6050 as has been the case in the past
6051 - All cal/exf related options are currently set in
6052 single header file. Should remain so until we
6053 agree on a consistent new policy.
6054 o Removed all CPP options for cal package.
6055 cal has no more CPP options.
6056 o modified STOREs in GAD_ADVECTION
6057 o corrected key comp. for passkey
6058
6059 checkpoint52b_post (2003/11/23)
6060 o new version: "thsice" of thermodynamic sea-ice pkg:
6061 - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
6062 - modify fluxes but do not change theta directly;
6063 - light cleaning of bulk_force pkg (still needed with thsice).
6064 - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
6065 + output_thsice.txt to test thsice & bulk_force pkgs.
6066 o put back grid & coriolis monitor output.
6067 checkpoint52b_pre (2003/11/23)
6068
6069 o call "do_the_model_io" at the beginning (=> dump initial state)
6070 o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
6071 o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
6072 (need info on NUMBER_OF_PTRACERS)
6073 o missing PTRACERS headers in some routines
6074 o default tamc.h in pkg/autodiff supposed to crash
6075 to ensure proper customization
6076
6077 checkpoint52a_post (2003/11/17)
6078 o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
6079 - moved surfaceTendencyTice from pkg/seaice to main code
6080 - subroutine FREEZE_SURFACE now limits only surface temperature
6081 and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
6082 => new output.txt for global_ocean.cs32x15 & global_with_exf
6083 - keep the old version of FREEZE for backward compatibility;
6084 global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
6085 - corresponding modifs for TAF directives
6086 o added surface flux output variables to TIMEAVE_STATVARS
6087 o time-averaged output for pkg/ptracers
6088 o fix problem with ECCO-related divided adjoint
6089 snapshot file was missing some ad-variables,
6090 but no warning issued by TAF
6091
6092 checkpoint52a_pre (2003/11/12)
6093 o some bug fixes for #undef REAL4_IS_SLOW
6094
6095 checkpoint52 = ecco_c52_e35
6096 o after testing adjoints of checkpoint51u_post
6097
6098 checkpoint51u_post (2003/11/06)
6099 o this is the post-merge tag of the ecco-branch
6100 (needs another clean checkout and re-testing)
6101 o various natl_box_adjoint configs and results
6102 but no input fields
6103 o obcs adjoint not yet merged!
6104 o adding ECCO global 1x1 and 2x2 degree configs
6105 o updated/extended some store directives for seaice
6106 o pkg/ecco now containes ecco-specific part of cost function
6107 o top level routines the_main_loop, forward_step
6108 supersede those in model/src/
6109 previous input data.cost now in data.ecco
6110 (new namelist ecco_cost_nml)
6111 o in ctrl/ cleaned some cross-dependencies and updated CPP options
6112
6113 checkpoint51t_post (2003/11/04)
6114 o this is the pre-merge tag of the ecco-branch
6115
6116 checkpoint51s_post (2003/11/04)
6117 o cleanup: removed various obsolete #define-s
6118 o pkg/grdchk
6119 - renamed 'ph-grd 3' to 'grad-res'
6120 - merged from ecco-branch
6121 (remaining bug fixes for obcs gradient checks)
6122 - additional high-precision output for testreport
6123 (grep for 'precision_grdchk_result')
6124
6125 checkpoint51r_post (2003/11/03)
6126 o cleaned up or removed CPP_OPTIONS.h files
6127 o updated results for some of the tests to reflect the new
6128 optfiles (-ieee: -O0 instead of -O3)
6129
6130 checkpoint51q_post (2003/10/30)
6131 o cd_code:
6132 - moved cd_scheme.F -> cd_code_scheme.F
6133 - separate read_checkpoint from cd_code_ini_vars.F
6134 - separated cd_code part from write_checkpoint
6135 - updated AD_SOURCE, generated .flow
6136 - added CD_CODE_VARS.h to the_main_loop
6137 - Moving cd_code specific store dir.s to pkg/cd_code
6138 o ctrl package totally restructured
6139 - pack/unpack now optional and decoupled from
6140 xx_/adxx_ I/O
6141 - ctrl_pack/unpack cleaned
6142 (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
6143 - confined inclusion of AD_CONFIG.h to where necessary.
6144 o genmake2: changed AD dependencies from SRCFILES to AD_FILES
6145
6146 checkpoint51p_post (2003/10/30)
6147 o create initial cd_code package
6148 - WARNING: the initialization of fields within packages
6149 is broken because INI_FIELDS (where READ_CHECKPOINT is
6150 called) is called *before* PACKAGES_INIT_VARIABLES.
6151 This seems to be backwards since
6152 1) its important to initially zero the entire field including
6153 the "halo" region
6154 2) zeroing needs to be done *before* reading pickup info
6155 and the pickup call might or might not happen in any
6156 particular run
6157 - this needs an overhaul for R2
6158 o cleanup verification/*/code/GMREDI_OPTIONS.h
6159 o cleanup testreport
6160
6161 checkpoint51o_post (2003/10/27)
6162 o bringing AD-related verif's up to date with genmake2
6163 - carbon/
6164 - global_ocean.90x40x15/
6165 - hs.94.1x64x5/
6166 - (front_relax/ )
6167 o (more) consistent directory structure for AD-related verif.'s
6168 o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
6169 o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
6170 o bug fix in find_alpha.F for MDJWF:
6171 - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
6172 change rho -> rho-rhoConst
6173 - replace call find_rho to find_rhonum
6174 o initialisation of rFlx extended to full array (required by TAF)
6175 and shifted to thermodynamics
6176 o removed PTRACERS.h in ptracers routine
6177 o added surfacetendencyPtr to S/R parameter list pracers_forcing
6178 o Correcting initialisations for fVerU, fVerV.
6179 o helping TAF to recognize dependency on kUp for
6180 fVerU, fVerV
6181 o Replacing delZ by delR in pkg/ctrl/
6182 checkpoint51o_pre (2003/10/24)
6183
6184 o undid all of cp51 pending some cleanups and discussion
6185 o added the [#include "AD_CONFIG.h"] statement to all files that need
6186 it for adjoint/tl #defines
6187 o re-worked the build logic in genmake2 to support AD_CONFIG.h
6188 o removed tools/genmake since it no longer works
6189
6190 checkpoint51n_post (2003/10/23)
6191 o modifications to make FREEZE flux visible to pkg/kpp
6192 - moved surfaceTendencyTice from pkg/seaice to main code
6193 - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
6194 - subroutine FREEZE now limits only surface temperature
6195 (this means new output.txt for global_ocean.90x40x15,
6196 global_ocean.cs32x15, and global_with_exf)
6197 o added surface flux output variables to TIMEAVE_STATVARS
6198
6199 checkpoint51n_pre (2003/10/23)
6200 o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
6201 o added [#include "AD_CONFIG.h"] to all files that use the following
6202 defines:
6203 - ALLOW_ADJOINT_RUN
6204 - ALLOW_TANGENTLINEAR_RUN
6205 - ALLOW_ECCO_OPTIMIZATION
6206
6207 checkpoint51m_post (2003/10/21)
6208 o incorporating changes to get TAMC/TAF working in genmake2
6209 - added new TAMC/TAF targets to the Makefile
6210 - various cleanups related to package handling
6211 - these changes should have no impact on the forward model
6212
6213 checkpoint51l_post (2003/10/20)
6214 o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
6215 - faster algorithm for cal_addtime.F
6216 - higher precision arithmetic, where needed
6217 - pkg/exf *startdate variables changed from calendar date to
6218 model integration time
6219
6220 checkpoint51l_pre (2003/10/17)
6221 o add salt flux to forcing fields (used when salty sea-ice forms or melts)
6222 o enable to apply restoring on S & T only in a latitude band.
6223 o update output (external_forcing_surf modif. change truncation errors)
6224 global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
6225
6226 checkpoint51k_post (2003/10/16)
6227 o change default to: useNHMTerms=.FALSE.
6228 - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
6229 adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
6230 - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
6231 exp1, ideal_2D_oce
6232 - change data file of oceanic exp (leave the results unchanged for now)
6233 exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
6234 o set gravitySign automatically according to the vertical coordinate used
6235 (and change sign: back to "logical" value: +1 when R increases downward)
6236 o added an include barrier to the default CPP_OPTIONS.h and
6237 removed the #include "PACKAGES_CONFIG.h" from it
6238 o fix a bug in mom_fluxform (from chk51j_post)
6239
6240 checkpoint51j_post (2003/10/10)
6241 o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
6242 o adjusted some flow directives (dynamics, thermodynamics)
6243 o added cubed-sphere case to test cost function
6244 o heckpoint_lev?_directives.h now include
6245 pkg-specific directives, whenever those are enabled.
6246 o Moving pkg-specific flow directives to corresponding pkg
6247 Moving pkg-specific differentiation list to corresponding pkg
6248 Moving pkg-specific checkpoint-lev storing to corresponding pkg
6249 ---> conventions are
6250 - pkg_ad.flow
6251 - pkg_ad_diff.list
6252 - pkg_ad_check_lev?_dir.h
6253
6254 checkpoint51i_post (2003/10/09)
6255 o merge of the branch-genmake2
6256 - knowingly breaks the older genmake
6257 - automatic generation of all ALLOW_${PKG_NAME} defines
6258 - new testreport supersedes older testscript
6259 o large number of package inclusion and header cleanups
6260 checkpoint51i_pre (2003/10/08)
6261
6262 o new output for adjoin of global ocean vector invariant
6263 o fix for checkpoint of thermodynamic seaice and bulk_force
6264 o Steph gchem various cleanups
6265
6266 checkpoint 51h_pre
6267 o fixed some single quotes
6268 o modify gchem pkg to be more versatile
6269 o modifications to clean up dic pkg
6270 o add pkg/cfc
6271
6272 checkpoint51g_post (2003/10/02)
6273 o provide links for ARPACK and ADM*TLM
6274 o start removing verification/vero/
6275 o update AD-related stuff
6276 (in particular some IF-statements in model/src/ routines)
6277 o adding to verification/global_ocean.90x40x15/ adjoint of
6278 vector invariant setup
6279
6280 checkpoint51f_post (2003/10/02)
6281 o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
6282 o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
6283 of tracer Green's fucntions for ocean inversion project.
6284
6285 checkpoint51f_pre (2003/08/07)
6286 o Added on-the-fly spatial interpolation capability
6287 "USE_EXF_INTERPOLATION" to pkg/exf.
6288 - This is a temporary Cartesian-grid hack until
6289 the super-duper ESMF coupler becomes available.
6290 - See verification/global_with_exf/README for usage example.
6291 - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
6292 flags and modified pkg/seaice accordingly.
6293 o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
6294 and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
6295 non-local transport term.
6296
6297 checkpoint51e_post (2003/08/03)
6298 o pkg/mom_vecinv:
6299 - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
6300 - add time-ave diagnostic of vorticity advection.
6301 o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
6302 o atmospheric geopotential: - include water vapor effect;
6303 - use p^kappa in p* scaling.
6304 o land pkg: read initial state from files.
6305 o AIM : add stratospheric drag in the upper level
6306
6307 checkpoint51d_post (2003/07/18)
6308 o change function ILNBLNK (=> last non-blank char.) to return zero
6309 (instead of the string length) when the string. char is empty
6310 o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
6311 o modif's to restore TAMC compatibility
6312 - avoid "_d" constructs in PARAMETER declarations
6313 - avoid interrupting lines by comment lines
6314 o Use cluster local disks for purely local I/O
6315 vs. globally visible disks needed for ctrl stuff
6316 (merged from ecco-branch)
6317 - new active_file_loc... and mdsio_..._loc routines
6318 - affected packages: autodiff, ctrl, grdchk, mdsio
6319
6320 checkpoint51c_post (2003/07/08)
6321 o introducing integer flag debugLevel
6322 - debLevZero: suppress all output
6323 - debLevA: standard
6324 - debLevB: equivalent to current debugMode=.TRUE.
6325 o introducing pathname variable mdsioLocalDir for mdsio
6326 that can be specified at runtime
6327 (relevant for cluster I/O to local disk)
6328 `
6329 >>>checkpoint51b_post
6330 adjoint of ptracers
6331 o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
6332 o extended state in checkpoint_lev?, etc.
6333 o alternative ctrl/cost with tr1 or ptracer
6334 o new comlev1_bibj_ptracers
6335 o new ptracers.flow
6336 o made ptracers_forcing same as external_forcing_s
6337 o added verification for adjoint with ptracers
6338 - adm. grdchk fail so far
6339 - tlm. grdchk OK
6340 - checked tapelev/comlev recomputations: OK
6341 <<<checkpoint51b_pre
6342
6343 checkpoint51a_post (2003/06/25)
6344 o added code for biogeochemistry package
6345 - new pkgs: dic, gchem
6346 - new subroutine in ptracers
6347 o modify code for biogeo packages
6348 - in model/src and pkg/ptracers
6349
6350 checkpoint51 (2003/06/24)
6351 o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
6352 - autodiff, ctrl, exf, grdchk, seaice
6353 kept separate packages
6354 - cost, ecco, obcs
6355 o updating verification/internal_wave, verification/lab_sea
6356 (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
6357
6358 checkpoint50i_post (2003/06/23)
6359 o Preparing next differentiable checkpoint and sync
6360 of MAIN vs. ecco-branch
6361 - 1st step: this one is differentiable
6362 - 2nd step: next(! not this) checkpoint will have updated packages
6363 from ecco-branch)
6364
6365 checkpoint50h_post (2003/06/20)
6366 o new package "land": provide surface BC for AIM.
6367 o pkg/ptracers: apply exchange to all tracers after reading a pickup.
6368 o AIM: use true log-P extrapolation for near surface temp (= as in
6369 F.Molteni paper) ; update aim.5l_cs output.
6370 o New variable in PARM03 for more flexible pickups
6371 o somewhat cleaned package initialisation sequence for
6372 ctrl/ cost/ ecco/ in packages_... routines
6373
6374 checkpoint50g_post (2003/05/23)
6375 o merged with release1_p17 (pkg/seaice and verification/lab_sea)
6376 - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
6377 - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
6378 made the default because of faster convergence than ADI
6379
6380 checkpoint50f_post (2003/05/23)
6381 o exf totally restructured
6382 - replaced all exf_set_ routines by one generic exf_set_gen.F
6383 and made sure it's still differentiable
6384 - split exf_getffields.F into new exf_bulkformulae.F
6385 - exf_inscal_/exf_outscal_ suffixes consistent with field names
6386 - updated adjoint/makefile and relevant verif. accordingly
6387
6388 checkpoint50f_pre (2003/05/23)
6389 o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
6390 + change Evap over land. (update aim.5l_cs output)
6391 o added missing .cvsignores and made uniform across expts
6392 o changed configuration of tidal_basin_2d expt
6393 o added pkg/debug functions for tracing code in fatal crashes
6394 o tidied pkg/monitor to use MONITOR_OPTIONS.h
6395 o new fn in pkg/monitor to stop model if solution grows too big
6396 o removed lots of single quotes from comments
6397
6398 checkpoint50e_post (2003/05/14)
6399 o make KPP work with PTRACERS
6400 - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
6401 nearly a copy of kpp_transport_s
6402 - there is no analogue to SurfaceTendencyS, so I have to use
6403 gPtr(of the surface layer) instead
6404 o add a new platform SunFire+mpi (SunFire 15000) to genmake
6405 checkpoint50e_pre (2003/05/13)
6406
6407 checkpoint50d_post (2003/05/13)
6408 o change kpp output from multiple-record state files to single-record state
6409 files analogous to write_state.F
6410 o reduce the output frequency of cg3d-related stuff to the monitor frequency,
6411 analogous to the cg2d-related output.
6412 o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
6413 so that writing to internal file fn (with length 512) fails.
6414 checkpoint50d_pre (2003/05/12)
6415
6416 checkpoint50c_post (2003/05/12)
6417 o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
6418 o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
6419 o add time-average diagnostic of U*V and vertical diffusive flux for theta.
6420 o bug fixed in convective adjustment diagnostic (multi-tile set-up).
6421 o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
6422
6423 checkpoint50c_pre (2003/04/30)
6424 Merging from release1_p13:
6425 o bug fix for pkg/seaice dynamic solver
6426 o Added SEAICE_initialHEFF to pkg/seaice
6427
6428 checkpoint50b_post (2003/04/17)
6429 o store u*,v* in gU,V instead of in guNm1,gvNm1
6430 o in order to put the momForcing out of the Adams-Bashforth:
6431 move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
6432 to timestep.F
6433 o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
6434 o re-generate output for highly sensitive test-exp:
6435 global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
6436
6437 checkpoint50b_pre (2003/04/17)
6438 o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
6439 o corrected CPP option mismatch in exf_Bulk... functions for case
6440 #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
6441
6442 checkpoint50a_post (2003/03/21)
6443 o Bug fix for merging between c50 and KPP.
6444 ikey was passed from thermodynamics to kpp_calc via
6445 common block rather than being recomputed in kpp_calc,
6446 in contradiction with new key itdkey.
6447 New key ikppkey created, and tamc.h headers updated.
6448
6449 checkpoint50 (2003/03/08)
6450 - 2nd step of merge with ecco-branch:
6451 merge changes in ecco-branch back into main trunk
6452 - bug fix in find_alpha
6453 - more storing in gmredi_calc_tensor.F, kpp_routines.F
6454 - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
6455 - merged some sliced AD support routines
6456
6457 checkpoint49 (2003/03/06)
6458 merged from ecco-branch:
6459 o exf:
6460 - Enable initialisation of forcing fields to constant
6461 (runtime) values.
6462 - in exf_getffields.F
6463 Reduce i-/j-loop to interior domain, discarding overlaps.
6464 That also fixes wrong TAF-key computations for key_1, key_2
6465 with bulf formulae.
6466 - exf_init.F modify #ifdef for exf_init_evap
6467 - exf_getffieldrec.F, ctrl_getrec.F
6468 The following INT-usages are not safe:
6469 fldsecs = int(fldsecs/fldperiod)*fldperiod
6470 fldcount = int(fldsecs/fldperiod) + 1
6471 and were modified.
6472 o autodiff: checkpoint_lev...
6473 - updated storing for bulk formulae (some arrays were missing)
6474 - added state for seaice package
6475 - synchronized with main branch
6476 o DIVA:
6477 Modif.s in
6478 - the_main_loop.F
6479 - the_model_main.F
6480 and added cost_final_restore.F cost_final_store.F
6481 o With these changes, it is possible to fully separate
6482 the first forward run to compute the cost function (mdthe_main_loop)
6483 and adjoint runs over individual DIVA intervals (adthe_main_loop)
6484 into separate model executions.
6485 This enables better tuning of DIVA to given queue sizes.
6486 o Loss of cost function value in consecutive DIVA runs is
6487 fixed by storing to 'costfinal' file.
6488 o Appropriate call of ctrl_unpack/_pack,grdchk_main at
6489 beginning/end of adjoint integration is accounted for.
6490 The current changes apply to TAF-1.4.26.
6491 TAF has one remaining bug, requiring one manual change
6492 (see MITgcm manual).
6493 o cal: synchronized between MAIN and ecco-branch
6494
6495 checkpoint48i_post (2003/03/05)
6496 o Changes to restore differentiability of code w.r.t. previous tag
6497 (mostly adding new routines to make list and replacing
6498 pressure by totPhiHyd).
6499 o Updated and merged grdchk package
6500 - has both ADM and TLM checks
6501 - works for single- and multi-proc.
6502 - output cleaned
6503 - worked successfully for parallel DIVA
6504 o genmake:
6505 - Adding -platform=SP4
6506 - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
6507 o Modif. for DIVA:
6508 ctrl_unpack should not be called in intermediate DIVA interval.
6509 (similar thing would apply for active files such as
6510 tbar, sbar, psbar, which should not be reinitialised;
6511 only relevant for ecco-branch)
6512
6513 checkpoint48h_post (2003/02/28)
6514 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
6515 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
6516 o Added SEAICE_initialHEFF to pkg/seaice
6517 o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
6518
6519 checkpoint48g_post (2003/02/18)
6520 --- EOS:
6521 o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
6522 store total Potential in totPhyHyd for diagnostics & EOS.
6523 o fix restart and overlap Pb when using Z-coord and EOS funct. of P
6524 --- Pressure/geopotential gradient:
6525 o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
6526 o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
6527 ( changes results of global_ocean_pressure )
6528 o NLFS + z-coord.: add eta*Rho' contribution.
6529 o accurate phiHyd when using interface-W at the middle between 2 centers
6530 ( changes results of ideal_2D_oce )
6531 o includes r* 2nd term in potential gradient.
6532
6533 checkpoint48f_post (2003/02/18)
6534 Merging from release1_p12:
6535 o Modifications for using pkg/exf with pkg/seaice
6536 - improved description of the various forcing configurations
6537 - added basic radiation bulk formulae to pkg/exf
6538 - units/sign fix for evap computation in exf_getffields.F
6539 - updated verification/global_with_exf/results/output.txt
6540 o Added pkg/sbo for computing IERS Special Bureau for the Oceans
6541 (SBO) core products, including oceanic mass, center-of-mass,
6542 angular, and bottom pressure (see pkg/sbo/README.sbo).
6543 o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
6544 to avoid negative values in shallow regions.
6545 - updated verification/natl_box/results/output.txt
6546 - updated verification/lab_sea/results/output.txt
6547 o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
6548 o Added useSingleCpuIO option (see PARAMS.h).
6549 o Updated useSingleCpuIO option in mdsio_writefield.F to
6550 work with multi-field files, e.g., for single-file pickup.
6551 o pkg/seaice:
6552 - bug fix in growth.F: QNET for no shortwave case
6553 - added HeffFile for specifying initial sea-ice thickness
6554 - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
6555 o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
6556 kpp_transport_t.F, forward_step.F, and the_main_loop.F
6557 o pkg/seaice:
6558 - adjoint-friendly modifications
6559 - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
6560
6561 checkpoint48e_post (2003/02/12)
6562 o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
6563 o dynamics: change definition of computational domain & adapt mom_fluxform
6564 accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
6565 o following exp works with Olx=Oly=2 (and pass through checkbounds option):
6566 adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
6567 exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
6568 global_ocean.90x40x15 global_with_exf global_ocean_pressure
6569 inverted_barometer solid-body.cs-32x32x1
6570 (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
6571
6572 checkpoint48d_post (2003/02/09)
6573 o in preparation for r*:
6574 a) use pre-computed gradient of hydrostatic potential:
6575 changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
6576 b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
6577 => affects results of glob_oce_pressure (different truncation error)
6578 update output.txt of ideal_2D_oce & global_ocean_pressure
6579
6580 checkpoint48d_pre (2003/02/08)
6581 o in preparation for r*:
6582 new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
6583 pass the 2 comp. of the grad. as arguments to momentum S/R.
6584 but for the moment, only used if it does not change the results.
6585 o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
6586
6587 checkpoint48c_post (2003/02/06)
6588 Modifications in treatment of initial flux forcing controls
6589 to avoid extra storing of flux fields.
6590
6591 checkpoint48c_pre (2003/01/21)
6592 o Added tidal_basin_2d experiment (currently 1D!)
6593 o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
6594
6595 checkpoint48b_post (2003/01/27)
6596 o r* coordinate added in #ifdef NONLIN_FRSURF block.
6597 (modification to pressure gradient not yet implemented)
6598 o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
6599 (for U & V) that are used for vertical advection of momentum.
6600
6601 checkpoint48a_post (2003/01/24)
6602 o In preparation for r*, use temp. array to compute vertical transport
6603 in flux-form momentum pkg. => change results of few test-exp.
6604 Update output of: exp4, exp5, front_relax, global_ocean_pressure,
6605 lab_sea, natl_box & plume_on_slope
6606
6607 checkpoint48 (2003/01/23)
6608 o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
6609
6610 checkpoint47j_post (2003/01/21)
6611 o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
6612 o moved adexch from forward_step to addummy_in_stepping
6613 o added exch in ctrl_map_...
6614 o aveFreq.=0. at end of cost_final to avoid overwrite in
6615 reverse checkpointing loop
6616 o Yet more changes in gmredi:
6617 * adgmredi_calc_tensor
6618 avoiding all recomputation of gmredi_slope_limit
6619 * adgmredi_x/y/rtransport
6620 added flag for excessive storing to avoid recomp. of
6621 u/v/rtans, dTdx/y/z
6622 -> this is not really necessary and very memory-consuming
6623 * adgmredi_slope_psi:
6624 consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
6625 * gmredi_slope_limit
6626 re-activated full calculation of taperfct for case 'ac02'
6627 o updating verification/ adjoints of carbon, global_ocean.90x40x15
6628
6629 checkpoint47i_post (2003/01/13)
6630 o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
6631 o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
6632 default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
6633 o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf)
6634 o gmredi: fix few bugs.
6635
6636 checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
6637 This will be a good checkpoint to plug into the ecco-branch.
6638 o few modif.'s to get latest version adjointed
6639 (mainly kick out code in ini_linear_phisurf)
6640 o modif's to run adjoint with exactConserv
6641 o case GM_BOLUS_ADVEC should be cleaned
6642 S/R gmredi_slope_psi should be cleaned
6643 o verification/carbon now has exactConserv=.TRUE.
6644
6645 checkpoint47g_post (2003/01/10)
6646 o time-average AIM output: becomes independent from statvars time-average
6647 (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
6648 o After TAF bug fix:
6649 Tested adjoint of gmredi package.
6650 Tests were done with checkpoint47 rather than with latest
6651 checkpoint47f_post since the latter is broken for the adjoint
6652 verification/carbon/ contains both ADM and TLM gradient checks.
6653 Here they are, before they get changed/lost/stolen.
6654 Mostly modif.'s to fix numerical sensitivities.
6655 Gradient checks OK for
6656 - GM_taper_scheme:
6657 * clipping
6658 * ac02
6659 * linear
6660 * glw91
6661 * dm95
6662 * ldd97
6663 - GMREDI_OPTIONS:
6664 * GM_VISBECK_VARIABLE_K
6665 * GM_NON_UNITY_DIAGONAL
6666 * GM_EXTRA_DIAGONAL
6667 * GM_BOLUS_ADVEC
6668 in conjunction with data.gmredi parameters to be checked in
6669 in a few minutes under verification/carbon/code/
6670
6671 checkpoint47f_post (2002/12/28)
6672 Merging from release1_p10:
6673 o modifications for using pkg/exf with pkg/seaice
6674 - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
6675 and SEAICE_EXTERNAL_FLUXES
6676 - pkg/exf CPP options EXF_READ_EVAP and
6677 EXF_NO_BULK_COMPUTATIONS
6678 - usage examples are Experiments 8 and 9 in
6679 verification/lab_sea/README
6680 - verification/lab_sea default experiment now uses
6681 pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
6682
6683 checkpoint47e_post (2002/12/27)
6684 o created a tag prior to creating a branch
6685
6686 checkpoint47d_post (2002/12/16)
6687 o fixed bug in the oceanic pressure coordinates code: vertical viscosity
6688 at the bottom boundary had an erroneous half slip boundary condition
6689 o added bottom drag and no slip boundary condition capabilities to
6690 oceanic pressure coordinates code
6691 o added new verification experiment global_ocean_pressure, this experiment is
6692 also described in the tutorial section of the manual
6693 checkpoint47d_pre (2002/12/16)
6694
6695 checkpoint47c_post (2002/12/16)
6696 o Added a verification experiment for a global cubed-sphere ocean run
6697 - verification/global_ocean.cubed32x32x30
6698 - uses pkg/therm_seaice and pkg/bulk_forcing
6699
6700 o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
6701 o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
6702 when using P-coordinate; only implemented for atmospheric config.
6703 o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
6704 NOTES: requires option NONLIN_FRSURF to be "#define".
6705 o update advect_xz/results/output.txt (left from checkpoint44g_post)
6706
6707 checkpoint47b_post (2002/12/05)
6708 Merging from release1_p9:
6709 o pkg/seaice
6710 - removed GOTO's and added taf directives
6711 - double precision constants to reduce the g77 (Linux)
6712 to F77 (SGI) differences reported in release1_p8
6713 o tools/genmake
6714 - added SGI options
6715 o verification/testscript
6716 - updated to that of checkpoint47a_post
6717 o verification/global_ocean.90x40x15/input/eedata
6718 - modified for SGI f77 compatibility
6719 o verification/lab_sea
6720 - added description of sea-ice model
6721 - added missing matlab routines
6722 - added test of thermodynamics parallelization
6723
6724 checkpoint47a_post (2002/11/23)
6725 o new pkg: aim_v23
6726 = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.
6727 for now, keep the same surface forcing as before.
6728 - Part-Cell implemented into AIM; check that Heat & Water are conserved
6729 - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
6730 - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
6731 o add diagnostic of surface correction term in monitor output
6732
6733 o bulk_force and therm_seaice
6734 - Two packages: bulk_force (Bulk forcing)
6735 and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
6736 - Earlier integration from Stephaine Dutkiewicz
6737 and Patrick Heimbach.
6738 - Two ifdef statements for compile time,
6739 ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
6740
6741 checkpoint47 (2002/11/15)
6742 differentiable version of checkpoint46n_post
6743 o bug fix in quasihydrostaticterms
6744 o * "clean" adjoint code (in terms of extensive recomputations)
6745 can now be obtained for all GMREDI options (i.e. for
6746 - GM_VISBECK_VARIABLE_K
6747 - GM_NON_UNITY_DIAGONAL
6748 - GM_EXTRA_DIAGONAL
6749 - GM_BOLUS_ADVEC )
6750 * However, wrong gradient check problem remains unsolved.
6751 * New CPP options have been introduced for different
6752 tapering schemes
6753 o external_fields_load now part of differentiation list
6754 o pressure needs multiple storing;
6755 would be nice to have store_pressure at beginning or
6756 end of forward_step, e.g. by having phiHyd global (5-dim.)
6757 (NB: pressure is needed for certain cases in find_rho,
6758 which is also invoked through convective_adjustment).
6759 o recomputations in find_rho for cases
6760 'JMD95'/'UNESCO' or 'MDJWF' are OK.
6761 o #define ATMOSPHERIC_LOADING should be differentiable
6762 o ini_forcing shifted to begining of initialise_varia
6763 o Incorporating QNVS line search routines into MITgcm
6764 (this is separate code, and therefore not under pkg)
6765 lsopt/, optim/
6766 o Updated verification/carbon/
6767 - #define GM_VISBECK_VARIABLE_K
6768 - GM_taper_scheme = 'ldd97'
6769
6770 checkpoint46n_post (2002/11/12)
6771 Merging from release1_p8:
6772 o verification/natl_box:
6773 updating new external_fields_load routine
6774 o New package: pkg/seaice
6775 Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
6776 The sea-ice code is based on Hibler (1979-1980).
6777 Two sea-ice dynamic solvers, ADI and LSR, are included.
6778 In addition to computing prognostic sea-ice variables and diagnosing
6779 the forcing/external data fields that drive the ocean model,
6780 SEAICE_MODEL also sets theta to the freezing point under sea-ice.
6781 The implied surface heat flux is then stored in variable
6782 surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and
6783 kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the
6784 non-local transport term. Because this call precedes model
6785 thermodynamics, temperature under sea-ice may not be "exactly" at
6786 the freezing point by the time theta is dumped or time-averaged.
6787 N.B.: fairly large differences in accuracy occur across
6788 different platforms/compilers; comparison between
6789 g77 (Linux) and F77 (SGI Origin 2000/MIPSpro)
6790 generated output gives:
6791 T S U V
6792 C D M c m s m s m s m s
6793 n p a R g m m e . m m e . m m e . m m e .
6794 f n k u 2 i a a d i a a d i a a d i a a d
6795 g d e n d n x n . n x n . n x n . n x n .
6796
6797 Y Y Y Y 5 5 7 7 7 8 10 9 6 6 6 6 7 5 7 5 7 FAIL lab_sea
6798 o GAD:
6799 - generated new common blocks to account for call of
6800 same gad routines with differing traceridentities
6801 (needed to modify tracerIdentity indices in GAD.h)
6802 - generated separate common blocks for case useCubedSphereExchange
6803 (Department of Futurology)
6804 - parameter lists to gmredi_?transport: added tracerIdentity
6805 - added new key indices to tamc.h
6806 o external_fields_load:
6807 - added this routine to TAF list
6808 - needed to make some common blocks global and additional storing
6809 along the same lines as exf package (checkpoint_lev?_directives.h)
6810 o exf:
6811 updated external forcing package
6812 - bug fixes carried over from ecco-branch
6813 (missing OBCS_OPTIONS.h in two routines)
6814 - enable easy to use "no forcing".
6815 - added exf I/O for atmospheric loading
6816 - added exf I/O for runoff data
6817 - transfered scaling between exf <-> MITgcm to exf namelist
6818 o Adding new verification experiment global_with_exf.
6819 This verification experiment is almost identical to the
6820 global_ocean.90x40x15 experiment, except that it uses
6821 the exf (and cal) package instead of the
6822 external_fields_load routine (cf README file).
6823
6824 checkpoint46m_post (2002/11/07)
6825 o modified testscript to return -- when there are no lines of "%MON" output
6826 o added new flag "quasiHydrostatic" for QH mode
6827 and new routine quasihydrostaticterms()
6828 o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
6829 New routine: mom_u_coriolis_nh()
6830 o fixed sign of non-hydrostatic metric terms in u and v equations.
6831 Depend on correct sign of gravitySign.
6832 o added work.pc* to .cvsignore in aim directories using ifc
6833 o introduced flag for controllin non-hydrostatic metric terms
6834 o removed gravitySign from PARM04
6835 o switched to g77/ifc from pgf77 in aim experiments
6836
6837 checkpoint46l_post (2002/11/01)
6838 o made convective adjustment work with pressure coordinates:
6839 - changed the direction of k-loop in convective_adjustment.F for the
6840 case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
6841 - adjusted the reference pressure k-index in convective_adjustment.F
6842 - adjusted the convection condition in convect.F (in analogy to
6843 calc_ivdc.F)
6844 - convective_adjustment no longer computes anything on the halos
6845 - removed the warnings about negative salinity from find_rho.F and
6846 find_alpha.F; instead the new routine look_for_neg_salinity, called
6847 at the beginning of find_rho, find_alpha, and find_beta, does a
6848 check of the entire slice, if CPP-option
6849 CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
6850 checkpoint46l_pre (2002/10/23)
6851
6852 checkpoint46k_post (2002/10/23)
6853 o fixed the verification/global_ocean.90x40x15 experiment:
6854 - new bathymetry (the world according to A., JMC, and M.)
6855 - new initial fields and forcing fields (*.bin files)
6856 - new POLY3.COEFFS (for the next release one should switch to a full
6857 equation of state: JMD95P or MDJWF)
6858 - fixed several errors and redundancies in the data file
6859 - experiment uses looped cells
6860 - added matlab directory with diagnostic scripts for plotting of output
6861
6862 o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
6863 - read AIM physics parameters from a file (data.aimphys)
6864 - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
6865
6866 checkpoint46j_post (2002/10/07)
6867 o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
6868 o move wVel computation at the end of the time step, in S/R integr_continuity
6869 o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
6870 o update timeave pkg for wVel diagnostic.
6871 checkpoint46j_pre (2002/09/27)
6872
6873 checkpoint46i_post (2002/09/25)
6874 o Clean up AIM package (and keep the results unchanged):
6875 include CPP_OPTION and use IMPLICT NONE in all routines ;
6876 declare all the variables _RL ; use _d 0 for all numerical constants.
6877 use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
6878
6879 checkpoint46h_post (2002/09/25)
6880 o cleaned up the use of rhoNil and rhoConst.
6881 - rhoNil should only appear in the LINEAR equation of state, everywhere
6882 else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
6883 and the dynamical equations are all divided by rhoConst
6884 o introduced new parameter rhoConstFresh, a reference density of fresh
6885 water, to remove the fresh water flux's dependence on rhoNil. The default
6886 value is 999.8 kg/m^3
6887 o cleanup up external_forcing.F and external_forcing_surf.F
6888 - can now be used by both OCEANIC and OCEANICP
6889 checkpoint46h_pre (2002/09/18)
6890
6891 Added code to convert surface volume flux (fresh water) into
6892 a mass flux when using P coordinates in the ocean (OCEANICP).
6893 Note: It assumes you have set rho0=rhoConst=density of fresh water.
6894
6895 checkpoint46g_post (2002/09/18)
6896 o Include a new diagnostic variable phiHydLow for the ocean model
6897 - in z-coordinates, it is the bottom pressure anomaly
6898 - in p-coordinates, it is the sea surface elevation
6899 - in both cases, these variable have global drift, reflecting the mass
6900 drift in z-coordinates and the volume drift in p-coordinates
6901 - included time averaging for phiHydLow, be aware of the drift!
6902 o depth-dependent computation of Bo_surf for pressure coordinates
6903 in the ocean (buoyancyRelation='OCEANICP')
6904 - requires a new routine (FIND_RHO_SCALAR) to compute density with only
6905 Theta, Salinity, and Pressure in the parameter list. This routine is
6906 presently contained in find_rho.F. This routine does not give the
6907 correct density for 'POLY3', which would be a z-dependent reference
6908 density.
6909 o cleaned up find_rho
6910 - removed obsolete 'eqn' from the parameter list.
6911 o added two new verification experiments: gop and goz
6912 (4x4 degree global ocean, 15 layers in pressure and height coordinates)
6913 checkpoint46g_pre (2002/09/16)
6914
6915 checkpoint46f_post (2002/09/16)
6916 o Enable tangent linear (forward mode) gradient checks:
6917 - extended active file handling to g_... files
6918 - added TANGENT_SIMULATION to theSimulationMode
6919 - extended grdchk package accordingly
6920 o added tangent linear setup in verification/carbon/code_ftl
6921 o added adjoint setup in verification/front_relax/code_ad
6922
6923 checkpoint46e_post (2002/09/05)
6924 o Added new equation of state -> MDJWF
6925 - EOS of McDougall et al., 2002, JAOT, submitted
6926 - caveat: the equation of state is only valid for a smaller (more
6927 realistic?) range of values than JMD95P/Z and UNESCO
6928 - added masks to the calculation of pressure in store_pressure
6929 - added more check values for density in check_eos (ini_eos.F), some of
6930 the old check values are out of the range of the MDJWF-eos, so don't
6931 expect perfect matches for those
6932 checkpoint46e_pre (2002/08/19)
6933
6934 checkpoint46d_post (2002/08/19)
6935 o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
6936 'OCEANICP', also initialised field pressure correctly in ini_eos in the
6937 case of pressure coordinates. eosType='JMD95Z' in
6938 combination with buoyancyRelation='OCEANICP' now causes an error.
6939 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
6940 in find_alpha/beta.
6941 checkpoint46d_pre (2002/08/15)
6942
6943 o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj)
6944 so that JMD95Z and JMD95P give approptiate static stability in find_rho.
6945
6946 checkpoint46c_post (2002/08/15)
6947 o Changes necessary for ocean in p-coordinates
6948 - Added new buoyancy relation = 'OCEANICP'
6949 - Added new parameters = gravitySign (this used to be contained inside
6950 the factor dRdZ which I added when we first switched to R coordinates).
6951 X GM/Redi is not compatible (yet)
6952 X bottom drag and no-slip need to be debugged.
6953 checkpoint46c_pre (2002/08/07)
6954
6955 checkpoint46b_post (2002/08/07)
6956 o Added new equation of state -> JMD95Z and JMD95P
6957 - EOS of Jackett and McDougall, 1995, JAOT
6958 - moved all EOS parameters into EOS.h
6959 - new routines ini_eos.F, store_pressure.F
6960 o Added UNESCO EOS, but not recommended because it requires
6961 in-situ temperature (see JMD95)
6962 o Modified formatting for knudsen2.f in utils/knudsen2 and added
6963 unesco.f to be used with POLY3
6964 checkpoint46b_pre (2002/07/31)
6965
6966 checkpoint46a_post (2002/07/31)
6967 o Added (atmospheric) pressure loading
6968 - new field in FFIELDS.h, etc...
6969 - new cpp flag ATMOSPHERIC_LOADING
6970 o Changed hFacC to _hFacC in calc_phi_hyd.F
6971 o Added SHORTWAVE_HEATING to some files for consistency
6972 checkpoint46a_pre (2002/07/13)
6973
6974 checkpoint46 (2002/07/13)
6975 further merges from release1_p5
6976 o new ctrl package
6977 - adopted from ECCO environment to enable optimization
6978 - added Eliassen Palm fluxes to controls
6979 o added Eliassen Palm flux controls to gradient check package
6980 o cost package
6981 - Compatible with new ctrl package
6982 - added Eliassen Palm cost hooks
6983 - modif's of existing cost functions
6984 o Adjoint-related bug fixes in kpp:
6985 - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
6986 - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
6987 o autodiff package
6988 - flow directives:
6989 + new for S/R do_the_model_io
6990 + enhanced for S/R checkpoint
6991 + new gmredi.flow
6992 - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
6993 disable adcommon.h/g_common.h by default.
6994 - fixed problem for adjoint of global_max
6995 o modified verification/carbon/
6996 o New setup for adjoint of global_ocean
6997 o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
6998 o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
6999 o incorporated hooks for sponge layer code (external_forcing.F)
7000
7001 checkpoint45d_post (2002/07/12)
7002 o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
7003 o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
7004 (affects plume_on_slope "cg2d" output)
7005 o add new parameter deltaTfreesurf for free-surface time stepping
7006 o exchange gT,gS when using staggerTimeStep & GM & Oly<4
7007 o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
7008 o change phiMin in exp1 (to agree with documentation)
7009 o add new flags:
7010 - T,S forcing inside/outside Adams-Bashforth
7011 - turn off temp,salt advection and/or forcing
7012 - for each tracer, define internal flag for multiDimAdvection & A-B
7013 o monitor: change definition of KE to check conservation of Energy
7014
7015 checkpoint45c_post (2002/05/30)
7016 o Removed f90 comments ("!")
7017 o Modified initialisations to enable exf package for MITgcm
7018 (without invoking ECCO_PACKAGE).
7019 o modifications to gradient check package (Martin Losch)
7020 - enable centered differences
7021 - modified format of standard output
7022
7023 checkpoint45b_post (2002/05/30)
7024 o cleaned exchange calls in cg2d
7025 o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
7026 o included CPP option SINGLE_LAYER_MODE in thermodynamics
7027 to configure barotropic setup (Martin Losch)
7028 o moved some initialisations within bi,bj loop in dynamics
7029 (TAF flow dependency)
7030 o in initialise_varia, moved call packages_init_variables
7031 before convective_adjustment_init
7032 (corresponding adjustment of TAF tape initialisation).
7033 o in calc_diffusivity/calc_viscosity extended domain to full overlap.
7034
7035 checkpoint45a_post (2002/05/01)
7036 o compute Rho over the whole domain (extend iMin,jMin indices)
7037 o specific exchange for X-slice domain (case Ny=1)
7038 o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
7039 o solve_for_pressure : set cg2d_x to zero where OBCS are applied
7040
7041 checkpoint44h_post = checkpoint45
7042 o Fix to restore differentiability:
7043 place at which packages_init_variables is called in
7044 initialise_varia is crucial for reverse control flow.
7045 o modifications in GMRedi to enable stable adjoint
7046 (corresponding modif's in thermodynamics, dynamics)
7047 o added missing hook for sponge layer code in external_forcing
7048 o modified test cost functions
7049 o storing in gad_advection (plus removal of write(0,*)!
7050 o missing headers TR1.h added in convective_adjustment routines
7051 o errorMessageUnit set non-equal zero in eeboot
7052 (conflict on some platforms, e.g. IBM SP3)
7053 o modified carbon verif.
7054
7055 checkpoint44h_pre (2002/03/14)
7056 o vertical grid option: allow to put the Interface at the middle between
7057 2 cell-centers ; replace delZ in pkg/kpp by drF.
7058 o GM Advective form: Tracers are advected using the residual transport (=
7059 Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
7060
7061 checkpoint44g_post (2002/03/05)
7062 o fix surface correction term in multiDimAdvection (affects plume_on_slope
7063 results) ; ifdef missing in thermodynamics.F
7064
7065 checkpoint44f_pre,checkpoint44f_post
7066 o added PTRACERS package
7067 This allows an arbitrary number of passive tracers to be integrated
7068 forward simultaneously with the dynamicaly model.
7069 + Implemented so far:
7070 - basic forward algorithm (time-stepping, advection, diffusion, convection)
7071 - I/O and checkpointing
7072 - GM/Redi *but* using the GM/Redi coefficient of Salt
7073 + Not implemented so far:
7074 - KPP
7075 - OBCS
7076 + No specific example supplied (yet) but global_ocean.90x40x15 has the
7077 necessary data.ptracer file. Simply use -enable=ptracers and uncomment
7078 line in data.pkg.
7079 + This package is disabled by default since it increases storage.
7080
7081
7082 o testscript: added -cleanup option
7083 o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
7084 b) enable to filter 2D fields.
7085
7086 checkpoint44e_pre,post
7087 o re-wrote convective adjustment to use pre-calculated weights
7088 Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
7089 Adds: model/src/convective_weights.F, convectively_mixtracer.F
7090 Original calls to convect() still in place.
7091
7092 chkpt44d_pre,post
7093 o added missing EXCLUDE_MONITOR flags
7094 o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
7095 (incompatible typ in MIN/MAX expressions caused problems
7096 on IBM SP3)
7097 o in genmake added variable MAKEDEPEND
7098 plus resetting for case SunOS
7099 o added timer_stats.c routine for IBM SP3
7100 o removed variables in dynamics
7101 !!! I forgot to create tag chkpt44d_pre !!!
7102 !!! But chkpt44d_pre = chkpt44c_post !!!
7103
7104 o real fresh water flux implemented with non-linear free-surface.
7105
7106 chkpt44c_pre,post
7107 o few fix (mask in shap_s2, EmPmR in external_field_load,
7108 USE_NATURAL_BCS in solve_for_P);
7109 o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
7110
7111 checkpoint44b_pre/_post
7112 o merge of relevant stuff from the ecco-branch:
7113 - genmake: removed $S64 overwrite for case SunOS
7114 - pkg/exf: update and corrections for field swapping and obcs
7115 - pkg/ecco: parameter lists for the_model_main, the_main_loop
7116 harmonized between ECCO and MITgcm
7117 - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
7118 updated checkpointing_lev... lists for obcs
7119 - model/src: minor changes in forward_step, plot_field
7120 added directive for divided adjoint in the_main_loop
7121 - pkg/mdsio: added mdsio_gl_slice
7122
7123 o check parameters & config (chkpt44a_pre,post)
7124 o OBC and NonLin_FrSurf.
7125
7126 checkpoint44 (2002/01/18)
7127 o fix bug in mom_vi_del2uv
7128 o select when filters are applied ; add options to zonal_filter (data.zonfilt)
7129 o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
7130 o update AIM experiments (NCEP input files)
7131 o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
7132 o added some stuff for AD
7133
7134 checkpoint43 (2001/09/28)
7135 o added two new advection tests
7136 o added global 4x4 degree ocean test
7137 o added test of H&S94 with free surface on cube
7138 o some final mods for gradient check, adjoint,...
7139
7140 checkpoint42 (2001/09/27)
7141 Fixed AD-related problems:
7142 o Store directives up-to-date with re-arranged Adams-Bashforth
7143 (mainly thermodynamics.F)
7144 o New store directives for multi-dim. advection schemes
7145 * new CPP flag ALLOW_MULTI_DIM_ADVECTION
7146 * new common block and key passkey
7147 (mainly gad_advection.F)
7148 o Modified store directives for split of dynamics/thermodynamics
7149 for the case ALLOW_KPP
7150 o Cleaned argument list for timestep_tracer.F
7151
7152 checkpoint41 (2001/09/27)
7153 o re-formatted/added comments in prologues of key subroutines
7154 to work with protex
7155
7156 checkpoint40 (2001/09/27)
7157 o moved calc_gs, calc_gt and calc_tr1 back to model/src
7158 o added FLT (floats) package from Arne along with demo. experiment
7159 o re-arranged Adams-Bashforth scheme for tracers to allow easier
7160 implementation of forward-in-time forcing terms
7161 o more mods for non-linear free-surface including new variable
7162 o modified multi-dim method to work on cube
7163 o bug fix in KPP (from DM)
7164
7165 checkpoint40pre9 (2001/09/27)
7166 o added DST advection schemes
7167 o fix MPI bug on SGI's
7168 o modifications for non-linear free-surface
7169 o fixed conditionals for fixed flow/passive tracer only mode
7170 o added tension/strain form of stress tensor
7171 o changes to commenting of arguments for TAF/TAMC
7172 o added/updated many matlab scripts
7173 o added multi-dimensional advection method for tracers
7174
7175 checkpoint40pre8 (2001/09/05)
7176 o new package rw/
7177 Added method for dumping intermediate local arrays:
7178 mdsio_writetile - same as mdsio_writefield except works from inside
7179 bi,bj loop
7180 mdsio_writelocal - same as mdsio_writetile except works for local
7181 arrays
7182 write_local_r? - higher-level wrapper for mdsio_writelocal
7183 Controlled by diagFreq. Defaults to zero (ie. no dumps)
7184 Example given at end of mom_vecinv.F that dumps some local arrays.
7185 o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
7186 control flux-form versus vector invariant code.
7187 Switch is runtime flag vectorInvariantMomentum (defaults to false)
7188 or genmake -DISABLE ...
7189 o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
7190 (additional storing is now needed for case vecinv;
7191 currently nothing implemented to switch this storing off
7192 in case fluxform is used since no CPP flag available).
7193
7194 checkpoint40pre7 (2001/08/14)
7195 o bug fix in dynamics.F
7196 calc_viscosity called before k=1,Nr loop.
7197 o added some #ifdef's ALLOW_PASSIVE_TRACER
7198 o cleaned initialisations in ctrl_map_ini
7199 related to TAF
7200
7201 checkpoint40pre6 (2001/08/13)
7202 o split dynamics into thermodynamics & dynamics
7203 o corresponding split of calc_diffusivity into
7204 calc_diffusivity, calc_viscosity
7205 (kpp_calc_diff, kpp_calc_visc).
7206 o Added diffkr, kapgm to control variables
7207 o bug fix in gmredi_slope_limit for ldd97
7208
7209 checkpoint40pre5 (2001/07/31)
7210 o proper initialization of Adams-Bashforth time stepping
7211 + uses forward step for very first step of model (iter=0)
7212 o re-generated *all* output since almost all output is modified by this
7213 change (sorry but we've been putting this one off for about 2 years)
7214 + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
7215 *not* regenerated since they are already out of date and I don't
7216 want to create the impression that they are suddenly working.
7217 o removed KAP stuff for DEC's
7218 o modified/added many .cvsignore files in */code and */input
7219 o added new expt "solid-body.cs-32x32x1"
7220 + this uses an alternative form of ini_curvilinear_grid.F which
7221 is not necessarily any better than the current one...
7222
7223 checkpoint40pre4 (2001/07/30)
7224 o added re-initialisations of utrans,vtrans,rtrans in
7225 calc_common_factors which are crucial for TAF.
7226 o extended iMin,jMin range for calc_common_factors,
7227 calc_diffusivity
7228 o added option ALLOW_PASSIVE_TRACER
7229 o a few minor updates and fixes
7230
7231 checkpoint40pre3 (2001/07/13)
7232 o created calc_gtr1.F for gad package
7233 o split the_main_loop and re-introduced forward_step
7234 o some recomputations of nIter0 for TAMC
7235
7236 checkpoint40pre2 (2001/07/13)
7237 o Updated to latest branch of AJA, JMC
7238 o Added gradient check package
7239 o Added routines for passive tracer handling
7240 o Added carbon sequestration sensitivity experiment
7241
7242 checkpoint39 (2001/05/14)
7243 o Modifications and fixes to support TAMC
7244 (mainly missing or wrong directives)
7245 o Corrected common blocks when fooling TAMC to produce adjoint I/O
7246 in addummy_in_stepping
7247 o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
7248 o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
7249 o Included following packages:
7250 cal: calendar
7251 exf: external forcing
7252 ecco: essential routines to control use of cal, exf
7253 (NB: this is not the full ECCO environment)
7254 o disabled some packages by default in genmake
7255
7256 checkpoint38 (2001/04/10)
7257 o see notes_c37_adj.txt
7258 o corrected wrong layer index in external_forcing_t
7259 o replaced the_main_loop/forward_step by the_main_loop
7260 o removed forceoutput from write_state
7261 (replaced criteria for initial/final state)
7262 o added runtime flag for pre-C35 pickups: usePickupBeforeC35
7263
7264 checkpoint37 (2001/03/13)
7265 o mdsio.F routine split and packaged in pkg/mdsio
7266 (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
7267 used unless genmake -disable=mdsio)
7268 o allow a more precise surface-geopotential gradient for the atmosphere
7269 taking into account the change in space of Alpha (=1/rho) at the surface.
7270 o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
7271 (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
7272 o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
7273 Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
7274 [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
7275 o Time-Average diagnostics defined as a pseudo package "timeave".
7276 o pickup files : old pickup (before c35) did not work with new code (c35
7277 and after) unless activating 2 commented lines in initialise-varia.
7278 o Non-Hydrostatic pickup file Pb fixed.
7279 o bug with Rigid-lid version (since c35) fixed.
7280
7281 checkpoint36 (2001/02/20)
7282 o implement Crank-Nickelson barotropic time-stepping
7283 o recover Time-Average diagnostics
7284 o fix Pb in checkpoint (PR#19)
7285 o AIM become a standard package ; clean unused CPP_kees
7286
7287 checkpoint35 (2001/02/08)
7288 o subtantial rewrite of dynamics.f
7289 o allows staggered time-stepping
7290 o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
7291 o added bottom drag (linear + quadratic)
7292
7293 checkpoint34 (2001/01/30)
7294 o Modified exchange routines for correct reverse simulation.
7295 o Added verification output to comply with bug fix in impldiff.F
7296 as of c33 (exp2, natl_box).
7297 o Corrected store directives in dynamics.F
7298 o Corrected array boundaries in impldiff.F
7299 o Corrected array dimensions in gmredi.
7300 Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
7301 o Added routine GLOBAL_SUM_INT to global_sum.F
7302 o Added mdsio_gl.F for ECCO purposes.
7303
7304 checkpoint33 (2000/11/30)
7305 o Fixed bug in lower BC in impldiff.F
7306 o Fixed confusion about units of forcing arrays in FFIELDS.h
7307 namely Fu,Fv,Qnet,Qsw,EmPmR:
7308 - Removed verification/natl_box/code/external_fields_scale.F
7309 (did not differ from that in model/src)
7310 - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
7311 (see FFIELDS.h for description)
7312 - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
7313 kpp_calc.F and kpp_transport_t.F
7314 - Removed model/src/external_fields_scale.F and calls to it
7315 - verification/natl_box uses flux data with "atmospheric" sign so
7316 a special version of external_fields_load.F is used to
7317 change the data as it's read in. This way, the arrays
7318 have the right units and signs at all times tha a user could
7319 possibly use them.
7320 o Corrected genmake to delete a temporary file during configuration
7321
7322 checkpoint32 (2000/11/13)
7323 o Scaling of forcing fields moved from external_forcing.F to
7324 external_fields_scale.F, called directly after loading fields.
7325 o Surface relaxation terms added to surface tendency fields in
7326 extra subroutine.
7327 o impldiff.F changed to avoid storing by TAMC of huge intermediate
7328 fields.
7329 o Changes in GMRedi to comply with packaging structure.
7330 o Modifications and bug fixes in KPP package.
7331 o Verification experiment for KPP added (verification/nat_box/)
7332
7333 checkpoint31 (2000/09/11)
7334 o Packages interface brought in line with defined standard
7335 -> new routines packages_...F
7336 -> changes in initialise_fixed.F, initialise_varia.F
7337 -> enables initialisation interface for ECCO package
7338 o Rescaling of external forcing fields immediately after read
7339 (removed from external_forcing.F)
7340 -> new: surface_fields_scale.F
7341 -> affects ini_foorcing.F, external_fields_load.F
7342 o Computation of surface tendencies before tendency updates.
7343 -> new: external_forcing_surf.F
7344 o Change of variable names useGMRedi, useKPP, useECCO
7345 o Further changes in dynamics.F, impldiff.F for TAMC
7346 o Tested for experiments 0, 2, 4.
7347 - not yet tested for GMRedi.
7348 - not yet tested for KPP.
7349
7350 checkpoint30 (2000/07/13)
7351 o Updates for OBCs
7352 o New experiment for test OBCs (internal_wave)
7353 o New output.txt in verification/exp4/results/
7354 o Updates for KPP: calculation of viscosity corrected, new variables
7355 kpp_dumpFreq and kpp_taveFreq
7356 o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
7357 and entry for T90 in genmake
7358
7359 checkpoint29 (2000/06/21)
7360 o packaged KPP and GM/Redi
7361
7362 checkpoint28 (2000/06/09)
7363 o Corrected initialization of hFacMin for difference vertical coordinates
7364 o Modified calculation of partial cell thickness to more robust algorithm
7365 o config_summary.F: replaced write_1D_... by write_0D_...
7366 read_write.F: added subroutines write_0D_...
7367 o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
7368 included some initialisations required for TAMC.
7369 o routine calc_isoslopes: modified sqrt computation to make it
7370 differentiable for zero argument.
7371 o routines dynamics, impldiff:
7372 included store directives and tape key computations required for TAMC.
7373 o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
7374
7375 checkpoint27 (2000/04/10)
7376 o fixed calc_isoslopes() to so that cancellation of terms in tensor
7377 formulation works properly with variable resolution.
7378 o restructured the calling tree between the_model_main() and dynamics()
7379 o split initialise() into initialise_fixed() and initialise_varia()
7380 o introduced initialization file pSurfInitFile for free surface (cg2d_x)
7381 in new routine ini_psurf()
7382
7383 checkpoint26 (2000/04/05)
7384 o moved some #ifdef in optional routines to encompass everything
7385 except the argument declarations. This was using up some memory.
7386 o fixed macros like _ADT to work with both versions of Linux cpp
7387 o cleaned up some unused and uninitialized variables
7388 (helps when debugging with strict compile options)
7389 o split up CPP_EEOPTIONS.h into options and macros
7390 (macros are now in eesupp/inc/CPP_EEMACROS.h)
7391 o patch for 2 processor JAM mode
7392
7393 checkpoint25 (2000/03/15)
7394 o updates for OBCs and NH
7395 o dramatically reduced memory usage
7396 o added "JAM" routines for use on Artic network
7397 o parameterization of convection by implicit vertical diffusion
7398 o added a diagnostic of convective index
7399 o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
7400 (this is was partly for OBCs and NH but also in anticipation of
7401 an explicit free-surface option)
7402 o initial state input files for U and V
7403
7404 checkpoint24 (1999/08/02)
7405 o Removed some spurious "REAL"s
7406 o Updated KPP to latest version from JPL
7407 o Added a COS(latitude) in horizontal viscosity
7408
7409 checkpoint23 (1999/05/26)
7410 o Added del^4 diffusion for salt and temperature
7411 o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
7412
7413 checkpoint22 (1999/05/18)
7414 o Made many small changes: implicit none, format(i5), etc...
7415 o Introduced KPP mixing scheme (compiles and runs but *not* tested)
7416
7417 checkpoint21 (1999/05/18)
7418 o Introduced new I/O package that supports direct-access records (mdsio.F)
7419 o Split-up mid-level I/O routines
7420 o Updated input data for experiments 0,1,2,4 and 5
7421 o Finally removed the genmake.* scripts (everyone seems happy with genmake)
7422
7423 checkpoint20 (1999/03/22)
7424 o Tidied up open-boundaries some more
7425 o Added non-hydrostatic code
7426 o Fixed some input data
7427 o Modified MPI start-up to work in "coupled" context.
7428
7429 checkpoint19 (1998/12/15)
7430 o Tidied up directory structure for verification experiments.
7431 o Added new code for open boundaries.
7432 o Corrected advective terms near boundaries.
7433 o Added CPP flag for "old UV" geometry and corrected spherical geometry.
7434 o Implemented free-slip/no-slip BCs and del^4 dissipation.
7435 o Split default parameters out of ini_parms.F into set_defaults.F.
7436
7437 checkpoint18 (1998/11/30)
7438 o Further changes for optional code generation with
7439 CPP - ugh!
7440
7441 checkpoint17 (1998/11/03)
7442 o Beginning to incorporating modularity
7443 for supporting atmos. and ocean configs.
7444 o Small changes for TAMC complinace
7445 o New ultra simple test case. Barotropic box
7446 configuration "exp0".
7447
7448 checkpoint16 (1998/10/28)
7449 o Minor changes to exchange routines to support
7450 accumulation in reverse mode. Adjoint of an
7451 assignment is an addition.
7452 o Changes to support compilation by TAMC (LR(1)
7453 syntax) and by g77 under Linux ( 72 character
7454 limit ).
7455
7456 checkpoint15 (1998/09/29)
7457 Rewrote exchange routines to allow
7458 o General tile <-> tile connectivity.
7459 o TAMC reverse mode flag ( is this really needed? )
7460 o Variable width overlap and exchange region widths.
7461 o Hooks for sharing data via DMA, Arctic, Memory Channel,
7462 shmput/shmget, VIA, SYSV shmem and every other cool
7463 communication method.
7464
7465 checkpoint14 (1998/09/09)
7466 Consistent isomorphism chages made. These allow dynamical core
7467 to support both pressure and meters as a vertical coordinate.
7468
7469 checkpoint13 (1998/07/17)
7470 Release which corrects global_max problem and a couple
7471 of KGM time-averaging diagnostic errors. Also contains
7472 a double-gyre experiment setup as well as the baseline
7473 4 degree global template. The double gyre template is
7474 organised to allow it to be applied automatically to
7475 the baseline configuration.
7476
7477 branch-point-rdot
7478 A few tidy-ups have been made bt the real point of this
7479 check-point (excuse the pun) is to allow a branch to be
7480 made for the purposes of adding the rDot alterations.
7481 I don't want to commit the rDot to the main-trunk until
7482 we've actually tested it...
7483
7484 checkpoint12 (1998/07/08)
7485 Tidy up and added generic genmake script (formerly
7486 configure script).
7487 Released to testers.
7488
7489 checkpoint11 (1998/07/02)
7490 Re-arranged initialise() and introduced ini_vertical_grid()
7491 and ini_masks_etc().
7492
7493 checkpoint10 (1998/07/01)
7494 Introduced the configure script.
7495 Separated out the diags package.
7496 Added template for writing time-averages of tile/intermediate quantities.
7497 Updated SIZE.h in exp2 and made the data big-endian.
7498
7499 checkpoint9 (1998/06/22)
7500 MPI fix. Filename changes (meta/data). salbin*y stuff.
7501 General tidy-up.
7502 SST.bin SSS.bin added to verification/exp2
7503
7504 checkpoint8 (1998/06/22)
7505 Inludes time-dependant forcing and time-averaging.
7506 Works at 4x4 and 2.8125x2.8125 global
7507
7508 checkpoint7-4degree-ref
7509 Branch from checkpoint7. Released for application to
7510 global modeling and general modeling - process studies, regional
7511 model etc..
7512 Configured for verification/exp2 - 4 degree global, two process.
7513
7514 checkpoint7 (1998/06/15)
7515 Created by cnh
7516 Simple 4 degree global simulation
7517 configuration.
7518 Includes climatological wind,
7519 hydrography, bathymetry etc
7520 Does not include Heat Flux and E-P
7521
7522 checkpoint6 (1998/06/08)
7523 Created by cnh
7524 merged checkpoint5 with CD and
7525 spherical polar code.
7526 Still some problems with GM Redi
7527 abd full topography.
7528
7529 checkpoint5 (1998/06/08)
7530 Created by AJA
7531 contains updates to GM Redi
7532 and reordered timestepping loop
7533 for Implicit Diffusion.
7534
7535 checkpoint4 (1998/05/30)
7536 Created by cnh
7537 Contains memory saving macros ( _rdxc etc..) for when
7538 grid variations are limited.
7539 Contains polynomial coeffs for EOS and knudsen program
7540 for generation.
7541
7542 checkpoint3 (1998/05/26)
7543 Created by cnh
7544 Added extra flags for runtime options
7545 Added this file
7546 Added implicit free-surface
7547 Added pre-conditioner
7548 Put compare01 into repository ( compare01/... )
7549 Put data and eedata into repository ( verification/exp1 )
7550
7551 checkpoint2
7552 Created by AJA
7553 Added GM/Redi
7554
7555 checkpoint1
7556 Created by AJA
7557 Restructured kloop in dynamics.F
7558 Added non-linear EOS
7559
7560 baseline
7561 Original checked in code

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