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Revision 1.2322 - (show annotations) (download)
Thu Apr 6 16:29:09 2017 UTC (6 years, 10 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint66f
Changes since 1.2321: +2 -1 lines
new tag: checkpoint66f

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.2321 2017/04/05 03:49:11 jmc Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 checkpoint66f (2017/04/06)
8 o model/src:
9 - add specific run-time param to select level of printed plot-field-maps,
10 set by default to debugLevel. Remove internal param "printDomain".
11 o pkg/seaice:
12 - add flag to add snow mass to seaiceMassC/U/V, the default is
13 SEAICEaddSnowMass=.FALSE., not to change previous results
14 o pkg/bling
15 - Bug fix in bling_production regarding unit conversion for diagnostics
16 being put in the wrong place
17 o model/src:
18 - add back recomputation of rSurfW & S to ensure consistent column thickness
19 (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
20 when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
21 revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
22 o pkg/autodiff:
23 - clean-up "checkpoint.flow"
24 o pkg/rw (Contribution from Jody Klymak):
25 option to set mds file suffix as function of time in simulation:
26 *) new input parameter "rwSuffixType" (read from PARM03 namelist)
27 to select file suffix format; by default (=0), use iteration number;
28 *) add simple routine to return file suffix according to rwSuffixType;
29 *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
30 use new S/R to get file suffix, except for debug output file (diagFreq)
31 and pkgs offline & rbcs input files.
32 o pkg/rw:
33 - uniform processing of "I10" suffix across writing fld routines; used to
34 simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
35 (similar to cg3d.F, cg3d_ex0.F)
36 o pkg/mom_vecinv:
37 - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
38 vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
39 o pkg/bling:
40 - Many small changes intended to clean the code.
41 Unnecessary ADJOINT_SAFEs removed ;
42 removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
43 diagnostics added.
44
45 checkpoint66e (2017/03/14)
46 o pkg/exf:
47 - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
48 definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
49 use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
50 avoid any dynamic allocation ;
51 - S/R EXF_CHECK: add new check & stop when file-name is defined but not
52 read-in ; add warning when file is read-in but not used within pkg/exf ;
53 + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
54 - update exf_summary.F (print {FLD}RepCycle).
55 o verification/global_with_exf:
56 - switch on exf interpolation in AD test (just like the forward test)
57 o pkg/mom_vecinv:
58 - add storage directives to avoid recomputations within mom_vecinv.F
59 which were generating seg. fault with gfortran -devel
60 o pkg/ctrl, pkg/smooth:
61 - initialize array halos which were generating seg. fault with
62 gfortran -devel in adjoint mode
63 o pkg/exf:
64 - for each input field, enable to specify a field specific repeat-cycle
65 ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
66 o verification/lab_sea:
67 - update AD results of primary test and noseaicedyn test after switching
68 to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
69 check stays about the same.
70 o pkg/exf:
71 - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
72 - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
73 o pkg/bling, USE_EXFCO2 code:
74 - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
75 - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
76 o pkg/exf:
77 - rename S/R EXF_INIT to EXF_INIT_VARIA ;
78 - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
79 repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
80 and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
81 - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
82 EXF_INIT_FLD) and update calls in exf_init_varia.F
83 - For now, for backward compatibility, keep a simplified version of S/Rs
84 EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
85 - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
86 to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
87 o tools/genmake2:
88 - replace "bc -l" (only used once) by "expr" (already used).
89 o verification/global_ocean.cs32x15:
90 - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
91 Note: exf setting (data.exf) can be compared to other exf secondary exp
92 "seaice" (kept with useCAL=T) which has same time dependent forcing.
93
94 checkpoint66d (2017/02/13)
95 o pkg/exf:
96 - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
97 early on (in packages_boot.F) to stress this change in pkg setting.
98 - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
99 o model/src:
100 - move call to ecco_phys to end of time step; this may induce minor
101 cost function changes by shifting time averages by one time step
102 for some variables; this revision resulted in changed adjoint results
103 in MITgcm_contrib/verification_other/global_oce_cs32
104 o pkg/exf:
105 - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
106 this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
107 e.g. precip, are not available.
108 o pkg/flt:
109 - flt_init_varia.F: use pickupSuff if specified
110 - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
111 intermediate, step towards completing pkg/exch2 support within pkg/flt;
112 ifdef DEVEL_FLT_EXCH2 then:
113 - flt_init_fixed.F: comment out stop
114 - flt_exch2.F: conserve ipart, jpart (grid coordinates)
115 - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
116 - flt_mapping.F: attempt to fix longitude diagnostic near date-line
117 - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
118 o tools/genmake2 & pkg/pkg_depend:
119 - define new type of pkg dependency rule ("=pkg_x"), less strict than
120 the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
121 (-pkg_x in packages.conf).
122 - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
123 - add "+cal" to dependency list of pkg/ecco (needed to compile).
124 - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
125 o utils/matlab:
126 - adding ocean_basin routines for defining basin masks.
127 o pkg/exf:
128 - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
129 arguments, allowing to check (and stop) if parameter setting of
130 {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
131 useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
132 for backward compatibility.
133 - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
134 exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
135 o pkg/bling (USE_EXFCO2 code):
136 - fix missing setting of apco2StartTime according to apco2startdate1 & date2
137 by adding a call to S/R EXF_GETFFIELD_START.
138 o pkg/exf:
139 - allows to compile without pkg/cal (but disabled by current dependency
140 rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
141 run with useCAL=F ; this involves setting directly {FLD}StartTime instead
142 of {FLD}startdate1 & date2 ; consistency check not yet coded.
143 o verification/global_ocean.cs32x15:
144 - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
145 corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
146 o pkg/exf:
147 - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
148 calculations); change FWD experiment global_ocean.cs32x15
149 (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
150 o pkg/exf:
151 - In preparation for addition to NAMELIST, rename internal (_RL) parameter
152 {FIELD}startdate to {FIELD}StartTime
153 Note: new name also fit better the content, i.e, a start time in second.
154 o eesupp/src:
155 - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
156 o pkg/exf:
157 - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
158 to allow to read-in Sensible & Latent Heat flux ;
159 - simplify pkg/exf main options:
160 1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
161 exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
162 compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
163 2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
164 ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
165 3) improve options documentation in EXF_OPTIONS.h.
166 o pkg/ecco:
167 - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
168 ecco_summary.F: add passive tracer cost functions to gencost;
169 m_ptracer and m_boxmean_ptracer
170 o pkg/ctrl:
171 - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
172 parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
173 of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
174 xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
175 o model/src:
176 - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
177 parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
178 o pkg/exf:
179 - exf_getffields.F: add to list of implemented gentim2d contol parameters:
180 xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
181
182 checkpoint66c (2017/01/19)
183 o verification:
184 - add new option "-src" to testreport to only produce source code (*.f),
185 including taf output src code (if using '-adm'/'-tlm' option).
186 o pkg/exf:
187 - add saltflx :: Net upward salt flux in psu.kg/m^2/s
188 o pkg/diagnostics:
189 - add run-time variable diagMdsDir to specify a subdirectory for
190 diagnostic output when mds is being used and mdsioLocalDir is not.
191 o pkg/mnc:
192 - mnc_utils.F: edit stop message
193 o pkg/autodiff:
194 - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
195 add HAVE_SYSTEM bracket around system call to mkdir
196 o pkg/profiles:
197 - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
198 profiles_readparms.F: call ALL_PROC_DIE before 'stop'
199 - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
200 add HAVE_SYSTEM bracket around system call to mkdir
201 o pkg/smooth:
202 - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
203 - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
204 - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
205 o pkg/exf:
206 - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
207 issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
208 generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
209 - summary: skip detailed field report if not used (empty file-name).
210 o tools/xmakedepend:
211 - In case line editor "ed" is missing, switch to "sed" command to clean-up
212 Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
213 o pkg/exf:
214 - change definition of "hflux" input file to always include Short-Wave;
215 this is now consistent with hflux computation (if using bulk-formulae)
216 and hflux diagnostic & documentation (in EXF_FIELDS.h).
217
218 checkpoint66b (2016/12/01)
219 o model & momentum pkgs:
220 - implement fully implicit bottom friction combined with implicit surf.
221 pressure, for now, only in hydrostic formulation:
222 + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
223 and run with selectImplicitDrag=2 ;
224 + currently missing diagnostics of bottom drag and vert. viscosity tendency;
225 - partial implicit time-stepping (bot. friction + vert. visc first, then
226 surf. press) corresponding to selectImplicitDrag=1 should be applicable
227 to NH formulation but not available until we solve for surf. pressure
228 increment (instead of full etaN).
229 - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
230 with implicit vertical viscosity.
231 o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
232 - this is a first version that includes many regularisations that may
233 not all be necessary, to be sorted out,
234 - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
235 - change one verification experiment in seaice_itd to use and test new code
236 - seaice_growth: catch a case where the argument of log can be zero
237 or smaller (important for code stability)
238 o model/src:
239 - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
240 & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
241 similar A.X'=Y' system (with same matrix A) in subsequent calls;
242 switch based on errCode (In/Out) argument value; in calling routines,
243 initialise errCode before first call.
244
245 checkpoint66a (2016/10/18)
246 o pkg/bling:
247 - BLING package now loads in atmospheric pCO2 file using exf package routines
248 Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
249 o model/src & pkg/ptracers:
250 - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
251 GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
252 implicitDiffusion (respectively) are used (even without momImplVertAdv
253 or temp,salt,PTRACERS_ImplVertAdv).
254 o model/src & generic_advdiff:
255 - add parenthesis in main diagonal calculation of implicit vertical
256 diffusion matrix (impldiff.F & gad_implicit_r.F).
257 This affects results at machine truncation level; update output of many
258 verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
259 o pkg/mom_commom & generic_advdiff:
260 - add deep atmosphere and anelastic scaling factor in implicit vertical
261 advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
262 o model/src:
263 - remove few unnecessary temp array copies in solve_tridiagonal.F
264 & solve_pentadiagonal.F
265
266 checkpoint65z (2016/09/28)
267 o pkg/seaice: fix multithreading for seaice_fgmres.F
268 - remove unecessary variables from common blocks
269 - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
270 basis, that are stored in commom blocks (including integer variable i1)
271 - clean up code a little by removing commented lines that refer to
272 original code
273 - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
274 o MITgcm manual:
275 - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
276 preliminary documentation for generic controls (8.3; ctrl.tex),
277 a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
278 ecco_costfunction.tex
279 o pkg/ecco:
280 - update and cleanup list of CCP options
281 - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
282 is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
283 - add checks that retired run-time options are not used, and in relation
284 to gencost_mask and gencost_errfile
285 - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
286 gencost_nrecperiod
287 - fix m_eta computation for virtual salt flux case
288 - add m_horflux_vol case (selected via gencost_barfile) that computes
289 transports via cost_gencost_boxmean (gencost_flag=-3)
290 - use gencost_flag more systematically (i.e., avoid using gencost_name)
291 for code switches (aside from physical variable selection)
292 o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
293 attempt appears to be a bit of a hack and my need some repair down the road
294 o pkg/exf:
295 - interpolation near South Pole: fix criteria on input field latitude.
296 o pkg/icefront & pkg/exf:
297 - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
298 from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
299 o pkg/exf:
300 - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
301 "exf_output_interp" (in namelist: EXF_NML_04); change output file name
302 (add suffix "_out" instead of a prefix); keep same record number as in
303 input file but always write record 1 first (to avoid a STOP in I/O S/R).
304 Change output file content by writing interpolated field before applying
305 land-sea mask (helpful for debug).
306 - 2 compon. vector interpolation with rotation: apply scaling factor on
307 each compon. (Eastward and Northward) just before rotation.
308 o pkg/bling:
309 - Cleaned package. Removed not needed code and comments.
310 - adjoint example now works
311 (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
312 o pkg/ptracers:
313 - add Bruno Deremble's code to complete the linear surface correction
314 for tracer conservation;
315 - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
316
317 checkpoint65y (2016/07/29)
318 o pkg/debug (stats):
319 - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
320 proc/thread mapping);
321 - fix Min & Max for case where 1 thread has only empty tiles;
322 - use RL variable to count number of wet grid points (with big domain,
323 can be too large to fit into integer*4).
324 o pkg/monitor:
325 - use RL variable to count number of wet grid points (but used only for del2)
326 - add new routine to compute Advective CFL within tracer time-stepping with
327 writing delayed until next monitor output.
328 o pkg/obcs:
329 - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
330 o pkg/cal:
331 - calandar-dump: treat case myTime < timePhase in the same way as in
332 eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
333 o pkg/dic & seaice:
334 - fix compilation of ocean component for coupled atm+ocn model with
335 seaice dynamics & dic.
336
337 checkpoint65x (2016/06/11)
338 o add a license text file in main MITgcm tree.
339 o added pkg/bling:
340 - intermediate complexity biogeochemical model
341 - see bling_description.txt for details
342 - verification experiment is global_oce_biogeo_bling (for now, in
343 Contrib/verification_other/); tested daily on baudelaire with gfortran.
344 - add entry point in pkg/gchem for new pkg "bling".
345 o pkg/seaice: fix tensile stength computation
346 - replace global field tensileStrength by tensileStrFac
347 - tensileStrFac can be computed once in S/R seaice_init_varia
348 - fortunately that does not affect any verification results
349
350 checkpoint65w (2016/05/12)
351 o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
352 with ECCO_CTRL_DEPRECATED defined
353 o verification/global_ocean.cs32x15:
354 - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
355 with "selectNHfreeSurf=1".
356 o model/src (non-hydrostatic free-surface):
357 - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
358 was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
359 - Calculate surface vertical velocity after 2-D solver adjustment (accounts
360 for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
361 and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
362 This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
363 - Update output (changes at machine truncation level) of verification exp:
364 exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
365 short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
366 o pkg/seaice: ITD code
367 - fix picking up from a single category model by initialising
368 heff/area/hsnowITD = 0. in seaice_itd_pickup.F
369 - split a long warning message in seaice_check_pickup.F into two lines,
370 because NEC SX-ACE cannot deal with the long line.
371 o model/src:
372 - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
373 o pkg/seaice:
374 - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
375 o pkg/seaice:
376 - add basal stress as parameterisation for grounding ice
377 following Lemieux et al. (2015)
378 - turn on by setting new parameter SEAICEbasalDragK2 to a value
379 larger than 0. Lemieux et al. (2015) recommend 15.
380 - The adjoint complains with extra recomputations so there is also a
381 new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
382 order to postpone the problem
383 - compile the new code in lab_sea
384 o verification/halfpipe_streamice:
385 - update both TAF and OpenAD adm output (machine truncation differences)
386
387 checkpoint65v (2016/04/08)
388 o verification/advect_xz:
389 - increase overlap size from 3 to 4 and add new secondary test for PQM
390 advection scheme (with mono & wino limiter).
391 - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
392 o model/src:
393 - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
394 added phi0Ref) to set vertical axis origin and phiRef origin;
395 keep Ro_SeaLevel for backward compatibility (with a warning).
396 According to coordinate and fluid type:
397 OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
398 ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
399 OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
400 ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
401 - remove Ro_SeaLevel from ATM experiment parameter files;
402 - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
403 complement; update output.txt (changes at machine truncation level).
404 o pkg/seaice/seaice_evp.F
405 - simplify computation of deltaZ and zetaZ to simple averaging following
406 Bouillon et al. (2013). This removes a lot of code, but also changes
407 verification experiment lab_sea.hb87 -> updated
408
409 checkpoint65u (2016/03/14)
410 o pkg/generic_advdiff:
411 - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
412 with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
413 Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
414 testing and not for actual use.
415 o model/src:
416 - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
417 origin r = rF(1);
418 - add options (parameter selectP_inEOS_Zc) to select which pressure to use
419 in EOS for height coordinate: enable to include NH Pressure or to use
420 more accurate pressure vertical profile; options not linked to EOS type
421 (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
422 - start to implement variable gravity (along vertical): for now, only with
423 z-coords (not even z*).
424 - add Ideal Gas equation of state for height coordinate.
425 - update OpenAD output (affected at machine truncation level) of exp:
426 global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
427 o pkg/exf:
428 - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
429 of exf interpolation (before any rescaling, rotation or interpolation
430 to velocity point) for each field that gets loaded from file. This option
431 identically mimics the input file organization (e.g. record numbers in year
432 by year input files) besides the change in horizontal grid.
433 - add rotateStressOnAgrid run-time switch so that wind stress fields
434 can be provided on the A-grid in zonal/meridional direction and
435 rotated on the fly. This only applies to the case when the exf
436 interpolation is off and rotateStressOnAgrid is false by default.
437 o model/src:
438 - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
439 it's also used with pkg/atm_phys) and add few more parameters (but still
440 inactive, src code yet to come)
441
442 checkpoint65t (2016/02/10)
443 o pkg/atm_phys:
444 - from Ruth Geen: add optical depth dependence on CO2 concentration.
445 o model/src:
446 - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
447 for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
448 Update output of exp. deep_anelastic (changes at truncation level).
449 o tools:
450 - add a hack in "remove_comments_sed" (used only with TAF) for recent
451 version of OpenMPI (shipped with FC.23): comment out the new header
452 file "mpif-sizeof.h" which causes problems to TAF.
453 o pkg/seaice:
454 - change the termination criterion so that maxits (SEAICElinearIterMax)
455 has an effect
456 - unify iteration parameters for implicit solvers (JFNK and Picard)
457 SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
458 SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
459 SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
460 SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
461 SEAICEnonLinTol replaces JFNKgamma_nonlin
462 - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
463 - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
464 use with SEAICEuseKrylov
465 o pkg/seaice/seaice_lsr.F
466 fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
467 relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
468 an effect.
469 o pkg/seaice: add two new parameters
470 - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
471 parameter is not in any namelist)
472 - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
473 a preconditioner for the non-linear Newton iteration of the JFNK
474 solver
475 o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
476 affects some experiments at truncation level:
477 - global_ocean.cs32x15.icedyn (11 digits),
478 - global_ocean.cs32x15.seaice (11 digits),
479 - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
480 - also update global_ocean.cs32x15 adjoint and tangent-linear results
481 o pkg/salt_plume & pkg/thsice:
482 - for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
483 connect salt_plume flux to ATM-OCN coupling pkgs interface:
484 a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
485 export to coupler interface) even without compiling pkg/salt_plume ;
486 b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
487 (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
488 o pkg/dic:
489 - use the updated seaice fraction (from seaice pkgs) for DIC forcing
490 instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
491 called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
492 - move also update with values from ATM-OCN Coupler in the same new S/R
493 (previously done in ocn_apply_import.F).
494 o tools/adjoint_options:
495 - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
496 has been changed on Jan 14, 2016.
497 o pkg/ggl90:
498 - add alternative discretisation of vertical shear (off by default), to
499 compute the mean (@ grid-cell center) of vertical shear compon instead of
500 vertical shear of mean flow (@ grid-cell center).
501 - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
502 results on adjacent faces of cubed-sphere grids; this fix the restart.
503 o pkg/atm_compon_interf:
504 - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
505 pass last value, stored directly before export to CPL ;
506 Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
507 - remove atmSLPr from pickup files (no longer needed for restart)
508
509 checkpoint65s (2016/01/13)
510 o eesupp & genmake2:
511 - first check for Function ETIME and, if it fails, then check for subroutine
512 ETIME and consistent output; use the appropriate version in timers.F
513 o model/src:
514 - to check restart test, add option to apply EXCH to U,V earlier, just before
515 integr_continuity; turned off by default.
516 o pkg/dic:
517 - remove CPP option USE_ATMOSCO2 (not needed)
518 o tools/tst_2+2:
519 - try to ignore difference between +0 and -0 in binary file, causing test
520 to fail for no good reason.
521 o eesupp & genmake2:
522 - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
523 but also check (in genmake2) that test runs and returns meaningful results.
524 o coupler pkgs:
525 Finish implementation of optionally-exchanged variable switches (started on
526 Nov 12) with addition of few more exchanged fields, including 2-way exchange
527 of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
528 advection in OCN component; this requires sequential coupling.
529 coupler (pkg/atm_ocn_coupler):
530 - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
531 routines (useful for debug).
532 - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
533 flux, DIC fields) if corresponding switch is ON.
534 - add option to export RunOff to OCN (to use for DIC river input)
535 - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
536 components (pkg/atm_ & ocn_compon_interf):
537 - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
538 optionally exchanged fields; add a check & stop in cpl_readparms.F.
539 ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
540 OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
541 - rename: fracIce -> sIceFrac_cpl (<- match coupler var name)
542 + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
543 - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
544 - hold in common block coupler optionally-exchanged variable switch
545 and set default "useImportXXX" accordingly; + check & stop if inconsistent.
546 - add diagnostics for all imported fields from coupler (in both OCN & ATM);
547 this is intended to replace the OCN cplFldtave.* output files (not updated
548 to contain new additional exchanged fields).
549 o pkg/dic:
550 - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
551 o pkg/thsice:
552 - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
553 and writing of thsice pickup files.
554 o pkg/atm_compon_interf:
555 - move all field individual export-call out of cpl_export_import_data.F
556 into new S/R ATM_EXPORT_FIELDS
557 o pkg/atm_compon_interf:
558 - store state variables (for now, only thSIce fields) just before beeing
559 exported (in cpl_export_import_data.F, like on ocean side) instead of from
560 atm_store_my_data.F like all exported fluxes.
561 - new version of pickup_cpl: write field names into meta file and read meta
562 file to find field postion in pickup. Also only write/read fields meeded for
563 restart (same logic as main pickup file ; also using pickupStrictlyMatch)
564 o pkg/dic:
565 - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
566 o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
567 pressure replacement method (=1., default) or original Hibler (1979) (=0.)
568 value can be from domain [0,1] to average between the two methods
569 o pkg/atm_phys:
570 - allow to provide 2-d map of albedo and mixed-layer depth from files (but
571 hold fixed in time).
572
573 checkpoint65r (2015/12/21)
574 o pkg/seaice:
575 fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
576 solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
577 o pkg/seaice:
578 - fix a bug in computing areaS in (J-J -> J-1) that affects runs
579 when SEAICEscaleSurfStress=.TRUE.,
580 - apply areaW and areaS in S/R seaice_calc_lhs
581 o pkg/atm_phys:
582 - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
583 (shortwave & longwave, net & downward) and diagnostics of temp. tendency
584 for individual contribution (convection, LSC cond, radiation)
585 - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
586 information); activated with: solar_exponent=0. and wv_exponent=-1.
587 o pkg/ggl90:
588 - within IDEMIX add upper limit for horizontal group velocity to
589 avoid instability problems in the explicit horizontal diffusion term for
590 long time steps or high resolution
591 o pkg/diagnostics:
592 - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
593 (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
594 o testreport:
595 - remove "-v" (verbose option) in default mpirun command.
596 o pkg/seaice/seaice_growth:
597 - catch potential division by zero in ITD code, does not change
598 verification results
599 o pkg/ecco:
600 - retire old codes to the Attic. The calls to retired functions are
601 left in a commented form in case they ever need to be re-activated.
602 - ecco_check.F: issue warning if any old CPP option is
603 defined that corresponds to retired codes -- then stop.
604 o pkg/atm_compon_interf:
605 - change seaice fraction (use for OCN dic surf.flux) stored and sent to
606 coupler: use last time-step value instead of average over cplSendFrq_iter
607 time-step, similar to what is done for seaIceMass.
608 This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
609 o eesupp & genmake2:
610 - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
611 <= remove until a fix is found for some ifort version on ia32 machine.
612 o pkg/seaice/seaice_evp:
613 - refine residual computation
614
615 checkpoint65q (2015/11/18)
616 o pkg/seaice/seaice_evp:
617 - fix residual computations so that they no longer affect the actual
618 simulation code
619 - fix seaice_readparams to be able to actually set new parameters
620 SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
621 o model/src:
622 - fix wrong truncation (single prec) from "FLOAT" function in expressions
623 like: deltaT*FLOAT(myIter) when myIter is large:
624 a) replaced by DFLOAT (if not seen by TAF);
625 b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
626 o pkg/aim_v23:
627 - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
628 when pickupSuff is set ; do write rolling pickups + at the end of the run.
629 o pkg/atm_ocn_coupler + ocn_compon_interf:
630 - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
631 coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
632 add corresponding call in DO_OCEANIC_PHYS.
633 o coupler pkgs:
634 Start a new way to set-up optionally-exchanged variables (previously, only
635 there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
636 data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
637 send switch to ATM & OCN compon before reading their own "data.cpl" (so that
638 compononent param default can be set accordingly).
639 Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
640 but rather applies to a group a fields (going both ways like for DIC)
641 and corresponds to an option of coupling config.
642 coupler (pkg/atm_ocn_coupler):
643 - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
644 and read namelist directly (without eessup S/R calls) instead of
645 in the very un-flexible old way, 1 param per line, in fixed order;
646 - add error-counter to track errors (e.g., missing "data.cpl") and to stop
647 cleanly in CPL_CHECK_CPLCONFIG
648 - add new coupling-exchange selectors (some not yet active) including
649 cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
650 and ocnCpl_exchange_DIC=T in OCNIDS.h);
651 - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
652 component ; called directly from coupler.F, after comp. registrations;
653 - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
654 atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
655 -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
656 components (pkg/atm_ & ocn_compon_interf):
657 - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
658 CPP header file in all pkg source files.
659 - move checking of comp. configs out of cpl_exch_configs.F into new S/R
660 ATM/OCN_CHECK_CPLCONFIG;
661 - add error-counter to track errors (e.g., in "data.cpl") and to stop
662 cleanly in ATM/OCN_CHECK_CPLCONFIG;
663 - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
664 from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
665 before PACKAGES_READPARMS;
666 verification/cpl_aim+ocn/:
667 - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
668 "data.cpl" for coupler (in input_cpl).
669 o eesupp/inc:
670 - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
671 #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
672 to always cumulate tile local-sum in the same order (still uses
673 MPI_Allreduce like standard code).
674 - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
675 that are now identical to standard version (in eesupp/inc).
676 o pkg/shelfice:
677 - add SHELFICETransCoeffTFile for initializing spatially varying
678 heat and salt transfer coefficients
679 o pkg/atm_compon_interf & ocn_compon_interf:
680 - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
681 S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
682 - move bi,bj loops inside S/R OCN_STORE_MY_DATA
683 o pkg/atm_ocn_coupler:
684 - initialise to zero ATMVARS.h & OCNVARS.h arrays.
685 o pkg/rbcs:
686 - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
687 to compile with maskLEN=1 when all tracers use the same RBCS-mask.
688 - add a short report (to STDOUT) about RBCS-mask settings.
689
690 checkpoint65p (2015/10/23)
691 o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
692 there is no adjoint test for EVP, we don't know what it does to the adjoint
693 solution, but at least there are no more recomputation warnings left
694 o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
695 a chance of giving the same results as a fully converged VP (JFNK) solver
696 o tools/adjoint_options/adjoint_diva:
697 - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
698 o pkg/streamice:
699 - spotted bug in streamice_driving_stress using dyG where should have been dxG
700 o pkg/exf:
701 - remove STOP statement that prevented to use wind or (wind-)stress
702 interpolation for constant-in-time forcing fields (wind/stress period = 0).
703 o pkg/seaice:
704 - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
705 5 additionals 2D fields and 6 new store directives
706 - change logic in seaice_readparms.F: EVP code can now be turned on in
707 various ways, setting SEAICE_deltaTev is no longer required,
708 alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
709 or SEAICEaEVPcoeff
710 o pkg/shelfice/shelfice_thermodynamics.F
711 - redefining uLoc/vLoc to u/v, instead of 2u/v
712 o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
713 - this is an intermediate state of a truely converging EVP that has
714 the potential of outperforming implicit VP methods, I do not recommend
715 using it yet.
716 - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
717 and all parameters are hardwired
718 - for convergence it still requires very smooth regularisations, that means,
719 if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
720 different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
721 specific averaging appears to be required, still subject to tuning
722 - still needs cleaning and I need to turn parameter into runtime parameters
723 - add code to compute and print residuals of iteration, compile with
724 defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
725 o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
726 that entered with r1.54 on Sep04, 2015, -> update results
727
728 checkpoint65o (2015/09/14)
729 o pkg/mom_vecinv & mom_common:
730 - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
731 called from there.
732 - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
733 allows to use Vector-Invariant form in deep atmos and anelastic formulation
734 o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
735 and Koenig-Beatty+Holland (2012)
736 - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
737 - global 2D field tensileStrength, computed in seaice_calc_ice_strength
738 - requires an extra input argument for S/R seaice_calc_viscosities
739 - tensileStrength's depth dependence is different from Itkin et al. (2015)
740 (to be changed and played with, for now exponential)
741 o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
742 - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
743 by AREA according to Connelly et al. (2004), JPO.
744 - For EVP and the LSR solver, the implicit part of the drag term is
745 the only non-zero term in the denominator when there is no ice (which
746 prevented running the model with zero ice-ocean drag). If
747 SEAICEscaleSurfStress = .TRUE., this results in a division by zero
748 (or zero main diagonals BU/BV) which need to be caught. A practical
749 consequence is that for open water, the momentum equation reduce
750 to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
751 they happen to be zero, often leading to a non-zero solution over
752 open water.
753 o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
754 efficient EVP method.
755 - introduce area-weighted averages for e12 (analogously to
756 seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
757 remain, but also changing the order of terms in the previous average
758 changed the results as much) -> update experiment
759 - add SEAICE_DELTA_SMOOTHREG code
760 - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
761 TEM-code
762 - adjust loop bounds so that only required fields are computed
763 - add new averaging code for zetaZ/deltaZ (again similar to
764 seaice_calc_viscosities.F), inactive by default for now (will change
765 results again), but will replace old code eventually
766 o eesupp/src:
767 - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
768 to always cumulate tile local-sum in the same order
769 (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
770 Still uses MPI_Allreduce (like standard code) but on array of tiles
771 and should be faster than GLOBAL_SUM_SEND_RECV code.
772 - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
773 (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
774 - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
775 aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
776 fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
777 natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
778 tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
779
780 checkpoint65n (2015/07/29)
781 o pkg/thsice:
782 - add a warning when used with pkg/aim but without updating SST
783 (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
784 o pkg/offline:
785 - change where Offline-Fields are loaded, from load_fields_driver.F to
786 directly within FORWARD_STEP, just after updating iter number and time;
787 - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
788 S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
789 These changes allow:
790 a) to recover exactly on-line results using deltaToffline=deltaTClock,
791 tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
792 both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
793 time-step, both with GM & KPP files and with recomputing these fields;
794 b) no needs to switch on staggerTimeStep anymore;
795 c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
796 - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
797 o pkg/offline:
798 - change (rarely used) offset-iteration parameter to an offset time (in s):
799 can easily recover previous offset-iter effect by setting offset-time
800 (offlineTimeOffset) to offset-iter x deltaToffline;
801 - do not turn-off Temp & Salinity surface relaxation when using KPP (used
802 in KPP as part of surface buoyancy forcing) in offline run.
803 - fix ptracers KPP non-local term in the case where KPP is re-computed.
804 o OpenAD
805 - Adding preliminary ggl90 test to OpenAD verification.
806 Config. with ggl90 currently diverges after 64 time steps
807 so will need more work to become more stable
808 - Adding preliminary kpp test to OpenAD verification.
809 required small tweakes in kpp_routines.F
810 - Merge and update from Krishna Narayanan's contrib area:
811 * Add one variable for preliminary OpenAD DIVA
812 * Add replacement time-stepping for OpenAD DIVA
813 * genmake2 flag -diva (but only for OpenAD; preliminary)
814 * required modifs for OAD_support
815 successful preliminary test for tutorial_global_oce_biogeo/
816 o pkg/seaice:
817 - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
818 - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
819 delta with a smooth function in s/r seaice_calc_viscosity
820 (no effect on EVP)
821 - rename local suffix "sqr" into "sq" for more consistent variable names
822 o pkg/seaice:
823 add new parameter SEAICE_deltaMin that is used ***only***
824 for regularizing Delta (and nothing else, like the parameter
825 which is also used for all sorts of things SEAICE_EPS).
826 Defaults to SEAICE_EPS for backward compatibility only.
827 o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
828 the wrong key by inialising it before use -> fixes a recomputation
829 problem but does not fix the gradient
830 o pkg/layers:
831 - move resetting of flux arrays to outside the iLa loop
832 (this caused layers_diapycnal to not work with more than one layer coord.)
833 - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
834 o pkg/layers:
835 - remove from common block 3D layers fields (used to diagnose transport
836 in tracer coords) and declare them as local arrays in layers_calc.F
837 o pkg/seaice:
838 - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
839 in lab_sea forward experiment (changes results -> updated)
840 - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
841 o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
842 computations; for SEAICE_VECTORIZE_LSR
843 - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
844 sweep to the outside,
845 - remove store directives and add "CADJ loop sequential" directives
846 in analogy to model/src/solve_tridiagonal.F
847 - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
848 boundaries to yield more readable code. This has also the charming side
849 effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
850 SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
851 seaice_lsr_tridiagu/v now requires either of these flags, vectorization
852 still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
853 an additional option)
854 The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
855 but the adjoint gradients (which are affected by this change) still explode.
856 o coupler (atm & ocn _compon_interf):
857 - avoid using Exch2 IO mapping if not suitable.
858
859 checkpoint65m (2015/06/15)
860 o pkg/layers:
861 - clean-up old parameters setting (from Sep 2012):
862 + remove old parameters setting from common block (declared locally);
863 + stop if any old parameter is mixed with new parameters;
864 + check for valid or consistent parameter setting (e.g., layers_name)
865 - check that layers_bounds for Pot.Density are in the right range;
866 this is supposed to catch un-updated setting after recently shifting
867 potential density field "prho" by -1000 (now in "sigma" scale).
868 o pkg/layers:
869 - Added missing call to layers_fill for keeping track of tottend in
870 pkg/diagnostics/diagnostics_fill_state.F
871 o pkg/layers:
872 - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
873 of diapycnal fluxes
874 o pkg/layers:
875 - reverted changes to interpolation to previous treatment; there
876 was never actually a problem
877 o pkg/layers:
878 - fix interpolation of layers tracers in the presence of partial cells
879 - add lots of new functionality to compute water mass transformation
880 (enabled by CPP flag LAYERS_THERMODYNAMICS)
881 - add new calls from main code (diags_oceanic_surf_flux.F,
882 thermodynamics.F, impldiff.F) and gad to save the necessary fields
883 for layers_thermodynamics calculations
884 o pkg/ptracers:
885 - add capability of stepping a passive tracer forward without advection
886 by setting PTRACERS_advScheme to 0.
887 o pkg/diagnostics:
888 - add few (threads) _BARRIER around any update of "diag_pkgStatus".
889 o pkg/layers:
890 - shift potential density field "prho" by -1000 for density layer averaging so
891 that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
892 Note that density bin boundaries (layers_bounds in data.layers) have
893 to be set accordingly (i.e., shifted, in sigma scale).
894 o pkg/layers:
895 - fix snap-shot output of layer thickness @ V.pt and output of pot.density
896 - fix calculation of layer non-weighted velocity and layer probability
897 - add diagnostics for pot.density used for layer averaging
898 o pkg/seaice:
899 - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
900 positiveness, modify a few comments and improve variable names,
901 - the changed computation of deltaC affects most seaice-related
902 experiments at the truncation level.
903 seaice_itd.thermo is affected by far the most, with
904 only 7 digits of agreement remaining; update experiments.
905
906 checkpoint65l (2015/05/04)
907 o pkg/shelfice:
908 - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
909 factor drKp1 to zero where it is negative (ie. do not use
910 SHELFICEBoundaryLayer if hFacC>1)
911 - the same for factor drLoc in shelfice_forcing.F
912 o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
913 with modules in ptracers, when using testreport option "-small_f"
914 o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
915 - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
916 o verification/testreport
917 - add new option -small_f
918 with this option testreport first makes the target small_f (*.f files)
919 before running make (all). This is useful for explicit inlining when
920 all sources need to be full available.
921 o pkg/exf/exf_interp.F:
922 remove previous changes related to reverse (decreasing) input grids latitude
923
924 checkpoint65k (2015/04/01)
925 o pkg/ecco:
926 fix missing cosphi initialization; use eccoiter in place of optimcycle;
927 if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
928 instead of active read/write
929 o pkg/ctrl:
930 if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
931 instead of active read/write.
932 o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
933 return if .NOT.useAUTODIFF
934 o pkg/seaice: add CPP brackets (cost function related).
935 o model/src:
936 add useAUTODIFF run time switch.
937 o pkg/exf/exf_interp.F:
938 add code to allow input grids with latitude starting in the north (i.e. when
939 j=1 corresponds to northern edge of field); modify global_with_exf to test
940 this feature.
941 o verification/testreport:
942 - replace "grep -A3" with POSIX conformal sed command, because there are
943 implementations of grep that cannot do contextual searches
944 - replace "cat -n" by "nl" (two occurrences), because not all implementations
945 of "cat" have the option "-n"
946 o model/src:
947 add new file gsw_teos10.F that contains 3 functions, more or less a copy
948 of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
949 convert from conservative to potential temperature. For now they are not
950 called anywhere.
951 o pkg/ggl90: make "useIDEMIX" useful
952 - re-organize code in s/r ggl90_calc a little to move computations that
953 are different for idemix into separate loops (changes verification
954 experiment idemix at truncation level, 12 digits remain -> updated)
955 - requires 2 new 2D fields KappaM, verticalShear
956 - make hFacI and recip_hFacI local 3D variables that are passed to
957 s/r ggl90_idemix
958 - fix and improve some comments
959
960 checkpoint65j (2015/02/25)
961 o pkg/openad
962 - synchronize seawater.F with version in model/src: replace routine
963 body of sw_temp by calling sw_ptmp and fix/add a few comments.
964 o pkg/mnc:
965 - change default value of pickup_read/write_mnc params to FALSE
966 (since few features are missing in reading MNC pickup files).
967 o model/src:
968 - change default (background) vertical diffusivity for salt to be the
969 temperature (background) vertical diffusivity.
970 - change background vertical diffusivity in vertical mixing pkgs ggl90,
971 kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
972 This makes ptracers default diffusivity (that uses salt diffKr) more
973 consistent with vertical mixing schemes.
974 o verification/testreport:
975 - fix typo in "-pcls" option ;
976 - put temp files in /tmp (instead of in local dir)
977 - add option "-ncad" to use genmake2 new option "-nocat4ad"
978 - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
979 o pkg/ggl90 (idemix code):
980 - apply few fixes ; add some missing "_d 0" ; update output of exp.
981 global_ocean.90x40x15.idemix
982 o OpenAD
983 - enable active file I/O and begin removal of work-around code
984 for OpenAD for handling control variables (memory vs. active files)
985 - new CPP options file OPENAD_OPTIONS.h
986 - revert to genarr2d gradient check for hs94.1x64x5
987 - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
988 - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
989 o tools/genmake2:
990 - add option for an alternative Makefile (from Martin) where multiple
991 source files are sent to TAF (instead of all in one file).
992 o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
993 - code provided by Carsten Eden as an extension of ggl90
994 - so far the code is turned on within ggl90 by setting a CPP-flag at
995 compile time; a runtime flag implementation is not yet complete
996 - tested in new verification experiment global_ocean.90x40x15.idemix
997 o verification:
998 - reduce length of the AD test run by half for experiments
999 global_ocean.cs32x15 (std + thsice) and isomip
1000 - enable active file I/O for OpenAD, adjust verifications accordingly
1001 - halfpipe_streamice: change gradient check from genarr2d to gentim2d
1002 o verification/testreport:
1003 - fix two non-POSIX sed statements so that there are no error messages
1004 on Mac OS X
1005 - replace hostname -s with hostname | sed 's/\..*$//'
1006 o model/src/seawater.F:
1007 - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
1008 (following the matlab code), which would have avoided the bug caught
1009 by Matt (see below) in the first place
1010 o pkg/shelfice:
1011 - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
1012 and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
1013 - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
1014 ice-shelf case (i.e., within surface level).
1015 - add config summary in shelfice_check.F
1016 - remove global variable recip_SHELFICElatentHeat and replace by a local
1017 variable recip_latentHeat
1018 - introduce diagnostics for friction velocity uStar (in case of
1019 SHELFICEuseGammaFrict)
1020 - change verification experiment isomip.htd:
1021 + start from pickup (as input_ad at nIter0=8640)
1022 + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
1023 + test SHELFICEuseGammaFrict = .TRUE.
1024 + test SHELFICEadvDiffHeatFlux = .TRUE.
1025 o model/src:
1026 - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
1027 in-situ Temp) and in routine SW_TEMP (in pkg/openad);
1028 update output of experiments global_with_exf.yearly and isomip (all 6).
1029 o pkg/shelfice:
1030 - change setting of kTopC to also be zero where there is no ice-shelf.
1031 - zero out surface forcing arrays (for now, for T & S + EmPmR) where
1032 ice-shelf is.
1033 - first attempt to get RealFreshWaterFlux effects: for now, only without
1034 SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
1035 o pkg/seaice: add the option to prescribe a fixed thickness PDF
1036 for thermodynamic calculations
1037 - because of divisions of the type 7/7 not exactly equal to 1, this change
1038 affects results of some verification experiments by up to 4 digits:
1039 global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
1040 seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
1041 adjoint: lab_sea, lab_sea.noseaicedyn
1042 -> updated
1043
1044 checkpoint65i (2015/01/23)
1045 o model/src:
1046 - change units of frictionHeating field from W to W/m^2
1047 - fix bug in frictional heating from stratospheric drag in
1048 S/R ATM_PHYS_TENDENCY_APPLY_V
1049 - with synchronous time-stepping: move resetting to zero of frictionHeating
1050 field from load_fields_driver.F to thermodynamics.F ;
1051 - add diagnostics for frictional heating.
1052 o model/src & gmredi K3D:
1053 - add frictionHeating field to pickup-files (for synchronous time-stepping)
1054 - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
1055 - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
1056 and name in pickup file).
1057 - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
1058 o model/src:
1059 - move (from ini_forcing.F) initialisation of all arrays in header file
1060 FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
1061 (since Nov 2012) with option selectAddFluid=1.
1062 o pkg/shelfice:
1063 - change units (+ document) of newly added field "shelfIceMassDynTendency"
1064 - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
1065 o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
1066 o pkg/seaice: two new runtime parameters:
1067 - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
1068 long overdue
1069 - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
1070 parameterization of tensil stress for fast ice (does not do anything yet)
1071 o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
1072 for LSR: move checking overlaps out of JFNK-if-block
1073 o pkg/atm_phys:
1074 - move copy of grid and dynamical fields out of atm_phys_driver.F into
1075 new S/R ATM_PHYS_DYN2PHYS.
1076 - fix level height for Linear Free-Surf case (to be consistent with
1077 fixed-in-time pressure levels).
1078 o pkg/mom_common (bottomdrag):
1079 - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
1080 to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
1081 update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
1082 o pkg/shelfice (u/v_drag):
1083 - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
1084 - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
1085 (now similar to shelfice_u_drag.F)
1086 - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
1087 from mom_vecinv.F (similar to mom_fluxform calls).
1088 o pkg/mom_common (bottomdrag):
1089 - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
1090 - add options for alternative discretisation of velocity norm in quadratic
1091 bottom drag: averaging of grid-cell-center KE to U.point and V.point
1092 (selectBotDragQuadr=0, original code) can produce noisy patterns; this
1093 improves when averaging only the other component (e.g. vVel for U bottom
1094 drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
1095 - add options (bottomVisc_pCell) to account for partial-cell in bottom
1096 friction (no-slip BC) thus getting the true distance from the bottom;
1097 off by default since this also reduces model stability (explicit bottom
1098 friction). Changes produce different machine truncation with linear-drag
1099 + no-slip BC: update output of experiments exp4.stevens (10 digits) and
1100 front_relax (bvp & mxl, 10 & 11 digits).
1101 o model/src & mom pkgs:
1102 - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
1103 since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
1104 - for now and until vertical mixing scheme are updated to fill up level Nr+1,
1105 just copy level Nr value to level Nr+1.
1106 o doc:
1107 - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1108 o pkg/shelfice:
1109 - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1110 SHELFICE.h: move array shelficemass to init_varia, initialise
1111 from array shelficemassinit, which is set in init_fixed and
1112 has option to be set from file; introduce array
1113 shelficeMassDynTend array, set thru file in init_fixed
1114 - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
1115 shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
1116 pkg/streamice
1117 - shelfice_thermodynamics.F: call shelfice_step_icemass if
1118 SHELFICEMassStepping = .true.
1119 - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
1120
1121 checkpoint65h (2014/12/17)
1122 o verification/global_ocean.90x40x15, global_ocean_ebm:
1123 - update to generic controls.
1124 o pkg/ctrl:
1125 - ctrl_map_ini_genarr.F: test for igen>0
1126 - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
1127 - move gentim2d part of ctrl_map_ini_genarr.F to
1128 new separate routine : ctrl_map_ini_gentim2d.F
1129 - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
1130 add time variable weights and cyclic controls (time mean,
1131 seasonal cycle, etc) capabilities to gentim2d
1132 o pkg/ecco:
1133 - move reading of error, conversion to weights from
1134 ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
1135 o global_oce_llc90, cs32:
1136 - activte sbo.
1137 - CTRL_SIZE.h : add maxCtrlProc.
1138 - activate the new genctrl capabilities.
1139 - update following reorganization of global_oce_input_fields.tar.gz
1140 o pkg/ctrl/ctrl_ad_diff.list:
1141 - add missing ctrl_init_rec.f
1142 o tools/OAD_support/keepOriginal:
1143 - add ctrl_init_rec.F
1144 o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
1145 - avoid recomputations of xx_gentim2d_dummy.
1146 o momentum diagnostics:
1147 - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
1148 mom_vecinv.F to timestep.F (to include Smag-3D contribution).
1149 o pkg/seaice/seaice_lsr.F:
1150 - fix computation of BU/BV, make sure they are non-zero, only necessary
1151 for cubed sphere exchanges and SEAICE_OLx/y>0.
1152 This makes calling s/r fill_cs_corner_rl obsolete (removed).
1153 o verification/global_ocean.cs32x15/input.seaice
1154 - add test for strong implicit coupling and restricted addtive Schwarz
1155 methods for LSR
1156 - update results/output.seaice.txt
1157 o verification/tutorial_global_oce_biogeo:
1158 - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
1159 and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
1160 update output_adm,_oadm,_tlm.txt
1161 o pkg/dic:
1162 - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
1163 - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
1164 for tracer 1 & 2 is set (to avoid double counting of dilution effect).
1165 o verification/tutorial_global_oce_biogeo:
1166 - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
1167 dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
1168 update output_adm,_oadm,_tlm.txt
1169 o eesupp/src:
1170 - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
1171 and call it in seaice_lsr when using nonzero SEAICE_OLx/y
1172 o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
1173 LSR (following Hutchings et al. 2004)
1174 - introduce zetaZ as a global variable (requires adjustments in
1175 seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
1176 in seaice_calc_viscosities.F
1177 - new flag SEAICEuseStrImpCpl (default off)
1178 - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
1179 momentum equations
1180 - JFNK-solver (preconditioner) adjusted to allow using this method
1181 (where it does not have any positive effect)
1182 o pkg/seaice
1183 - add overlap for restrictive additive Schwartz method also to LSR, but
1184 turn it off by default (because it only seems to work for non-cubed
1185 sphere/llc topologies)
1186 o pkg/autodiff
1187 - add extra exchanges in addummy_in_steppging also for mnc output
1188 o pkg/seaice:
1189 - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
1190 to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
1191 o pkg/obcs:
1192 - add option to specify domain-connected piece Id along OB though files
1193 (for now, only used to diagnose PhiVel; default =1 -> global correction)
1194 - modify obcs_diag_balance.F to process each connected-part separately;
1195 exclude OB where Id = 0 but keep the full divergence there (-> constant
1196 Psi along this portion of OB and all inflow derived from grad(Phi))
1197 - add example of OB-conect files in verification/so_box_biogeo/input.
1198 o pkg/diagnostics:
1199 - improve treatment of Open-Boundaries in Velocity-Potential calculation:
1200 a) use non zero matrix element across OB and solve for Phi 1 grid point
1201 outside OB (i.e, where tracer OBCS are applied).
1202 b) global imbalance of inFlow/outFlow across OB: instead of modifying
1203 velocity across OB, spread it uniformly along the OB in the RHS.
1204
1205 checkpoint65g (2014/11/19)
1206 o pkg/diagnostcis:
1207 - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
1208 o pkg/my82,pp81,kl10:
1209 - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
1210 field diffKr as background diffusivity to set minimum diffusivity value.
1211 o pkg/seaice:
1212 - add new parameter SEAICEuseEVPrev (for revisited EVP by
1213 Bouillon et al 2013)
1214 - add SEAICE_evpAlpha/Beta to namelist
1215 - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
1216 involve trivial re-ordering of divisions/multiplications that should not
1217 have any effects, but ... they do change the results of lab_sea.hb87 so
1218 that only 2 digits of agreement remain, in line with the general
1219 instability/fragility of the evp-code. For now, I do not care and just
1220 update the verification experiment
1221 o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
1222 - remove xx_genarr2d_numsmooth etc
1223 - use xx_genarr2d_preproc etc instead
1224 - carry out smooth_correl2D at initialization stage rather than during
1225 time stepping.
1226 - get smoothOpNb from xx_gentim2d_preproc
1227 o global_oce_cs32 :
1228 - add test of generic ecco capabilities.
1229 o pkg/exf/exf_getsurfacefluxes.F :
1230 - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
1231 o pkg/ctrl,ecco :
1232 - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
1233 is defined.
1234 o pkg/seaice: add diagnostics for Delta (deformation parameter)
1235 o model/src:
1236 - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
1237 diffusivity (background) is specified but ignored.
1238 o verification:
1239 - in testreport, convert hostname to lower case for default output dir name
1240 o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
1241 o pkg/dic: add modifications from Hajoon:
1242 - add iron sedimentation flux function of the flux of PO4 out of bottom layer
1243 - light attenuation: add self-shading effect by climatological Chlorophyll
1244 (read from file).
1245 o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
1246 compiles when SEAICE_ALLOW_DYNAMICS is undefined
1247 o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
1248 AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
1249 ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
1250 approach where CPP_OPTIONS.h includes an omnipotent
1251 ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
1252 o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
1253 ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
1254 o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
1255 to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
1256 (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
1257 o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
1258 add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
1259 - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
1260 - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
1261 - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
1262 o pkg/ctrl,ecco,exf :
1263 - remove variables associated with NON-generic costs,
1264 unless ECCO_CTRL_DEPRECATED is defined.
1265 - remove NON-generic NON-obcs controls,
1266 unless ECCO_CTRL_DEPRECATED is defined.
1267 o pkg/ctrl : added ctrl_local_params.h
1268 o pkg/ecco : added ecco_local_params.h
1269 o verification : added ECCO_CTRL_DEPRECATED to most as and oad
1270 experiments, which will progressively be removed once the
1271 experiments are revised to use only generic controls/costs.
1272
1273 checkpoint65f (2014/10/13)
1274 o pkg/ctrl, ecco, seaice : minor changes in headers
1275 o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
1276 cost function and control capabilities added since checkpoint65c.
1277 o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
1278 o pkg/ecco: increase modularity and improve logic
1279 - ecco_toolbox.F (new) : basic operations that are often used,
1280 including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
1281 ecco_addcost, ecco_add, ecco_div, ecco_readbar.
1282 - cost_gencal.F (new) : determine filnames and records.
1283 - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
1284 - cost_generic.F : use spzeroloc rather than hard-coded -9999,
1285 and exploit the above functions leading to more compact code.
1286 - cost_genread.F : rm un-necessary arguments, re-arrange args order.
1287 - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
1288 using_ers, using_gfo, using_mdt is now only defined within gencost)
1289 o pkg/ecco: extend generic cost capabilities
1290 - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
1291 capabilities via gencost_preproc (+ _c,_i,_r related params),
1292 gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
1293 gencost_outputlevel arguments to cost_generic
1294 - pkg/ecco/cost_genread.F (new) : interface between cost_generic
1295 and active_read, making room for gencost_preproc to take effect.
1296 Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
1297 - pkg/ecco/cost_generic.F :
1298 compute and store misfit maks*(model-data) in localdif that is
1299 then used in cost and for output, output misfit if outlev.GT.0
1300 - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
1301 rather gencost_barfile for deciding whether to write barfile
1302 - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
1303 - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
1304 ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
1305 - pkg/ecco/ecco_summary.F : report gencost variables
1306 - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
1307 o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
1308 o pkg/ecco: internal re-organization
1309 - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
1310 (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
1311 mv relevant variables definition from ecco_cost.h to ecco.h,
1312 make sure gencost routines only include ecco.h)
1313 - throughout : add missing CCP switches, rm unused variables,
1314 and rm un-necessary CPP switches
1315 - throughout gencost routines : replace modelstartdate with
1316 gencost_startdate when needed
1317 - cost_bp_read.F : use arguments, instead of common blocs
1318 so that it can be used also by (new) cost_gencost_bpv4.F
1319 - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
1320 - ecco_phys.F : compute etanFull
1321 - ecco_readparms.F : rename using_topex as using_tpj, add
1322 bpv4-grace to gencost list, initialize added parameters
1323 - ecco_summary.F : include SIZE.h needed for augmented ecco.h
1324
1325 checkpoint65e (2014/09/28)
1326 o pkg/obcs:
1327 - replaced the just-added CPP options with run-time variables
1328 (see pkg/obcs/OBCS_PARAMS.h for details)
1329 o pkg/obcs:
1330 - add additional CPP options for sponge boundary layers
1331 (see pkg/obcs/OBCS_OPTIONS.h for details)
1332 o pkg/atm_phys:
1333 - implement simple (obliquity only, assuming circular planet orbit)
1334 seasonal cycle for incoming insolation ; used when run-time parameter
1335 "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
1336 o pkg/exf, pkg/ecco, pkg/ctrl:
1337 - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
1338 - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
1339 - implement gentim2d for xx_tauu, xx_tauv
1340 o pkg/ctrl, pkg/ecco :
1341 - fix and complement the generic controls implementation
1342 o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
1343 pkg/shelfice/shelfice_thermodynamics.F,
1344 verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
1345 verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
1346 - add weight in CTRL_GET_GEN calls
1347 o pkg/ctrl :
1348 - ctrl_get_gen.F : add weight as input parameter, and apply
1349 it directly rather than using smooth_correl2Dw (to be retired).
1350 - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
1351 o pkg/ctrl :
1352 - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
1353 ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
1354 - re-activate ctrl_summary (call in ctrl_init.F)
1355 o pkg/ctrl/ctrl_cost_gen.F :
1356 - fix CCP brackets, remove un-necessary myiter, mytime
1357 o pkg/ecco, pkg/ctrl :
1358 - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
1359 - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
1360 - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
1361 - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
1362
1363 checkpoint65d (2014/09/15)
1364 o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
1365 - add xx_genarr2d_bounds,xx_genarr3d_bounds,
1366 xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
1367 o pkg/ctrl/ctrl_map_ini_genarr.F :
1368 - remove compilation failure
1369 - replace hard coded example
1370 - use ctrl_map_ini_gen2D, 3D
1371 o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
1372 - on/off switch based upon xx_genarr2d_weight,3d
1373 o src/packages_init_variables.F :
1374 - regroup pkg/estimation calls
1375 - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1376 (moved to ctrl_init_variables)
1377 o cost/cost_init_varia.F :
1378 - remove ecco_cost_init_varia
1379 (moved to ecco_init_varia)
1380 o ctrl/ctrl_init_variables.F :
1381 - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1382 - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
1383 o ctrl/ctrl_map_ini.F :
1384 - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
1385 (moved to ctrl_init_variables)
1386 o ctrl/ctrl_map_ini_ecco.F :
1387 - remove ECCO_PHYS (mv to ecco_init_varia)
1388 - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
1389 o ecco/ecco_ad_diff.list :
1390 - add ecco_init_varia.f
1391 o ecco/ecco_init_varia.F
1392 - new routine
1393 o pkg/streamice:
1394 - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
1395 to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
1396 - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
1397 o pkg/generic_advdiff:
1398 - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
1399 o pkg/exf:
1400 - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
1401 xxg_precip capability
1402 - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
1403 o pkg/ctrl:
1404 - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
1405 o model/src/load_fields_driver.F :
1406 - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
1407 so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
1408 o OpenAD verification experiments:
1409 - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
1410 in src files (to enable to skip the ECCO_CPPOPTIONS.h);
1411 for now, only in pkgs used in OpenAD verification experiments.
1412 - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
1413 specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
1414 instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
1415 This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
1416 o OpenAD verification tests:
1417 - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
1418 - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
1419 tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
1420 - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
1421 and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
1422 o model/src & generic_advdiff:
1423 - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
1424 forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
1425 dynamics requires valid tracer forcing only over tile interior but, for
1426 some diagnostics, may need to extend it over 1 point in tile halo region.
1427 - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
1428 tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
1429 setting in temp/salt/ptracer_integrate.F
1430 o pkg/dic:
1431 - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
1432 gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
1433 in gchem_forcing_sep.F
1434 o pkg/autodiff & obcs:
1435 - add storage of current OB values for U & V (was already done for T & S).
1436
1437 checkpoint65c (2014/08/30)
1438 o pkg/dic:
1439 - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
1440 and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
1441 AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
1442 o verification:
1443 - new experiment testing OBCS and DIC pkgs, using params & output from
1444 tutorial_global_oce_biogeo but limited to a sub-domain around Drake
1445 passage: take OBCS from the last year of a 2 yrs simulation and initial
1446 conditions from t=1.yr while keeping the same forcing.
1447 o model/src:
1448 - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
1449 (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
1450 o pkg/diagnostics (Stats-Diags):
1451 - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
1452 a) refine region where stats are computed, excluding where arrhFac=0 ;
1453 b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
1454 c) extend regional stats over the region edges (for U or V pt location).
1455 o pkg/gchem:
1456 - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
1457 pkg/dic is currently changing/updating ptracers values beyond the OB).
1458 o verification (hs94):
1459 - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
1460 bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
1461 hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
1462 apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1463 o pkg/ptracers:
1464 - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
1465 switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
1466 - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
1467 with AB-2 code (so that it get tested).
1468 o model/src:
1469 - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
1470 with AB-2 code (previously only available with AB-3 code).
1471 Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
1472 to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
1473 there, by calling CYCLE_AB_TRACER).
1474 o pkg/generic_advdiff:
1475 - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
1476 GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
1477 + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
1478 S/R temp/salt/ptracers_integrate.F
1479 o model/src & pkg/ptracers:
1480 - remove common block variables gT,gS (in DYNVARS.h), except when
1481 USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
1482 - remove common block variable gPtr.
1483 o model/src & pkgs:
1484 - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
1485 ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
1486 IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
1487 GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
1488 + change accordingly all calling S/R.
1489 - use local temperature/salinity/ptracer tendency array (without bi,bj)
1490 in S/R temp/salt/ptracers_integrate.F
1491 o pkg/seaice:
1492 - move computation of stress contributions to rhsU/V in s/r seaice_lsr
1493 to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
1494 - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
1495 in seaice_lsr
1496 - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
1497 in s/r seaice_lsr_calc_coeffs
1498 o pkg/mdsio:
1499 - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
1500 (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
1501 too long (e.g., > MAX_LEN_FNAM/2 )
1502
1503 checkpoint65b (2014/08/12)
1504 o pkg/matrix:
1505 - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1506 o model/src:
1507 - fix initialisation of geothermalFile; compile geothermal-flux code in
1508 natl_box verification experiment.
1509 o model/src & pkg/down_slope:
1510 - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1511 - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1512 field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1513 results at machine truncation level: update output of experiments
1514 global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1515 o pkg/diagnostics (Stats-Diags):
1516 - do not cumulate the full volume when DIAGNOSTICS_FILL is
1517 called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1518 This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1519 times (but Min,Max and StD are still wrong).
1520 o model/src:
1521 - add geothermal flux forcing: read in ini_forcing.F as time-constant
1522 field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1523 o model/src:
1524 - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1525 _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1526 arrays are already updated while adjustments (filters, conv.adjustment) are
1527 still applied later, in S/R TRACERS_CORRECTION_STEP.
1528 o model/src:
1529 - store in common bloc array "rhoInSitu" the virtual potential temperature
1530 anomaly that is used to compute geopotential: this make the atmos code
1531 more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1532 o pkg/seaice/seaice_lsr.F
1533 - rename integer variable ilcall to ipass (that's what it is called
1534 in the residual diagnostics
1535 - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1536 default) for improved non-linear convergence of the first few steps
1537 - adjust a few comments and add new ones to explain some of the store
1538 directives
1539 o pkg/generic_advdiff (& ptracers):
1540 - re-work the code to check for valid advection scheme and for minimum
1541 size of overlap (now stored in local common bloc in gad_advscheme.F)
1542 o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1543 - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1544 - add an auxilliary variable "bet" and fix store directives and keys in
1545 seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1546 less exact gradients in my tests); but there are still
1547 recomputation warning (although gradients are sort of OK), when
1548 SEAICE_LSR_VECTORIZE is not defined, so this flag and
1549 SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1550 - update verification experiments lab_sea.
1551 - change some comments in S/R seaice_calc_viscosities
1552 o model/src:
1553 - if staggerTimeStep=T, always apply exchange to velocity field in
1554 do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1555 (independent of using multi-dim advection or not); no effect on FWD run
1556 but affects AD results (at machine truncation level): update output of
1557 experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1558 and isomip (oad: 12.d).
1559 o pkg/generic_advdiff:
1560 - stop if doAB_onGtGs is set to FALSE but ignored
1561 - refine warning related to stability of tracer time-stepping
1562 regarding internal wave dynamics.
1563 - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1564 on staggerTimeStep & implicitIntGravWave (will now get a warning
1565 if potentially unstable).
1566 o pkg/kl10:
1567 - add new pkg "kl10" for mixing due to internal wave breaking, from
1568 http://www.sciencedirect.com/science/article/pii/S1463500310000144
1569 (contribution from Jody Klymak), tested in verification experiment
1570 verification/internal_wave/input.kl10/
1571 o isomip experiment:
1572 - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1573 (input.htd) and update the output.
1574 o cd_code experiments:
1575 - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1576 #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1577 global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1578 update the corresponding output.
1579 o pkg/seaice:
1580 - reduce the number of include files and store directives in
1581 S/R seaice_lsr_tridiagu/v
1582 - change the order of loops in one case in S/R seaice_lsr_tridiagv
1583 (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1584 get rid off one store directive (a TAF bug?)
1585 - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1586 S/R seaice_lsr_tridiagv to change the loop range for consistency
1587 - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1588 - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1589 S/R seaice_lsr_tridiagu/v (requires update of
1590 offline_exf_seaice/input.dyn_jfnk)
1591
1592 checkpoint65a (2014/07/27)
1593 o model/src:
1594 - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1595 surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1596 (topo in p-coords, ice-shelf in z-coords); update output of experiments
1597 tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1598 o model/src:
1599 - collect momentum forcing tendency into local 2-D array (passed as argument
1600 to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1601 parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1602 affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1603 - collect T & S forcing tendency into local 2-D array (passed as argument to
1604 apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1605 affects results at machine truncation level (e.g., ocean: if using
1606 SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1607 correction due to vertical advection).
1608 - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1609 global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1610 seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1611 obcs_ctrl (ad & fwd grd @ 12 & 7).
1612 o pkg/ptracers & diagnostics:
1613 - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1614 title (to avoid some unexpected truncation); sort out ptracers diags units.
1615 - collect ptracer forcing tendency into local 2-D array (passed as argument
1616 to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1617
1618 checkpoint65 (2014/07/18)
1619 o pkg/fizhi:
1620 - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1621 affects results at machine truncation level. Update output of experiments
1622 fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1623 o pkg/seaice: more clean up
1624 - rename TAF common block tapes to be more consistent and remove
1625 unnecessary duplicates
1626 - add store directives to remove more recomputations, but use smaller
1627 tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1628 The idea behind this flag is to reduce the memory footprint when the
1629 adjoint of the LSR is not required. As of now, defining the flag
1630 SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1631 a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1632 For experiment offline_exf_seaice, this means on a linux box with gfortran
1633 nearly a factor of 10 (but keep in mind there is mostly seaice code in
1634 this experiment):
1635 > size mitgcmuv_ad
1636 text data bss dec hex
1637 5100659 1216 220458952 225560827 d71c8fb
1638 5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1639 but only a moderate increase of 36% for global_ocean.cs32x15:
1640 text data bss dec hex
1641 6695027 1648 1014578664 1021275339 3cdf6ccb
1642 6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1643 - note: there are still recomputations in global_ocean.cs32x15 and
1644 offline_exf_seaice and the gradient agreement changes (gets a
1645 little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1646 - in general, the AD gradients still are wrong
1647 o OpenAD
1648 - clean up code_oad/ directories somewhat by moving files
1649 dontCompile, dontTransform, keepOriginal to OAD_support/
1650 o model/src:
1651 - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1652 (not currently tested): add dissipation terms before NLFS rescaling of
1653 tendencies (previously done after).
1654 o pkg/diagnostics:
1655 - write stats-diags in ascii file with more digits (same as in monitor).
1656 o pkg/down_slope:
1657 - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1658 NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1659 o model/src:
1660 - new file "apply_forcing.F" containing all the code previously in
1661 external_forcing.F, but with new argument list: pass, as new argument,
1662 the current level tendency array to update (instead of a direct update
1663 of the common bloc array). Change the corresponding calls.
1664 - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1665 EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1666 o pkg/seaice/seaice_lsr, a little bit of clean up
1667 - rearrange some code blocks, so that now all calculations for
1668 setting up the right-hand-sides done within one single block
1669 (I find that easier to read and understand)
1670 - rearrange freedrift-code to reduce the number of ifdefs
1671 - adjust some indentations and comments
1672
1673 checkpoint64z (2014/07/10)
1674 o model/src and several pkgs:
1675 - change argument list of all S/R called from external_forcing.F and
1676 called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1677 to pass, as argument, the current level tendency array to update
1678 (instead of a direct update of the common bloc array).
1679 - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1680 - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1681 o pkg/seaice/seaice_lsr.F
1682 - always initialize local arrays in seaice_lsr_tridiagu/v
1683 - add more local tapes to seaice_lsr_tridiagu/v
1684 - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1685 keep it in bi/bj loop; this seems to be essential
1686 - gradients are still wrong but only by 4-7 orders of magnitude
1687 instead of 15 orders of magnitude, lab_sea improves a little
1688 o pkg/seaice
1689 - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1690 generates unnecessary code in seaice_lsr_ad
1691 - add more store directives in seaice_lsr to avoid unnecessary code
1692 in seaice_lsr_ad
1693 - exclude some residual computations in seaice_lsr when
1694 ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1695 in seaice_lsr_ad
1696 - add more storing, a new tape (model/src/the_main_loop.F) and
1697 another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1698 and klockey should be checked by a specialist)
1699 - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1700 and update lab_sea after previous changes in pkg/seaice below
1701 o pkg/autodiff:
1702 - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1703 viscFacInAd : run time parameters allowing for adjoint switches
1704 note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1705 o pkg/ecco:
1706 - introduce cost_gencost_boxmean.F that computes a box mean
1707 temperature (for use in adjoint sensitivity studies).
1708 o model/src/set_defaults.F : initialize viscFacAdj to 1.
1709 o pkg/mom_common/mom_calc_visc.F:
1710 - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1711 o pkg/seaice/seaice_summary.F:
1712 - statement for SEAICEadjMODE now in autodiff_readparms.F
1713 o pkg/seaice:
1714 - remove some store directives and add new ones in an effort to get
1715 finally rid off the recomputation warnings. This is successful
1716 when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1717 defined (i.e. no extensive recomputation warnings left), but there
1718 are still too many recomputations on the solver iteration level
1719 - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1720 - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1721 SEAICE_SIZE.h
1722 - add a store directive in S/R seaice_calc_viscosities
1723 o pkg/seaice (ITD code):
1724 - fix definition of Hlimit for multi-threaded case
1725 - use double precision arithmetic to compute Hlimit: this affects results;
1726 update output of experiment seaice_itd.
1727 o replace content of verification/seaice_itd
1728 - instead of a 1D column use the configuration of offline_exf_seaice
1729 to test the ice thickness distribution code with ridging
1730 - this is a first shot at this experiment
1731 - change of some defaults of ridging parameters SEAICEhStar (from
1732 100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1733 and lot of new comments.
1734
1735 checkpoint64y (2014/06/20)
1736 o pkg/seaice/seaice_reg_ridge.F:
1737 - modify the regularization of very small volumes of ice; only check
1738 total volume HEFF, and do not apply correction to individual ice
1739 classes because that leads to funny patterns in the heat and fw-fluxes
1740 into the ocean. Adjust seaice_itd/results/output.txt
1741 - replace nITD by SEAICE_multDim in loop-ranges
1742 o pkg/exf:
1743 - add code to process the case field period = -12. with UV interpolation.
1744 - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1745 into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1746 o verification/global_with_exf:
1747 - switch all fields period to -12. (was previously untested) in input/data.exf
1748 (but keep secondary test ".yearly" unchanged); update the reference output.
1749 o pkg/cal:
1750 - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1751 o pkg/exf:
1752 - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1753 to replace logical switch "exf_verbose"
1754 - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1755 o pkg/sbo:
1756 - update from Katherine Quinn: evaluate mass directly from density and SSH
1757 (budget using Finite Volume method) instead of from bottom pressure.
1758 - allow testreport to collect few selected SBO output ; tested in exp.
1759 global_ocean.90x40x15 (after updating the results, to include SBO output).
1760 - fix some multi-threading issues (in output part).
1761 o model/src & most packages:
1762 - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1763 - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1764 PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1765 "data.{pkg}" exist ; and leave the S/R (return) just after.
1766 - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1767 + call LAND_READPARMS from packages_readparms.F
1768 o pkg/seaice:
1769 - remove code that resets useThSice in S/R seaice_readparms and
1770 replace it by a warning in S/R seaice_check
1771 - remove parameter MULTDIM, replace with nITD and runtime
1772 parameter SEAICE_multDim (still hard-wired to nITD if
1773 SEAICE_ITD is defined)
1774
1775 checkpoint64x (2014/05/24)
1776 o verification/lab_sea:
1777 - update adjoint and TLM output following changes to pkg/salt_plume
1778 - un-do the update after putting back local recip_Cp in few places.
1779 o pkg/salt_plume: modifications by An Nguyen:
1780 - add capability to do brine rejection (salt-plume) as function of
1781 volume+tracers (instead of only salinity tracer).
1782 - conserve volume by exchanging volume from each kLev to above to
1783 accommodate in-coming brine volume
1784 - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1785 - switch KPP surf buoyancy due to brine forcing to 3-d
1786 (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1787 - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1788 - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1789 in East/West Arctic.
1790 o pkg/sbo:
1791 - incorporate modifications from Katherine Quinn to enable the use of sbo
1792 pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1793 output for future testreport verification (unfinished).
1794 o pkg/atm_phys:
1795 - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1796 skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1797 output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1798 o pkg/seaice
1799 seaice_calc_ice_strength.F: modify expression to avoid divisions
1800 (affects truncation)
1801 seaice_do_ridging.F: clean up the insectarium
1802 - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1803 - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1804 - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1805 - add some debugging information and error messages (warnings)
1806 o model/src: modifications relatd to atmosphere p*:
1807 - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1808 - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1809 of vertical profile tRef in geopotential background and anomaly.
1810 - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1811 and pkg/atm_phys.
1812 - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1813 fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1814 o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1815 o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1816 not used right now, but can be used in BGC packages to fix conservation.
1817 o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1818 other packages too.
1819 o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1820 SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1821 o model/src:
1822 - since we have several heat capacity (even in model/src), define "recip_Cp"
1823 as local variable (no longer in common block) to avoid any confusion.
1824 - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1825 o pkg/exf:
1826 - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1827 air density as function of air Temp, Humidity and atm pressure.
1828
1829 checkpoint64w (2014/05/02)
1830 o verification:
1831 - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1832 seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1833 code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1834 seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1835 (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1836 o model/src: for atmosphere in p* coords:
1837 - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1838 - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1839 but not yet activated.
1840 o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1841 - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1842 - this changes the results (but not for any verification experiment, because
1843 none tests this), but avoids having an extra field in the restart files
1844 o pkg/seaice: remove global variable TICE (not needed)
1845 - replace by TICES or local variable where necessary (cost_seaice_test,
1846 seaice_diagnostics_state)
1847 - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1848 - use specific read/write routines for reading and writing individual leves
1849 of a multilevel field
1850 o pkg/ctrl & model/inc:
1851 - move additional anomaly fields of control vars (related to options:
1852 ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1853 from DYNVARS.h into new header file: CTRL_FIELDS.h
1854 o pkg/seaice: some small modifications to the ridging code
1855 - make fw2ObyRidge a global variable and add the freshwater flux to
1856 seaice_growth
1857 - pass actual thickness from seaice_prepare_ridging, so that it is
1858 computed only in one place and compute it in the same way as in
1859 seaice_growth
1860 - initialise more fields in seaice_do_ridging that where cause floating
1861 point exceptions over land
1862 o pkg/seaice: preparations for ridging code and first real ridging code
1863 - move most of "PART 1" of S/R seaice_growth into a new and separate
1864 S/R seaice_reg_ridge that will both regularize the state variable after
1865 advection call the actual ridging routine;
1866 - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1867 d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1868 - remove ridging code from seaice_advdiff
1869 - clean up remaining part 1 of seaice_growth in an attempt to make it
1870 more readable (this is probably subjective)
1871 - call seaice_itd_redist once in the initialisation phase to have the initial
1872 conditions in the correct category
1873 - finally: add new ridging routine for ITD code
1874
1875 checkpoint64v (2014/04/11)
1876 o pkg/ecco:
1877 - add runtime parameters mdt[start,end]date[1,2]
1878 - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
1879 o pkg/seaice:
1880 - make deltaC a global variable, so that it can be used in ridging code
1881 - first step towards ridging: introduce new routines that compute
1882 ice strength based on ridging parameters
1883 - add diagnostic for HSNOWITD
1884 - add opnWtrFrac as a global variable (required for ridging scheme)
1885 o pkg/salt_plume + pkg/seaice/seaice_growth.F
1886 - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
1887 AREA exceeds a threshold (code contributed by I.Fenty in 2011)
1888 o verification/hs94.1x64x5:
1889 - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
1890 - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
1891 o autodiff:
1892 - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
1893 and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
1894 For now, only in pkgs used in verification/hs94.1x64x5.
1895 - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
1896 which are specific to TAF/TAMC).
1897 - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
1898 since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
1899 is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
1900 - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
1901 building mitgcmuv_ad (make adAll).
1902 o pkg/ecco:
1903 - cost_gencost_seaicev4.F:
1904 reformulate proxy cost as function of sst and local param SEAICE_freeze
1905 change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
1906 - add stop statement if old names siv4-[sst,vol] are used
1907 - add snapshots + cost reports for atmospheric longwave
1908 - remove factor 0.1 in front of wtau[u,v]
1909 - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
1910 ALLOW_TMI_SST_COST_CONTRIBUTION
1911 o pkg/atm_phys:
1912 - add some diagnostics for Short-wave and for convection S/R.
1913 o pkg/seaice/seaice_growth:
1914 - fix a bug in the lateral melt parameterization for SEAICE_ITD
1915 in seaice_growth; tempFrz needs to be computed inside the i/j-loop
1916 - rearrange loop order for better vector code in the same code block
1917 - rewrite the floeDiameter formula to have fewer divisions
1918 - (miraculously) none of this changes the results of seaice_itd
1919 o pkg/smooth:
1920 - move param smooth2Ddiffnbt to pkg/ecco
1921 o pkg/salt_plume:
1922 - salt_plume_frac.F:
1923 clean up local param names
1924 reformulate (1-frac) to frac; original 1-frac was based on swfrac code
1925 o pkg/rw:
1926 - add RS version of S/R READ_MFLDS_LEV.
1927 o pkg/streamice:
1928 - fix the restart test by writing/reading pickup_streamice files.
1929 o pkg/seaice:
1930 - refine checks for jfnk-related parameters
1931 - comment out if statement with SEAICEuseIMEX parameter as long as there
1932 is no IMEX code to avoid confusion and surprises
1933
1934 checkpoint64u (2014/03/07)
1935 o verification/MLAdjust:
1936 - rename secondary test suffix:
1937 1.leith -> A4FlxF + switch to flux-form & add side-drag
1938 0.leithD -> AhFlxF + switch to flux-form
1939 0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag
1940 0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag
1941 o pkg/mom_vecinv:
1942 - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
1943 to be before mom_calc_visc.F)
1944 - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
1945 - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
1946 this is simpler for the adjoint and for diagnostics.
1947 o model/src + pkg/momentum:
1948 - add input files for 2-D additional Western and Southern cell-edge wall
1949 (e.g., to add "thin-wall" where it is =1).
1950 - fix sideDrag option for thin-walls with Non-Lin Free-Surf
1951 using 2nd hFacZ that is computed from initial (fix domain) hFac
1952 - known limitations of thin wall implementation: not yet coded for sigma
1953 coords; not working with CD-scheme neither.
1954 o pkg/seaice:
1955 - rename recently introduced parameters from (wrong name) AB to
1956 BDF (backward difference time discretisation)
1957 - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
1958 o tools/adjoint_options:
1959 - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
1960
1961 checkpoint64t (2014/02/01)
1962 o pkg/ecco
1963 - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
1964 runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
1965 - replace hard-coded record number and period which only work for monthly
1966 with read-in runtime param that works for other periods (month,day,year)
1967 o pkg/thsice
1968 - corrected store directive fixes thsice adjoint gradient checks
1969 o genmake2 & testreport:
1970 - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
1971 in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
1972 Update testreport accordingly. No need to set "export OPENAD=true"
1973 in adjoint_options/adjoint_oad anymore (will be removed later).
1974 o pkg/shelfice:
1975 - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
1976 only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
1977 so that surface forcing applies to k=kSurf if using pkg/shelfice.
1978 o pkg/ctrl, pkg/grdchk, pkg/ecco:
1979 - Changes to make GENARR more modular (i.e. invisible if not used)
1980 o model/src/temp_integrate.F and salt_integrate.F
1981 - re-include store directives that were removed on Dec 27th.
1982 o model/src/external_forcing_surf.F
1983 - add storage directives for EmPmR and PmEpR to avoid recomputation of
1984 seaice_model in the adjoint that is problematic when seaice_model is
1985 turned off in the adjoint. The resolved issue dated back to July when
1986 EXTERNAL_FORCING_SURF call was moved.
1987 Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
1988 o pkg/exf/exf_check.F
1989 - fix a small bug again (originally found by Wentao Liu, now found again)
1990 - streamline error output
1991 o pkg/streamice and aim_v23:
1992 - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
1993 Apple's /usr/bin/cpp knows what to do:
1994 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
1995 Target: x86_64-apple-darwin13.0.0
1996
1997 checkpoint64s (2014/01/05)
1998 o tools/adjoint_options:
1999 - switch to fastopt.net TAF server (instead of default fastopt.de) for
2000 AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
2001 o model/src:
2002 - remove some unnecessary TAF storage directives in forward_step.F and
2003 in dynamics.F (note: not always removed by TAF, e.g., double storage
2004 of kappaRU,kappaRV in former version of dynamics.F).
2005 o model/src & pkg/ptracers:
2006 - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
2007 salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
2008 and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
2009 - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
2010 - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
2011 - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
2012 o useSingleCpuInput separates single-CPU input from single-CPU output;
2013 for now only implemented for in exf_interp_read.F
2014 o verification/advect_xy:
2015 - fix missing EXCH call in local version of ini_salt.F and update output.
2016 o momentum diagnostics:
2017 - fix which deltaT is used in Total-Tendency diagnostics.
2018 - fix typo in diagnostics for momentum tendency from AB.
2019 o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
2020 SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
2021
2022 checkpoint64r (2013/12/08)
2023 o verification/*/results:
2024 - Update reference output of experiments that were passing with just 13 digits
2025 (make it easier to detect future changes in results)
2026 o model/src & pkg/ptracers:
2027 - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
2028 inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
2029 to inside ptracers_integrate.F ; remove ptracers_advection.F
2030 o coupling interface pkgs:
2031 [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
2032 - change the config check to test the agreement of Ocean Depth
2033 with ATM land/sea mask (instead of ATM orography);
2034 - send to coupler the number of coupler time-steps to do for this run:
2035 this allows to check for consistency and don't need anymore to be
2036 specified in parameter file "data";
2037 in coupler:
2038 - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
2039 - improve report to log-file of config setting (pass log-file unit to few S/R)
2040 o pkg/compon_communic:
2041 - add coupling send/receive for non-tiled integer vector;
2042 - add S/R to check and stop if any proc has an error (similar to
2043 eesupp/src/stop_if_error.F but single thread and across Comm_World).
2044 o pkg/exch2:
2045 - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
2046 through list of all tiles my proc owns.
2047 o model/src:
2048 - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
2049 from rTrans) to simplify dependencies (no need to store rTrans anymore in
2050 calling S/R); this affects AD results at machine truncation level:
2051 update AD-output (TAF) of experiments: 1D_ocean_ice_column,
2052 bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
2053 o tools/build_options:
2054 - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
2055 o coupling interface pkgs:
2056 [compon_communic, atm_compon_interf & ocn_compon_interf]
2057 - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
2058 to each S/R that needs it; remove un-used variables.
2059 - change component tile registration (cpl_register.F in both compon_interf
2060 and mitcomponent_tile_register.F) to pass the full list of tiles
2061 information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
2062 - with pkg/exch2: adopt the same convention used for I/O to define mapping
2063 towards coupler global array (unless W2_useE2ioLayOut=F):
2064 a) can now use different tiling between atm & ocn comp.
2065 b) no needs to modify the run-Off map when changing tiling (was needed
2066 even if using the same tiling between atm & ocn).
2067 c) will allow to run with blank-tiles in 1 component (e.g., for ocean
2068 full land tiles); not yet tested.
2069 - check for valid mapping from comp. tile to coupler global array
2070 - improve report of tile registration results to log file.
2071 o pkg/exch2:
2072 - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
2073 tile-registration (CPL_REGISTER);
2074 - activate (un-comment) definition and setting of "W2_tileIndex" list to
2075 store the local bi,bj indices of each tile;
2076 - also print bi,bj in local report to log file;
2077 - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
2078 Jun 2009 modif of pkg/exch2).
2079 o testing on baudelaire:
2080 - run 2 tests at a time: no significant slow down (since enough cpu) and
2081 get the full set of test done earlier
2082 - switch the ifort test to "-devel" ; run the OpenAD test everyday.
2083 o model/src/thermodynamics.F and routines called from it:
2084 - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
2085 gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
2086 velocity (outp) by adding bolus velocity.
2087 - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
2088 mass transport from velocity + lateral grid cell area
2089 - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
2090 - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
2091 in thermodynamics.F
2092 - remove k from thermodynamics.F and move it to temp_integrate.F
2093 salt_integrate.F and ptracers_integrate.F (now done inside the tracer
2094 loop).
2095 - compute locally (in thermodynamics.F) 3-D velocity field that is used to
2096 advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
2097 PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
2098 GAD_IMPLICIT_R and PTRACERS_IMPLICIT
2099 - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
2100 global_ocean.90x40x15, tutorial_global_oce_biogeo and
2101 tutorial_tracer_adjsens (+ TLM output).
2102 o tools/OAD_support and (verification/*/) code_oad:
2103 - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
2104 module conversion ; remove unneeded CPP_EEOPTIONS.h.
2105 - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
2106 version (closer to model/inc/CPP_OPTIONS.h).
2107 o model/src:
2108 - remove parameter "useOldFreezing" from PARAMS.h and push it to the
2109 retired list of parameters (routine FREEZE has been replace by surface
2110 freezing (10.yrs ago) and by pkg/frazil (interior freezing).
2111 o pkg/gmredi:
2112 - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
2113 velocity (same scheme but affects machine truncation) for GM_AdvForm.
2114 - update output of FWD experiments: front_relax.bvp,
2115 global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
2116
2117 checkpoint64q (2013/11/17)
2118 o verification:
2119 - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
2120 tutorial_global_oce_biogeo and global_ocean.90x40x15.
2121 - generate new output (growth & melt) for seaice_itd experiment after
2122 updating the input pickup_seaice files (previously wrong).
2123 o pkg/cost:
2124 - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
2125 (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
2126 o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
2127 cannot be applied to var in common block).
2128 o allows to get results independent of tile-per-proc setting (if using
2129 slower GLOBAL_SUM_SEND_RECV option).
2130 - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
2131 thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
2132 forward gradients: update output).
2133 - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
2134 S/R and, for most exp., also comment out GLOBAL_SUM_R8.
2135 o pkg/mom_common:
2136 - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
2137 code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
2138 viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
2139 ensure that all field value that are used are set.
2140 o tutorial_deep_convection (smag3d):
2141 - add missing scaling in mom_calc_smag_3d.F;
2142 - set smag3D_coeff in input.smag3d such that results do not change.
2143 o pkg/dic:
2144 - change dic_cost.F to compute cost on each tile first and then apply
2145 GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
2146 tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
2147 - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
2148 o eesupp/src & pkg/mdsio:
2149 - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
2150 (from pkg/mdsio) since they are no longer used for tape IO.
2151 - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
2152 (+ keep a copy in pkg/atm_ocn_coupler).
2153 o verification/isomip:
2154 - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
2155 o tools/build_options:
2156 - optfile linux_amd64_ifort11, fast (no ieee) case:
2157 to get a working restart for all experiments, add "-fp-model source"
2158 to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
2159
2160 checkpoint64p (2013/10/20)
2161 o pkg/autodiff:
2162 - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
2163 criteria, return to simple (default) tape IO format.
2164 o pkg/mdsio (+ eesupp/src):
2165 - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
2166 previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
2167 - fix globalFile and singleCpuIO options using simpler global mapping.
2168 - new pairs of scatter/gather vector S/R (one for each type, generated from
2169 template) corresponding to simpler global mapping.
2170 - adread_write.F: switch to new S/R (but leave old calls commented) and write
2171 to globalFile when parameter globalFiles is set to True.
2172 - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
2173 o pkg/autodiff:
2174 - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
2175 with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
2176 missing, just add a STOP if array type do not match.
2177 o pkg/exf:
2178 - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
2179 rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
2180 and rename array obsSIce to exf_iceFraction.
2181 o tutorial_deep_convection:
2182 - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
2183 for now all in this exp. code dir.
2184 - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
2185 testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
2186 o eesupp/src:
2187 - added SINGLE_DISK_IO option because reading of parameter files on
2188 very large number of processors did not work with existing set-up
2189
2190 checkpoint64o (2013/09/25)
2191 o pkg/atm_phys & atm_compon_interf:
2192 - allows for coupling of gray-atmosphere (atm_phys) with ocean.
2193 o tools/build_options:
2194 - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
2195 & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
2196 remove CPP setting (was identical to genmake2 default).
2197 o pkg/gmredi & model/src: Some updating and work done on the residual model.
2198 - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
2199 - fixed up the calculation of the eddy stress and how it is added to the
2200 external forcing via taueddy_external_forcing.F
2201 - at the moment, it is very experimental and only works with the variable eddy
2202 diffusivity calculated in gmredi_k3d.F
2203 o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
2204 lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
2205 o testreport (& tools/do_tst_2+2):
2206 - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
2207 o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
2208 - remove CPP='cpp -traditional -P' (this is genmake2 default)
2209 - add switch (for big setups) to use 'medium' memory-model (but leave it
2210 commented out for now). Note: needed with FC 19 to compile big setups.
2211 o pkg/atm_compon_interf:
2212 - regroup per field origin (model & pkgs) the coupling storage routines
2213 (which accumalate in time each coupling field)
2214 - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
2215 update accordingly + simplify aim_do_physics.F
2216
2217 checkpoint64n (2013/08/26)
2218 o pkg/bbl:
2219 - update formulation to reduce dispersion of tracer properties in bbl
2220 - replaced horizontal and vertical transport parameters with velocities
2221 - changes results for verification/global_with_exf.yearly
2222 o verification/halfpipe_streamice:
2223 - change to matrix construction; update both Fwd & AD output.
2224 o verification/tutorial_tracer_adjsens:
2225 - OpenAD test: switch to vector-invariant momentum since fluxform with
2226 rStar causes problems with OpenAD; update output.
2227 o tools:
2228 - genmake2: define a common prefix for all temp-file names ; move them
2229 to local /tmp disk (but would be easy to move them back);
2230 - xmakedepend: apply the same switch for temp-files.
2231 o pkg/offline:
2232 - changes for use with rStar (NLFS): assume that we continue to provide
2233 UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
2234 output files) and apply r* scaling at each time-step (function of the time
2235 varying Eta field); use normal pickup files (needed for restart with NLFS).
2236 o adjoint with OpenAD:
2237 - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
2238 package openad. This package has to be compiled for all runs with OpenAD
2239 instead of specifying code_oad_all as a modification directory.
2240 - link the fortran templates from tools/OAD_support to the build directory
2241 for preprocessing to avoid conflicts between different setups compiled
2242 simultaneously and simplify cleanup.
2243 o pkg/exf:
2244 - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
2245 main model or other pkgs are exchanged in EXF_MAPFIELDS).
2246 o model/src:
2247 - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
2248 (similar to do_fields_blocking_exchanges.F).
2249 o tools/genmake2:
2250 - remove TAF output src code just before calling staf (when not doing a fresh
2251 built, will stop if things go wrong with staf).
2252 - fix target "adobj" (left from TAF version-2 transition)
2253 o pkg/diagnostics:
2254 - add a parameter to track the status of pkg/diagnostics activation;
2255 this replace/extend the use of logical param "settingDiags" (to check
2256 when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
2257 New S/R to print error message and stop when pkgStatus is not right.
2258 - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
2259
2260 checkpoint64m (2013/08/13)
2261 o model/inc:
2262 - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
2263 8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
2264 o pkg/kpp & aim_v23:
2265 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
2266 o pkg/seaice:
2267 - restore (last time on 2011/12/24) ability to compile pkg/seaice with
2268 undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
2269 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
2270 o eesupp/src:
2271 - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
2272 in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
2273 o switch to TAF version-2:
2274 - add flow directives to "freeze" naming convention for ad-routines that
2275 are used in I/O routines of adjoint state and associated common blocks
2276 that are used in adcommon.h (backward compatible with version-1)
2277 - update all ad-optfiles (in tools/adjoint_options + few local to some
2278 verification exp) to switch to latest TAF version (currently 2.5.5);
2279 merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
2280 out except for diva).
2281 - the major change with TAF version-2 is that both the differentiated
2282 routines and the forward routines (new) are returned as part of the TAF
2283 output source code. Update genmake2 accordingly.
2284 - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
2285 with version-2 when compared to TLM or FWD gradient); other experiments
2286 output show minor changes (machine truncation level); update the few AD &
2287 TLM output with 12 matching digits only (some prior to version-2 switch).
2288
2289 checkpoint64l (2013/08/05)
2290 o model/src:
2291 - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
2292 - main_do_loop.F: no longer includes additional (AUTODIFF) header files
2293 when using TAF but only if using OpenAD.
2294 o pkg/mom_common+fluxform+vecinv:
2295 - always set horiz. viscosity arrays to background value before calling
2296 MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
2297 only when using variable horiz. viscosity (useVariableVisc=T);
2298 - simplify mom_vecinv.F (only 1 block for momViscosity).
2299 o pkg/mom_common: variable horiz. viscosity in NH code
2300 - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
2301 from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
2302 - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
2303 useBiharmonicVisc & useVariableVisc.
2304 - fix old bug (already in 1rst implementation of variable horizontal viscosity
2305 in calc_gw.F, version 1.27, 2006/06/20):
2306 horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
2307 even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
2308 - change background horiz viscosity in vertical momentum (gW) to always be
2309 viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
2310 any type of variable viscosity, e.g., viscAh/4Grid)
2311 - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
2312 viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing
2313 horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
2314 default viscAh,viscA4 is zero).
2315 o model/src:
2316 - extend length of drC & recip_drC from Nr to Nr+1.
2317 o Divided Adjoint (DIVA) with MPI:
2318 - genmake2: do not create local ./mpi_headers dir when no file to copy into.
2319 - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
2320 and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
2321
2322 checkpoint64k (2013/07/23)
2323 o tools/OAD_support:
2324 - avoid the need for file "oadtempflile" in insertTemplateDir.bash
2325 and remove it from genmake2.
2326 o tools/build_options:
2327 - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
2328 MPI_HEADER_FILES list (let genmake2 find the missing headers)
2329 o verification/halfpipe_streamice:
2330 - change to driving stress formulation; update both Fwd & AD output.
2331 o tools/genmake2 and Divided Adjoint with MPI:
2332 - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
2333 - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
2334 - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
2335 Makefile, which is set by genmake2, and check which mpi-headers are needed.
2336 Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
2337 - update target "CLEAN" (to also remove ./mpi_headers/ dir).
2338 o testreport:
2339 - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
2340 perform additional runs (number of additional runs is "add_DIVA_runs" taken
2341 from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
2342 o verification/lab_sea (AD test):
2343 - change to test Divided Adjoint Run in this set-up (both standard AD test
2344 and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
2345 o pkg atm_ & ocn_compon_interf:
2346 - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
2347 staggerTimeStep implementation) and disable (retired) corresponding
2348 parameter.
2349 o pkg/offline:
2350 - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
2351 - add S/R OFFLINE_CHECK to print offline parameter summary
2352 and stop if loading a file that is not used;
2353 - enable to calculate GMRedi tensor, KPP mixing and convective index
2354 when the corresponding file(s) is/are not specified (but pkg is used).
2355 - comment out resetting of monitorFreq (to endTime) since it still useful
2356 for monitoring CFL numbers and checking offline fields.
2357 o OpenAD:
2358 - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
2359 smaller standard output) and generate new (smaller) output (on baudelaire
2360 using gfortran with -ieee) for exp. tutorial_tracer_adjsens
2361 o model/src:
2362 - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
2363 (where external_forcing_adjust was called) and change list of arguments;
2364 - merge external_forcing_adjust.F into external_forcing_surf.F
2365 - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
2366 which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
2367 previously in file "balance_relax.F", now removed); remove corresponding
2368 arrays in FFIELDS.h.
2369 - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
2370 a hack for getting back surfaceForcingS (loaded from file) when using
2371 ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
2372 - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
2373 (was getting only 11 digits for AD-grad, due to different truncation
2374 error in AD code).
2375
2376 checkpoint64j (2013/07/04)
2377 o pkg/offline:
2378 - to enable the use of other features with pkg offline (e.g., obcs),
2379 also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
2380 - comment out "allowFreezing" (now active) in 2 offline testing exp.
2381 o pkg/exf ALLOW_RUNOFTEMP
2382 - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
2383 - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
2384 - changes verification/global_ocean.cs32x15/results/output.seaice.txt
2385 o pkg/atm_phys:
2386 - allows to add some damping on uVel,vVel (strength only function of k).
2387 o verification, ad-tests:
2388 - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
2389 global_ocean_ebm and offline_exf_seaice.thsice.
2390 o verification/halfpipe_streamice:
2391 - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
2392 flux input boundary conditions to be ignored; a fix for this bug changed
2393 verification results for forward test.
2394 - add adjoint test.
2395 o pkg/ptracers:
2396 - allow to restart without SOM pickup (resetting SOM to zero).
2397 o pkg/gmredi:
2398 - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
2399 - It uses mixing length theory and suppression by steering level effects to
2400 calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
2401 to JPO, for more details).
2402 - It also uses the diffusivity to calculate an eddy induced streamfunction
2403 based on a PV closure (rather than a buoyancy closure as in GM).
2404 - New files added to pkg/gmredi:
2405 gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
2406 induced overturning streamfunction (called from gmredi_calc_tensor)
2407 gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
2408 for use in gmredi_k3d
2409 gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
2410 the eddy diffusivity
2411
2412 checkpoint64i (2013/06/18)
2413 o pkg/cheapaml:
2414 - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
2415 that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
2416 with pkg/cheapaml.
2417 o utils/python: add subpackage for cubed sphere function, first example is
2418 simple cs.pcol to plot 2D fields on a map
2419 o pkg/streamice:
2420 - This is a new package in MITgcm, which solves dynamic equations for ice
2421 sheets and ice streams
2422 - At the moment it is independent of atmosphere/ocean dynamics, or any
2423 other physical packages in MITgcm, even ShelfIce (although it is anticipat-
2424 ed that this will change)
2425 - There is a new verification exercise that tests it, halfpipe_streamice,
2426 evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
2427 rectangular embayment
2428 - halfpipe_streamice is forward-only for now, will have TAF test soon
2429 - for questions, email dgoldber@mit.edu
2430 o pkg/thsice:
2431 - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
2432 of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
2433 - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
2434 call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
2435 - allow precip from pkg/cheapaml to make snow over seaice.
2436 o pkg/cfc:
2437 - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
2438 - remove atmos CFC 2-D arrays from common bloc (now local variables)
2439 - change some hard-coded constant to run time parameter for reading and
2440 and interpolating atmospheric CFC ; keep same default as previously.
2441 - more flexible reading of Atmos CFC (number of records no longer hard-coded)
2442 - put arguments in standard order: myTime, myIter, myThid
2443 - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
2444 atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
2445 - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
2446 - new routine to print summary of CFC params and check for consistency.
2447 o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
2448 similar to thsice_advdiff.
2449 Note that for the B-grid case the routine parameters uc/vc are overwritten.
2450 o pkg/cfc:
2451 - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
2452 update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
2453 - fix interpolation of atmphspheric CFC between Sorthern and Northern
2454 hemisphere value.
2455 o pkg/seaice:
2456 - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
2457 o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
2458 so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
2459 - requires an additional time level that is stored in the pickup
2460 - you can start with AB2 from a pickup without this time level with
2461 pickupStrictlyMatch = .false.
2462
2463 checkpoint64h (2013/05/26)
2464 o pkg/cheapaml:
2465 - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
2466 affect machine truncation (but exp cheapAML_box still pass with 13 digits).
2467 - consistent treatment of uWind,vWind location: assume everywhere in
2468 pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
2469 (Note: was already the case for Tair,Qair advection);
2470 add option (INCONSISTENT_WIND_LOCATION) to recover old results.
2471 - compute diabatic forcing only in the interior (excluding overlap regions)
2472 - fill in array "Qsw" (for short-wave heating);
2473 - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
2474 before any update (consistent with MITgcm state var diagnostics);
2475 - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
2476 non periodic ; + adjusted for uWind,vWind (C-grid).
2477 o pkg/seaice:
2478 - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
2479 add explicitly pkg/exf in experiments that currently use pkg/seaice.
2480 - allows to compile pkg/seaice without pkg/exf.
2481 o tools/OAD_support:
2482 - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
2483 of array "ourStepOf" in function rvNextAction (revolve.F90).
2484 o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
2485 - change pkg name (to be used with other atmospheric physics pkg)
2486 but by-pass CVS when making the new pkg so that we keep the CVS history.
2487 o pkg/offline:
2488 - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
2489 (previously called from pkg/dic_surfforcing_init.F)
2490 o model/src:
2491 - re-order sequence of calls within packages_init_variables.F, using
2492 standard order, except for:
2493 DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
2494 CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
2495 o new pkg: atm_phys
2496 - add entry point and source code (previously in contrib
2497 verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
2498 (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
2499 - re-order sequence of calls within packages_readparms.F,
2500 packages_init_fixed.F and packages_write_pickup.F
2501 (but skip packages_init_variables.F because of TAF issues).
2502 - update contrib/*/atm_gray/ experiment.
2503 o pkg/seaice (ITD code):
2504 - simplify and fix the writing of pickup-files for ITD case
2505 o pkg/seaice (ITD code):
2506 - introduce floe size dependent lateral melt for ITD case;
2507 - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
2508 - update seaice_itd experiment main output.
2509 o pkg/thsice:
2510 - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
2511 declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
2512 changed accordingly pkg/atm2d.
2513
2514 checkpoint64g (2013/05/01)
2515 o pkg/exf ALLOW_RUNOFTEMP
2516 - if defined, river and glacier runoff temperature can be read-in from
2517 runoftempfile; runoftempfile needs to have same format as runofffile
2518 o pkg/thsice (& pkg/bulk_force):
2519 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
2520 for energy content of Precip + RunOff & Evap (like with pkg/exf).
2521 - change computation domain to always be the interior (without overlap).
2522 - fix bug (wrong overlap) when using EXF and stressReduction > 0.
2523 o verification/tutorial_global_oce_biogeo:
2524 - add preliminary OpenAD setup (still has problems)
2525 o pkg/seaice:
2526 - turn some parameters for choosing the convergence criterion of
2527 the inexact Newton method (JFNK) into runtime parameters for convenience
2528 - clean up seaice_calc_viscosities.F: remove/retire two options for
2529 SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
2530 the results of lab_sea/input because a division has been replaced by
2531 a multiplication with the reciprocal (sumNorm)
2532 - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
2533 convergence of solver (changes results, of course), and to test some
2534 new features
2535 o model/src:
2536 - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
2537 - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
2538 - move forcing adjustment (balancing surface forcing) in specific S/R
2539 where might also be applied exchanges (if needed) to forcing arrays.
2540 o pkg/shelfice:
2541 - allow to specify the Ice-Shelf mass per unit area (instead of
2542 shelficeLoadAnomaly) and do the conversion from one to the other
2543 - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
2544 to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
2545 (b) will be loaded in time (before calling INI_PRESSURE) in case it is
2546 needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
2547 - update isomip experiment forward output (get machine truncation error
2548 from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
2549 o verification/offline_exf_seaice:
2550 revise data.seaice in input.thermo and input_ad and update results accordingly
2551 HO = 0.2, SEAICE_areaLossFormula = 2,
2552 SEAICE_growMeltByConv = .TRUE.,
2553 SEAICE_doOpenWaterMelt = .TRUE.,
2554 Improve consistency with input.thsice and fix the spurious 500m ice corners
2555 o verification/global_ocean.cs32x15:
2556 - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
2557 in icedyn (thsice+seaice-dyn) test and update output.
2558 o verification/offline_exf_seaice:
2559 - adjust list of tested variables (with testreport) and update
2560 standard test output with better slection of monitored fields.
2561 o pkg/cd_code:
2562 - swtich off Adams-Bashforth on the 1rst iteration. Update output of
2563 experiment lab_sea.hb87
2564 o tools/genmake2:
2565 - change default makedepend from the system default to tools/xmakedepend:
2566 When no makedepend is specified, select tools/xmakedepend it the test pass,
2567 otherwise select the system default (if exist and pass the test) or
2568 try to build cyrus-makedepend ; stop if none of the 3 works.
2569 o pkg/exf & pkg/thsice:
2570 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
2571 for energy content of Precip + RunOff & Evap. Assumes:
2572 1) Rain has same temp as Air.
2573 2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
2574 3) Run-Off comes at the temp of surface water (with same Cp)
2575 4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
2576 put directly into Latent Heat flux & should use water-vapor heat capacity.
2577 5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
2578 with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
2579 o pkg/seaice: simplify the use of CPP flags in JFNK-related files
2580 (compile when SEAICE_ALLOW_JFNK is defined)
2581 o pkg/thsice:
2582 - fix oceanic flux diagnostics & timeave (left from new sequence of calls
2583 implementation): move THSICE_AVE call after the advection (called directly
2584 from thsice_do_advect.F).
2585 o verification/global_ocean.90x40x15 and OpenAD:
2586 New experiment for OpenAD is identical to the one in input_ad except that
2587 multiDimAdvection=.FALSE.,
2588 There is still an issue with this.
2589 o pkg/thsice:
2590 - account for ice velocity (ocean relative velocity) in turbulent heat flux
2591 at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
2592 and offline_exf_seaice (main test).
2593
2594 checkpoint64f (2013/03/31)
2595 o verification/OpenAD:
2596 - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
2597 o verification/isomip, pkg/shelfice and OpenAD:
2598 - add OpenAD setup to this exp and make shelfice package work with OpenAD
2599 o verification/tutorial_global_oce_biogeo:
2600 - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
2601 o verification/offline_exf_seaice:
2602 - replace adjoint experiment (now similar to fwd input.thermo/ setup).
2603 o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
2604 - add OpenAD setup to this exp and make ptracers package work with OpenAD
2605 o pkg/seaice/seaice_evp.F:
2606 mask the asymmetric contribution of the ice-ocean stress (when
2607 the turningAngle is non-zero) over open water to avoid stripes
2608 in the EVP-solutions after many EVP-substeps. This does not change
2609 the verification experiment (because turningAngle=0 in that experiment),
2610 but will affect other EVP solutions with turningAngle.ne.0
2611 o verification, AD & TLM output:
2612 - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
2613 additions and multiplications which affect results at machine truncation
2614 level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
2615 lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
2616 (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
2617 digits of matching.
2618 o pkg/seaice:
2619 modify lsr-algorithm so that it vectorizes AND converges by using a
2620 "zebra" method: split vector loop into two with step size 2; this
2621 solves a general convergence problem for the JFNK solver on a vector
2622 computer. It has the potential to even improve convergence for
2623 non-vector machines, but it does change the results so it is turned
2624 off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
2625 SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
2626
2627 checkpoint64e (2013/03/05)
2628 o pkg/ecco and several verification experiments:
2629 Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
2630 from ecco package, and revert to unified routine in model/src/
2631 Adjust verification experiments accordingly, especially gloal_oce_llc90
2632 Should conclude long-standing work by Gael to reconsile the_main_loop with
2633 ECCO and will enable OpenAD's revolve loop in ECCO setup.
2634 o pkg/generic_advdiff:
2635 - implement compressible flow method for multi-dim advection (similar to
2636 gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
2637 TAF generates many recomputations) to use it; no yet coded with implicit
2638 vertical advection.
2639 - change experiment advect_cs (new output) and advect_xy (same output)
2640 to test compressible flow multi-dim advection.
2641 o pkg/generic_advdiff:
2642 - fix SOM advection for unusual cases (linear Free-Surf in r*, other
2643 cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
2644 o pkg/seaice:
2645 - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
2646 bug affects two verification experiments (lab_sea and lab_sea.hb87),
2647 recover old (wrong) results by setting noSlipFac = 2. in
2648 seaice_calc_strainrates.F;
2649 - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
2650 - add runtime parameter SEAICE_JFNKepsilon for that finite difference
2651 gradient in the Jacobian times vector operation (s/r seaice_jacvec)
2652 - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
2653 o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
2654 - new subroutines seaice_lsr_tridiagu/v
2655 - introduce loop bounds i/jmin/max to be able to use a restricted
2656 additive Schwarz method, but not used for now.
2657 - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
2658 - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
2659 o OpenAD support
2660 Reorganize S/R call for overall time-stepping loop to facilitate
2661 OpenAD revolve loop replacement
2662 (new S/R main_do_loop.F)
2663 o model/src:
2664 - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
2665 - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
2666 ADAMS_BASHFORTH2.
2667 o pkg/cheapaml:
2668 - add new parameter (default=F, same as before) to disable full domain
2669 (including land) periodicity in X & Y dir.
2670 - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
2671 prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
2672 into single S/R CHEAPAML_TIMESTEP.
2673
2674 checkpoint64d (2013/02/17)
2675 o pkg/monitor (angular momentum):
2676 - do not add Eta contribution to the total AM if using rigid-lid;
2677 - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
2678 - horizontal discretisation: compute Zonal wind contribution separately for
2679 each component (instead of from cell centered averaged) and use the 4
2680 grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
2681 - Check that AM is conserved with linear dynamics (momAdvection=F and linear
2682 FreeSurf) if using vectorInvariant momentum.
2683 o model/src (horizontal grid):
2684 - move initialisation of all horizontal grid arrays to null value
2685 from specific horizontal grid S/R to main S/R INI_GRID;
2686 - add 2 new arrays to project model C-grid velocity on to zonal direction
2687 (similar to AngleCosC & -AngleSinC but at U and V point location) and
2688 compute them in S/R CALC_GRID_ANGLES.
2689 o pkg/seaice: replace a hard coded parameter by a runtime parameter
2690 SEAICE_JFNK_tolIter
2691 o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
2692 preconditioner for JFNK (run LSR into the overlaps as far as possible,
2693 i.e OLx/y-2, but overwrite the solution in the overlaps)
2694 - extend loop range in seaice_calc_viscosity
2695 - add new parameters SEAICE_OLx/y (default = OLx/y-2)
2696 - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
2697 - slightly modify loops in tridiagonal solver lsr-preconditioner
2698 - by default remove the extra exchange in seaice_preconditioner with a
2699 replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
2700 - modify offline_exf_seaice so that old results without RAS are reproduced
2701 for output.dyn_jfnk.txt
2702 in seaice_fgmres.F (unrelated to RAS)
2703 - add a cpp-flag option for a re-ordered mapping (potentially more
2704 efficient), but because this changes the results, turn it off by
2705 default
2706 - replace the save statement by local common blocks
2707 o utils/matlab:
2708 - fix tile-offset in rdmnc.m when output was produced using EXCH2.
2709 - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
2710 instead of local script "load_cs.m".
2711 o pkg/seaice:
2712 - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
2713 to the scalarProductMetric and the unrolling. By chance this does not
2714 change the verification experiment, because of the particular domain
2715 decomposition
2716 o pkg/diagnostics:
2717 - change default missing_value from UNSET_RL to -999.
2718 o pkg/layers: improve vectorization of layers_fluxcalc.F
2719 - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
2720 time spent in this routine by more than a factor of 3 on an NEC-SX8
2721 - step 2: replace search algorithm by a bisection algorithm found in
2722 Press et al. Numerical Recipes in Fortran. This algorithm can be
2723 vectorized and finds the correct bin in approx. log2(Nlayers) steps.
2724 For now, use this algorithm only for TARGET_NEC_SX defined.
2725 - moved the search algorithm into a separate subroutine, that is kept
2726 within the same file for automatic inlining.
2727 - modified catching potential errors
2728 o pkg/ecco:
2729 - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
2730 o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
2731 - modifications for ALLOW_GENTIM2D_CONTROL
2732 -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
2733 -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
2734 -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
2735 -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
2736 o model/src:
2737 - account for moist thermodynamics in (dry) potential temperature equation;
2738 update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
2739 and cpl_aim+ocn.
2740 - also switch to standard compiler (gfortran, was using ifort previously)
2741 for fizhi-cs experiments reference output.
2742 o pkg/ctrl:
2743 - 1st step toward generic time-varying control variable (2D) via CPP option
2744 ALLOW_GENTIM2D_CONTROL
2745 - note new namelist ctrl_nml_genarr in data.ctrl
2746 o verification/global_ocean.cs32x15:
2747 - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
2748 thsice calling sequence and update "output.icedyn.txt" output file.
2749 o pkg/ptracers:
2750 - from Ryan A.: code to allow to restart a tracer at regular time interval
2751 specifying a reset frequency and a reset-phase (for each tracers).
2752 o pkg/thsice:
2753 - implement new sequence of calls for thsice+seaice:
2754 previously: ice-Dyn,ice-Advect,ice-Thermo(thsice)
2755 new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
2756 - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
2757 in CPP_OPTIONS.h) to recover old sequence;
2758 - update diagnostics for Intermediate State thsice diagnostics: now filled
2759 just before advection (instead of just after advection in old sequence);
2760 - update output of experiment offline_exf_seaice (standard test);
2761 - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
2762 by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
2763 o pkg/aim_v23:
2764 - use tiled array for aim_CO2 and surface wind speed for export to coupler;
2765 - use standard pkg/mdsio routines to read & write CO2 pickup file;
2766 - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
2767 - Implement new sequence of calls for seaice advection (with thsice and
2768 seaice diffusion): do ice advection after ice-Thermodynamic (previously
2769 was done before); change aim_do_physics.F (split the bi,bj loops block);
2770 - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
2771 o pkg/thsice:
2772 - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
2773 where just seaice diffusion is used without seaice-dynamics.
2774
2775 checkpoint64c (2013/01/18)
2776 o pkg/seaice:
2777 - add a parameter JFNKres_tFac that can replace JFNKres_t
2778 (= JFNKres_tFac*JFNKresidual before JFNK solver)
2779 - add a line search option to the JFNK solver
2780 - move update of u/vIce and computation of initial residual into a separate
2781 routine (same file); makes the code a little easier to read (?)
2782 - the line search requires computation of the residual and for some reason
2783 I cannot do the update of u/vIce at the beginning of the Newton loop
2784 without changing the results, so we move computation of the new residual
2785 also to the end of the Newton loop, even without the line search
2786 o pkg/mdsio:
2787 - write missing value (corresponding to undefined array value) to meta files;
2788 skip this if missing value is one (UNSET_RL would be a better value for the
2789 case of undefined missing value but it's current the default missing-value);
2790 Also update mdsio_read_meta.F (reading timeInterval & missing-value).
2791 o pkg/exf & thsice:
2792 - for diagnostics purpose, fill-up and update Qsw array (+ fill the
2793 diagnostics) even when SHORTWAVE_HEATING is #undef;
2794 o verification/cfc_example:
2795 - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
2796 illustrate how to use it).
2797 o verification/offline_exf_seaice:
2798 in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
2799 files to only one time-record.
2800 in input.thermo: narrow the 2 bands of low initial ice-concentration near
2801 N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
2802 snapshot output; same mcPheePiston value as in thsice with
2803 surf-current=0.2m/s.
2804 in input.thsice: similar set-up as in input.thermo (channel with same seaice
2805 initial conditions).
2806 o verification/cfc_example:
2807 - update file "data" with more standard choice (default rotationPeriod,
2808 exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
2809 set deltaTFreeSurf to deltaTtracer) and update the output.
2810 o pkg/layers:
2811 - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
2812 - ensure that "layers_bolus" is switched to False when useGMRedi=False.
2813 o verification/offline_exf_seaice:
2814 - set all {field}period to zero for constant-in-time forcing (not tested
2815 anywhere else).
2816 o verification/offline_exf_seaice:
2817 - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
2818 - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
2819 o model/src:
2820 - implement Finite-Volume method for (hydrostatic) presure gradient
2821 from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
2822 o pkg/seaice: implement EVP* by Lemieux et al. (2012).
2823 - In order to be compatible with the default EVP code, this requires changing
2824 the EVP code around a little; and because any small change immediately
2825 breaks the lab_sea.hb87 verification experiment, the reference output is
2826 updated two times (each time the remaining aggrement was only 2 digits):
2827 - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
2828 - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
2829 The adjoint test lab_sea.evp also needed to be updated.
2830 - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
2831 SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
2832 a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
2833 explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
2834 INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
2835 kept obscure, because I need to test it a little more.
2836 o pkg/cheapaml:
2837 - fix few incorrect type (_RL/_RS) in subroutine calls.
2838 o pkg/seaice:
2839 - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
2840 to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
2841 o model/src:
2842 - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
2843 change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
2844 experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
2845 o pkg/cheapaml:
2846 - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
2847 update output of experiment cheapAML_box.
2848 - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
2849 and set them only in one place (cheapaml_readparms.F).
2850 - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
2851 - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
2852 and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
2853 o model/src/the_main_loop.F:
2854 - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
2855 o pkg/seaice:
2856 - remove legacy branch code.
2857 - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
2858 o verification/*/code*/SEAICE_OPTIONS.h:
2859 - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
2860 SEAICE_CAP_HEFF).
2861 o pkg/cheapaml:
2862 - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
2863 to load new forcing fields.
2864 - add missing "_d 0" where it's needed; + some editing (improve indentation).
2865 - remove switch to "-r8" compiler option (no longer needed) in verification
2866 cheapAML_box, keep same output (small trucation error differences).
2867 o verification/offline_exf_seaice:
2868 - add thermodynamics only test.
2869 o verification/cheapAML_box:
2870 - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
2871 keep same output (same 14 digits for cg2d).
2872 - switch on "-r8" compiler option (some numerical values are missing
2873 the "_d 0") and update output (only 6 digits for cg2d were preserved).
2874
2875 checkpoint64b (2012/12/24)
2876 o pkg/cheapaml:
2877 - remove un-used variables (Qnet,EmPmR) from pickup files.
2878 - store tendency of advected variables into cheapaml pickup file
2879 and fix the AB-2 restart.
2880 o verification/offline_exf_seaice and lab_sea adjoint:
2881 - switch to new code (#undef SEAICE_GROWTH_LEGACY).
2882 - switch to 4 time steps in offline, consistent with lab_sea.
2883 - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
2884 - update results after change of experiment seaice.
2885 o pkg/seaice:
2886 - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
2887 parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
2888 still defined since SEAICE_multDim needs to be set to MULTDIM value (from
2889 SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
2890 o model/src:
2891 - add run-time parameter to select CG2D solver minimum-residual solution
2892 (in case of a poor convergence).
2893 o pkg/seaice/seaice_lsr.F
2894 - move calculation of matrix coefficients into new
2895 S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
2896 file; the main purpose of this change is to be able to reuse the code
2897 in S/R SEAICE_PRECONDITIONER
2898 - modify the computation of the residual so that the mass of sea-ice
2899 is not used twice; this simplifies the calculations, but since
2900 the residual is never used except when LSR_mixIniGuess.ge.4---and this is
2901 not tested in testreport---this does not affect the testreport results.
2902 o verification/seaice_obcs:
2903 - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
2904 verification/lab_sea/input.salt_plume; changes results/output.txt*
2905 o model/src:
2906 - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
2907 o pkg/seaice:
2908 - improve description of parameters in seaice_fgmres.F and start
2909 cleaning up the code
2910 - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
2911 second argument
2912 - add a metric based on grid cell area to SEAICE_SCALPROD; update
2913 results of offline_exf_seaice.dyn_jfnk
2914 - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
2915 o pkg/aim_v23:
2916 - fix an other bug in dissipation heating (grid-cell area was missing).
2917 o model/src + pkg/seaice:
2918 - add global (multi-tile) linear solver for pair of tri-diagonal system
2919 along X and Y lines, respectively for U and V component.
2920 Note: 1) MPI and cube-exchange not yet coded.
2921 2) probably not accurate for poorly conditioned / large size problem.
2922 - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
2923 default: not compiled and not used.
2924 o pkg/seaice:
2925 - first attempt at a multi-threaded fgmres solver for the JFNK solver:
2926 introduce bi/bj loops and use global_sum_tile_rl instead of
2927 mpi_allreduce in seaice_fgmres.F
2928 - improve diagnostics output for fgmres solver (seaice_fgmres.F)
2929 - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
2930 - add a verification experiment for JFNK in offline_exf_seaice
2931 o verification:
2932 - change (for now, only fwd test) offline_exf_seaice experiment:
2933 use a re-entrant channel with idealized coastline (trapezoidal shape)
2934 at southern boundary to explore seaice dynamics and thermodynamics
2935 with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
2936 secondary test (input.thsice) use thermodynamics only with SST relaxation.
2937 - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
2938 o pkg/exf:
2939 - disable "sstExtrapol" when Nr=1
2940 o verification:
2941 - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
2942 to test pkg/cheapaml.
2943 o pkg/aim_v23 & pkg/shap_filt:
2944 - fix dissipation heating (erroneous gravity multiplication factor).
2945 o pkg/seaice:
2946 - remove unused field pressPre from jfnk solver
2947 - rename two subroutines in seaice_preconditioner.F
2948 o eesupp/src:
2949 - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
2950 o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
2951 - remove wrong parts of the rhs and the lhs (were in there
2952 because I did not understand the concept of this preconditioner)
2953 - add an exchange between u- and v-sweep. This increases communication
2954 by a factor of two but improves the convergence of jfnk. Ideally,
2955 one would like the u- and v-sweep to be independent. So far within
2956 undocumented ifdefs
2957 - reorganize the extra computations for printing the residuals
2958 o tools/genmake2:
2959 - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
2960 since it's not necessary (and was preventing to use MNC in some cases).
2961
2962 checkpoint64a (2012/11/16)
2963 o pkg/autodiff:
2964 - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
2965 autodiff_readparms.F no longer depends on calling order (within
2966 packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
2967 rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
2968 and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
2969 o pkg/obcs:
2970 - adding tidal velocity forcing capability to obcs
2971 for usage example, see verification/seaice_obcs/input.tides
2972 o pkg/seaice:
2973 - turn the LSR-relaxation parameters WFAU/V into runtime parameters
2974 SEAICE_LSRrelaxU/V
2975 - introduce runtime parameter SEAICEetaZmethod (=0 by default)
2976 o pkg/aim_v23:
2977 - implement heating from friction (bottom friction and stratospheric drag).
2978 o pkg/shap_filt:
2979 - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
2980 dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
2981 o model/src:
2982 - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
2983 time-constant addMass field from file (addMassFile);
2984 - support for heating due to friction (and Kinetic Energy dissipation):
2985 add option, run-time switch and 3-D field array + support code ; each pkg
2986 or S/R can add heating contribution (if there is a sink of KE); the sum is
2987 accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
2988 o pkg/seaice:
2989 - complete merge of ITD code into seaice_growth.F
2990 from MITgcm_contrib/torge/itd/code/
2991 no verification so far, but Torge Martin tested
2992 "1-D test case and Beaufort set up;
2993 deliver okay results after 1 model year."
2994 - complete merge of SEAICE_SIZE.h into all relevant routines
2995 - move computation of eta at Z-points into calc_viscosities
2996 + introduce global field etaZ
2997 + add different methods for computing etaZ, for now the old
2998 method (simple averages of eta to Z-points) is hardwired
2999 + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
3000 seaice_preconditioner
3001 - simplify computations for SEAICE_ZETA_SMOOTHREG
3002 - seaice_preconditioner:
3003 + replace one remaining press by pressLoc (mistake)
3004 + adjust printing of residuals
3005 - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
3006 + add (SEAICE.h) and rename some counters (initiliased in
3007 seaice_init_fixed.F)
3008 + add _BEGIN/END_MASTER (myThid) around print statements
3009 + print total number of iterations and failures over SEAICE_monFreq
3010 interval to STDOUT
3011 - move control over output-messages by fgmres to seaice_jfnk to save
3012 some operations
3013 - move resetting initial guess for fgmres outside of seaice_fgmres_driver
3014 in order to make restarts with sol .ne. zero (fgmres with restarts)
3015 (seaice_jfnk.F, seaice_fgmres.F)
3016 - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
3017 a serious convergence problem when open boundaries are involved
3018 o pkg/ggl90: fix computation of control volumes for the case of
3019 ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
3020 up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
3021 o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
3022 o pkg/autodiff
3023 - Add inAdMode switch for SEAICEuseDYNAMICS:
3024 SEAICEuseDYNAMICSinAdMode
3025 (extend logic in ADAUTODIFF_INADMODE_SET)
3026 o pkg/seaice
3027 - Step 1 of merging ice-thickness distribution (ITD) code from
3028 MITgcm_contrib/torge/itd/ (author: Torge Martin)
3029 The code implements concept laid out in Thorndike et al. (1975);
3030 code is enabled via CPP flag SEAICE_ITD
3031 nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
3032 code is not complete yet!!
3033 - SEAICE_SIZE.h now included in almost all seaice routines
3034 o verification (using seaice):
3035 - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
3036 global_ocean.cs32x15.seaice ; update results.
3037 - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
3038 - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
3039 offline_exf_seaice (previously compiling B-grid).
3040 o pkg/exf:
3041 - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
3042 to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
3043 forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
3044 o pkg/layers (adjust changes from Sept 19):
3045 - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
3046 this allows to remove "layers_maxNum" dimension from all layers arrays.
3047 o pkg/layers (adjust changes from Sept 19):
3048 - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
3049 - snap-shot extended to all type of layers (not just the 1rst type);
3050 - remove layers variables when corresponding CPP option is undef.
3051 o pkg/layers:
3052 - rename pkg/layers variable and add new output (layer exist & un-weighted
3053 velocity in layer)
3054 o pkg/seaice:
3055 - simplify (?) ocean-drag coefficent computations by using
3056 the same routine in all three solvers (saves some code lines)
3057 - remove global fields DRAGA and DRAGS from C-grid code and
3058 declare them locally in lsr.F (the only place where they are
3059 still used)
3060 - update AD output of lab_sea.evp (very sensitive anyway).
3061 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
3062 (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
3063 and SEAICEuseJFNK=.true. A few things to note:
3064 - involves a FGMRES, that is parallel but very inefficient,
3065 because of many scalar products (global sums) in the Gram-Schmidt
3066 orthogonalization method. Needs to be replaced. Original code
3067 from J.-F. Lemieux
3068 - preconditioner for FGMRES is a stripped down version of LSOR
3069 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
3070 preconditioner. For the preconditioner, the default is set to 10.
3071 - Jacobian times vector is computed with finite differences
3072 - marginally related to JFNK-solver: add a smooth regularization for
3073 zeta with tanh that will improve convergence (Lemieux and Tremblay,
3074 2009) for any implicit solver (not implemented for EVP because EVP
3075 does not need this regularization in the first place). Define
3076 SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
3077 o eesupp/src:
3078 - check in genmake2 that intrinsic S/R flush is available.
3079 - add S/R to flush IO unit (if intrinsic S/R flush is available)
3080 - flush standard & error msg unit before MPI termination
3081 - if debugMode, flush IO unit after printing msg
3082 o pkg/ctrl:
3083 - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
3084 to ctrl_set_unpack_xyz.
3085
3086 checkpoint64 (2012/10/09)
3087 o pkg/shelfice
3088 - in mom_fluxform.F, mom_vecinv.F:
3089 CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
3090 Bug fix KappaRU -> KappaRV
3091 does not change verification/isomip but may change other setups
3092 (presumably constant KappaRU=KappaRV)
3093 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
3094 o pkg/obcs:
3095 - fixed some indexing bugs in obcs_seaice_sponge.F
3096 - added obcs relaxation subroutines for HSALT and HSNOW
3097 - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
3098 o pkg/seaice:
3099 - add "multicategory" parameterization for snow in analogy to ice,
3100 default is off for now.
3101 o pkg/obcs:
3102 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
3103 see verification/seaice_obcs/input.seaiceSponge for example application.
3104 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
3105 index setting by master-thread. This fix multi-threads Pb in previous modifs.
3106 o pkg/layers :
3107 - add diagnostics to pkg/layers
3108 - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
3109 (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
3110 o pkg/generic_advdiff/gad_implicit_r.F :
3111 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
3112 o pkg/seaice/seaice_growth.F:
3113 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
3114 o pkg/obcs:
3115 - change default setting of OBCS_UVICE_OLD from defined to undef;
3116 - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
3117 in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
3118 - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
3119 - change OB null index value (OB_indexNone) to -99 ; this fix the problem
3120 with Southern & Western OB at a tile edge (at least in a simple set-up).
3121 o pkg/obcs:
3122 - change settings of OB index in case OB coincides with tile edge (shared by
3123 2 tiles), so that common OB location is registered by both tiles (instead of
3124 only 1). However, for Southern and Western OB, index value = 0 is not
3125 recognized as valid OB index (=default null value) and needs to be fixed.
3126 - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
3127 - new parameter "OB_indexNone" for null index value (for now, still zero)
3128 to replace hard-coded null index value of zero.
3129 o pkg/exch2:
3130 - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
3131 always check buffer-size (but outside the loop); move checking for valid
3132 index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
3133 print each tile and point connection only if |W2_printMsg|>= 2 and 3.
3134 o pkg/ctrl (pack & unpack):
3135 - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
3136 (locally defined) for different variables (+ remove the variable-specific
3137 file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
3138 (to be extended to other local file names in ctrl.h).
3139 o pkg/flt:
3140 - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
3141 o pkg/mdsio:
3142 - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
3143 o tools/genmake2:
3144 - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
3145 (added by Alistair in version 1.51 for building without make depend);
3146 - remove Header files list (H_SRC_FILES) from the dependence of targets
3147 ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
3148 place in version 1.23): this save going through staf when unrelated header
3149 file has been modified.
3150 Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
3151 "make depend" step, still need to do "make links" before "make adtaf".
3152 o eesupp/src (+ few pkg src files) & genmake2:
3153 - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
3154 - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
3155 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
3156 upper/lower case ; account for space between "#" and undef/define)
3157 o pkg/flt (with exch2):
3158 - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
3159 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
3160
3161 checkpoint63s (2012/09/05)
3162 o pkg/ecco:
3163 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
3164 - add more relevant #ifdef ALLOW_SMOOTH ones.
3165 - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
3166 o pkg/ctrl:
3167 - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
3168 ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
3169 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
3170 doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
3171 ctrlSmoothCorrel3D (new).
3172 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
3173 - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
3174 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
3175 controls when useAtmWind, and vice versa.
3176 - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
3177 - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
3178 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
3179 - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
3180 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
3181 - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
3182 replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
3183 o pkg/smooth:
3184 - remove un-necessary includes.
3185 - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
3186 Those CPP options were never defined, and not necessary.
3187 o model/src:
3188 - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
3189 - standard treatment of useSMOOTH.
3190 o pkg/autodiff:
3191 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
3192 useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
3193 o pkg/exch2:
3194 - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
3195 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
3196 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
3197 and tiles to process mapping.
3198 - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
3199 moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
3200 rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
3201 from w2_eeboot.F to w2_readparms.F.
3202 o eesupp/src:
3203 - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
3204 ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
3205 also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
3206 - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
3207 is defined (remove condition on usingMPI) to match cases where MPI_INIT
3208 has been called.
3209 - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
3210 - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
3211 (so that on 1 proc, get same myPid independently of usingMPI)
3212 - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
3213 useCubedSphereExchange with EXCH-1 (safer).
3214 - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
3215 o pkg/ggl90:
3216 - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
3217 used in ALLOW_GGL90_SMOOTH code.
3218 o pkg/flt:
3219 - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
3220 floats at the Southern end of the domain).
3221 o eesupp/inc:
3222 - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
3223 but not used (and not to be used) anywhere, just for documentation.
3224 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
3225 - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
3226 a) can damage previously written records in any other multi-record files.
3227 b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
3228 o tools/genmake2:
3229 - define variable MAKE within Makefile and use it in place of 'make';
3230 - update AD_CONFIG.h (if needed) before building any of the executable
3231 (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
3232 and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
3233 - always print usual warning comment 'this file is automatically generated'
3234 from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
3235 o pkg/cheapaml:
3236 - updated to correspond to the code used in accepted paper (Nico Wienders).
3237 o pkg/exf:
3238 added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
3239 ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
3240 and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
3241 o pkg/exf, autodiff, ctrl, ecco and seaice:
3242 remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
3243 o pkg/ctrl, ecco:
3244 allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
3245 Depending on useAtmWind, one is inactive, and the other is active (see
3246 exf_getffields.F/exf_getsurfacefluxes.F).
3247 o tools/genmake2:
3248 - improve error msg when failing in 2nd test of check_for_broken_Ff
3249 - fix option '-makefile' short-name (-mf according to genmake2 -help)
3250 - source local config file "genmake_local" just after processing the genmake2
3251 command arguments (previously done before processing arg).
3252 o pkg/grdchk:
3253 - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
3254 to this routine from cost_final has been dropped in g_cost_final)
3255 - improve printed information (more explicit msg, no longer using "print *,"
3256 fix fcpertminus printed value).
3257 o model/src:
3258 - move call to COST_INIT_VARIA out of packages_init_variables.F directly
3259 into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
3260 this prevents getting cost-funct reset in adinitialise_varia recomputations.
3261 o pkg/dic:
3262 - move initialisation of "freefe" array from from dic_biotic_forcing.F to
3263 fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
3264 o pkg/grdchk:
3265 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
3266 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
3267 o pkg/autodiff/ctrl/grdchk :
3268 - attempt to sort out what works and what does not,
3269 with regard to I/O, and to warn/stop accordingly.
3270 o pkg/grdchk:
3271 - attempt to fix grdchk in the case of useSingleCpuIO.
3272 - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
3273 statements were moved from grdchk_main.F and into
3274 grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
3275 - a global sum is applied to record numbers icvrec/layer
3276 out of grdchk_loc so that they be passed to I/O routines.
3277 o pkg/smooth:
3278 - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
3279 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
3280 o verification/testreport:
3281 - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
3282 - can also use compressed (gzip) reference output file;
3283 - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
3284 to be easier to collect by testreport.
3285 - update existing TLM output (half out-of-date by more than 3 yrs).
3286 - report NETCDF & LAPACK settings (from genmake2) in output dir.
3287 - report run-time in each individual summary (previously only for AD test);
3288 for TLM test, add also TAF version.
3289 - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
3290
3291 checkpoint63r (2012/08/15)
3292 o tools/genmake2:
3293 - fix Makefile for target ftlall (+ update files to clean after make ftlall)
3294 o pkg/ecco/ecco_cost_final.F :
3295 - fix fc print statements (to stdout and costfunction0000) so
3296 that the printed value is always after the global sum.
3297 o pkg/seaice/seaice_dynsolver.F :
3298 - fix ice strength assymptote at SEAICE_area_max<1
3299 (no change for the standard case of SEAICE_area_max=1)
3300 o some cleaning:
3301 - pkg source files: ensure that all *.F files from each pkg included the
3302 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
3303 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
3304 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
3305 includes;
3306 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
3307 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
3308 is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
3309 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
3310 - update option-file CPP_OPTIONS.h of all AD experiments:
3311 * no longer include PACKAGES_CONFIG.h ;
3312 * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
3313 * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
3314 including ECCO_CPPOPTIONS.h).
3315 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
3316 - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
3317 separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
3318 not necessary accurate).
3319 - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
3320 pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
3321 deliberately break compilation (a remainder that it needs to be customized)
3322 - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
3323 - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
3324 - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
3325 o tools/genamke2:
3326 - check for lapack.
3327 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
3328 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
3329 jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
3330 from both packages.
3331 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
3332 - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
3333 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
3334 of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
3335 o pkg/cost : add comments to explain special and/or untested setups.
3336 o pkg/exf:
3337 - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
3338 (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
3339 o verification/*/code_ad:
3340 mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
3341 - reccord when this file is included (define ECCO_CPPOPTIONS_H)
3342 - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
3343 allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
3344 o pkg/seaice :
3345 - added possibility to change ice strength/PRESS0 relationship to
3346 HEFF, according to the following run time parameters
3347 SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
3348 SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
3349 SEAICEpresH0 :: HEFF threshold for ice strength (m)
3350 o pkg/ggl90 :
3351 - added run time flag mxlSurfFlag to include the code that ensure
3352 mixing between first and second level (previously included as a comment)
3353 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
3354 - add test of newly added dumpAdByRec=T option where
3355 we write all records to one file per variable.
3356 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
3357 - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
3358 to check that this code is ok with taf and compiles in adjoint.
3359 o pkg/autodiff :
3360 - added run time param dumpAdByRec : ad dump format switch.
3361 If true then write all records to one file per variable.
3362 Else write one file per record (remains the default).
3363 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
3364 o pkg/seaice:
3365 - Added SEAICEuseTILT run time switch : if set to
3366 false then omit the tilt term in seaice dynamics.
3367 - Fix free drift calculation.
3368 o pkg/shelfice:
3369 When initializing SHELFICEDragQuadratic, set default to be
3370 consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
3371 but retain option to set it independently
3372 (inconsistenty spotted by Veronique Dansereau)
3373 o eesupp/inc:
3374 - in EEPARAMS.h, add real-type constant for some frequently used simple number
3375 (0,1,2,1/2), with name explicitly referring to RS/RL type.
3376 o model/src:
3377 - move balancing of relaxation terms to new S/R balance_relax.F.
3378 o pkg/autodiff:
3379 re-write active I/O high-level (control) S/R:
3380 - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
3381 - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
3382 - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
3383 MDS_READ/WRITE_FIELD); change loops to multi-threads.
3384 - update and merge active_file_control_slice.flow into active_file_control.flow
3385 - update the calls in lower level S/R (active_file.F, active_file_g.F and
3386 active_file_ad.F) keeping the argument list and function unchanged.
3387 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
3388 =.TRUE.") and remove high-level (control) _loc version (not called anymore).
3389 - new low-level active I/O routines, one for each type (RL/RS), for active var
3390 of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
3391 fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
3392 right type.
3393 o autodiff and RS=real*4:
3394 - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
3395 ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
3396 - change argument type of 3-D mask argument to _RS to match type in the call
3397 (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
3398 o pkg/thsice:
3399 - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
3400 - option to correct ocean fresh-water flux for imbalance of Atmos+Land
3401 fresh-water flux: uniform correction or proportional to local precip.
3402 o pkg/ctrl:
3403 - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
3404 - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
3405 ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
3406 - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
3407
3408 checkpoint63q (2012/07/30)
3409 o pkg/autodiff:
3410 note about monitor and snap-shot of ad-variables:
3411 a) need to apply ADEXCH before monitor or output of ad-vars to include
3412 overlap contributions (was done for adjDump but missing for monitor).
3413 b) since ADEXCH implies adding overlap values to interior array, machine
3414 truncation error is expected when adding an ADEXCH call in the middle of
3415 the time-stepping (although mathematically identical).
3416 modifs:
3417 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
3418 declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
3419 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
3420 apply ADEXCH before monitor or snap-shot of ad-variables:
3421 =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
3422 - implement new method (copy+adexch) for snap-shot and monitor of main model
3423 ad-vars (initially not used by default -> output unchanged).
3424 - change default (set to 2) to use new method and update few output_adm.txt
3425 with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
3426 and both tutorial_tracer_adjsens tests).
3427 - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
3428 and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
3429 o pkg/ctrl:
3430 enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
3431 generic control variables via
3432 #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
3433 Only required customization should be S/R ctrl_map_ini_genarr.F
3434 (routine in repository contains example)
3435 o pkg/exf:
3436 - fix and refine checking of surface-relaxation setting when using EXF
3437 o verification (adjoint exp):
3438 - reduce length of simulation by half for experiment global_ocean.cs32x15
3439 (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
3440 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
3441 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
3442 of KE that can occur with aggressive optimization
3443 + put quadratic bottom drag calculation in separated loops (only done if
3444 using bottomDragQuadratic)
3445 o model/src: CG2D_NSA
3446 - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
3447 and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
3448 - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
3449 change cg2d residual target to be expressed in Wunits (=> do not normalise
3450 RHS ; this fix global_max Pb with TAF); update output.
3451 o verification/tutorial_tracer_adjsens:
3452 improve parameter consistency (and get rid of warnings):
3453 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
3454 - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
3455 - use staggerTimeStep (for stability) in som81; use default rotation period.
3456 o pkg/exch2:
3457 - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
3458 reset to 0 = 1 long line in X)
3459 o pkg/mdsio:
3460 - fix reading of dimensions from meta file for large-size domain
3461 o model/src:
3462 - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
3463 - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
3464 Cubed-Sphere Exch with CS-corners inside the domain;
3465 make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
3466 globalArea and to set hasWetCSCorners.
3467 - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
3468 metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
3469 - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
3470 useCDscheme and useCubedSphereExchange).
3471 o pkg/seaice/seaice_growth.F :
3472 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
3473 for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
3474 when the previous code was not correct.
3475 - in all cases diagnoze the boundary condition mismatch to SIaaflux
3476 - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
3477 that term to QNET (essentially to set the melt/freeze water to 0degC).
3478 when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
3479 o verification/global_ocean.cs32x15/input.seaice :
3480 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
3481 - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
3482 - update results (output.seaice.txt) accordingly.
3483 o verification/lab_sea/input/data.seaice :
3484 - remove SEAICEheatConsFix, which is now be tested
3485 in global_ocean.cs32x15. The presently coded fix
3486 is only consistent with real fresh water + nlfs.
3487 - update results (output.txt) accordingly.
3488 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
3489 o AD_CONFIG.h file:
3490 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
3491 - remove #include "AD_CONFIG.h" from all included OPTIONS files and
3492 add it explicitly in each fortran src file where it is needed.
3493 motivation: header file AD_CONFIG.h is generated/modified after "make depend"
3494 thus introducing potentially wrong dependency; therefore, better to include
3495 it only where it's really needed, and after any other included OPTIONS file
3496 (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
3497 or ALLOW_TANGENTLINEAR_RUN).
3498
3499 checkpoint63p (2012/07/06)
3500 o pkg/autodiff:
3501 - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
3502 - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
3503 which are now read from new parameter file "data.autodiff" (inAdExact
3504 previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
3505 - add file "data.autodiff" in all verification/*/input_ad/ directories.
3506 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
3507 mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
3508 o verification/tutorial_tracer_adjsens/
3509 - add extra sub-verification which uses "SOM" advection scheme
3510 (2nd Order-Moment Advection Scheme, Prather Limiter) with
3511 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
3512 and in data:
3513 multiDimAdvection=.TRUE.,
3514 tempAdvScheme=81,
3515 saltAdvScheme=81,
3516 o model/src:
3517 - introduce ALLOW_BALANCE_RELAX which allow the removal
3518 of the global mean of relaxation terms by setting
3519 balanceThetaClimRelax and balanceSaltClimRelax
3520 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
3521 This case is now treated appropriately in seaice_growth.F
3522 o pkg/seaice:
3523 - do balanceEmPmR and balanceQnet based on the net fluxes
3524 (SItflux) that enter the ocean+ice system rather than QNET
3525 and EMPMR. Works best in real fresh water.
3526 - SIatmFW, SIatmQnet, and SItflux computations had to be moved
3527 out of the diagnotics bloc, and stored in global arrays.
3528
3529 checkpoint63o (2012/06/29)
3530 o vertical mixing schemes:
3531 - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
3532 - replace computation of density (in Function STATE1, opps_calc.F) by a call
3533 to S/R FIND_RHO_SCALAR
3534 - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
3535 and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
3536 affects output (vermix.ggl90) at truncation level.
3537 o testreport:
3538 - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
3539 (nSx,nSy) for the number of threads (from eedata.mth)
3540 o model/src:
3541 - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
3542 related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
3543 o verification/tutorial_tracer_adjsens/
3544 - compile with ALLOW_CG2D_NSA
3545 - run with nonlinFreeSurf=3
3546 - update reference output_adm.txt
3547 o tools/genmake2:
3548 - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
3549 refine usePROFILES switching off (only when NetCDF is not available).
3550 o verification (atmospheric set-up):
3551 - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
3552 o pkg/profiles : refine profiles and files handling.
3553 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
3554 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
3555 - changes to use model/src/the_main_loop.F rather than the ecco version
3556 in ecco type adjoint runs.
3557 o model/src:
3558 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
3559 - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
3560 - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
3561 o model/src:
3562 - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
3563 update output of test experiment bottom_ctrl_5x5.
3564 o pkg/generic_advdiff:
3565 - implement vertical bi-harmonic diffusion (for now, only for T & S and
3566 only explicitly).
3567 o verification/bottom_ctrl_5x5/
3568 update reference output (results changed quite some time ago,
3569 not sure when; but new reference results look ok in terms of grdchk)
3570 o verification/1D_ocean_ice_column/
3571 For verification purposes, the exact adjoint rather than an approx.
3572 should be used (e.g., to comare against F.D. or TLM).
3573 removed autodiff_inadmode*_ad.F routines in code_ad/
3574 Update results/ accordingly.
3575 o pkg/cal:
3576 - change cal_getdate.F so that output date is function of input time only
3577 (less ambiguous, not mixed up with input iteration number).
3578 - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
3579 o pkg/diagnostics:
3580 - implement calendarDumps also for stats-diags
3581 - implement calendarDumps also for snap-shot output (negative freq)
3582 - for now, ignores calendarDumps if non-zero phase-lag.
3583
3584 checkpoint63n (2012/06/04)
3585 o model/src:
3586 - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
3587 between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
3588 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
3589 similar to calc_r_star.F); update results of experiment internal_wave and
3590 tutorial_global_oce_in_p (affected @ truncation level).
3591 o pkg/shelfice:
3592 - add parameterisation of advective-diffusive flux into the ice shelf
3593 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
3594 - simply eps3/3a computation
3595 o eesupp:
3596 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
3597 between tiles, just fill-in edges assuming locally periodic subdomain) and
3598 add corresponding exchange subroutines (EXCH0);
3599 - new CG-solver version (_EX0) for disconnected-tiles special case.
3600 o model/src (CG-solvers):
3601 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
3602 (similar final residual output and max-Iter number as with standard version);
3603 - allows to store and use lowest-residual solution (standard & _SR versions);
3604 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
3605 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
3606 o eesup/src:
3607 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
3608 ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
3609 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
3610
3611 checkpoint63m (2012/04/27)
3612 o pkg/shelfice:
3613 - account for partical cells in surface level below ice-shelf for hydrostatic
3614 pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
3615 o ad test experiments:
3616 - update and rename to "ad_optfile.local" local AD-optfile specific to a
3617 particular adjoint verification experiment (in verification/*/code_ad/)
3618 o pkg/seaice & pkg/exf:
3619 - Part two of ECCO-CLIVAR code merges.
3620 Completes merge of seaice area relax. code.
3621 Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
3622 to be set in EXF_OPTIONS.h since this pkg controls its I/O
3623 (and avoids second CPP option in SEAICE_OPTIONS.h)
3624 - change default value of costIceStart & costIceEnd to a valid date.
3625 - add snowPrecip to HSNOW in seaice_growth
3626 o pkg/ptracers:
3627 - move ptracers summary and setup check into separated S/R ; add a check for
3628 valid PTRACERS_Iter0 value (error+stop or just warning).
3629 o pkg/cal (+ pkg/ecco):
3630 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
3631 as input; and for AD, unless both are not differentiable (e.g., k index)).
3632 o model/src:
3633 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
3634 is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
3635 temporary set to usingZCoords value (to be changed to F when using shelfice).
3636 - hydrostatic pressure: implement partial cell near the surface also for
3637 Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
3638 usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
3639 o pkg/ctrl/ctrl_init.F:
3640 - add a formal parameter to s/r ctrl_init_rec to print
3641 xx_$(ctrl_valiable)_file for easier debugging
3642 - move call of cal_* routines into the if-block where they are really
3643 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
3644 to specify a startdate
3645 o pkg/seaice:
3646 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
3647 global_ocean.cs32x15/code versions).
3648 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
3649 verification experiment global_ocean.cs32x15.seaice and update results.
3650 o pkg/exf:
3651 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
3652 (according to useExfYearlyFields).
3653 o pkg/cal:
3654 - move calendar setting & summary (previously in cal_readparams.F) into new
3655 S/R CAL_INIT_FIXED to be called later in the initialisation process, once
3656 length of the simulation is set (after SET_PARMS call); This is an attempt
3657 to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
3658 - For safety: keep a record of pkg/cal parameter settings status
3659 to allow to STOP if one pkg/cal S/R is called too early.
3660 - add a stop in all basic pkg/cal subroutines if called before setting is done.
3661 - modify cal_getdate.F: stop when nothing was returned;
3662 if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
3663 this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
3664
3665 checkpoint63l (2012/04/04)
3666 o pkg/bbl:
3667 - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
3668 update global_with_exf output.yearly.txt file.
3669 o pkg/cal:
3670 - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
3671 - remove 2 unsused and very short (1 line only) functions ;
3672 - remove unsused subroutines from AD-Diff list.
3673 o model/src:
3674 - start to implement clean wait to stop in initialization S/R (config_check.F,
3675 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
3676 o folowing PRINT_MESSAGE changes:
3677 - remove reminder multiple print to the same file (STDOUT) when multi-threads.
3678 o pkg/bbl:
3679 - modification so it can work with z*
3680 - replace deltaT with dTtracerLev(k) for asynchronous time stepping
3681 - global_with_exf/input.yearly verification; changes output.yearly.txt
3682 o eesupp/src:
3683 - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
3684 writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
3685 - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
3686 # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
3687 - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
3688 - when using MPI, always set usingMPI=T ; set default accordingly and stop
3689 if not consistent.
3690 - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
3691 argument is zero (in case called within single-thread section).
3692 o pkg/fizhi:
3693 clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
3694 in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
3695 o pkg/exch2:
3696 - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
3697 activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
3698 - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
3699 but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
3700 with bad ones coming from a not-yet-updated halo.
3701 This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
3702 o pkg/frazil:
3703 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
3704 http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
3705 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
3706 o verification/lab_sea
3707 * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
3708 * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
3709 * nTimeSteps 3 -> 4
3710 * changed reference output accordingly
3711 o pkg/ctrl:
3712 * fix ctrl_get_gen for xx_sst, xx_sss
3713 o pkg/fizhi:
3714 - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
3715 update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
3716 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
3717 fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
3718 clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
3719 o pkg/gmredi:
3720 - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
3721 o pkg/fizhi:
3722 - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
3723 (old)aces open64 tuv test.
3724 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
3725 o pkg/mom_vecinv:
3726 - fix 1 loop range in mom_vecinv.F to be like all the other loops which
3727 set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
3728 with non-lin free-surf).
3729 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
3730 in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
3731 some compilers (gfortran 4.6.0 on MacOS)
3732 o momentum:
3733 - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
3734 & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
3735 fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
3736
3737 checkpoint63k (2012/03/17)
3738 o model/src:
3739 - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
3740 flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
3741 - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
3742 (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
3743 o model/src: solve_*diagonal.F
3744 - replace division with multiplication by inverse (similar to original version)
3745 update output of AD exp. global_ocean.90x40x15.
3746 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
3747 to enable the use of the vectorized & differentiable solve_tridiagonal.F
3748 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
3749 vertical advection (to get solve_tridiagonal tested in AD mode).
3750 o pkg/seaice: ECCO-CLIVAR merge:
3751 1. seaice AREA relaxation
3752 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
3753 * runtime flag: SEAICE_tauAreaObsRelax
3754 2. modified global mean cost imbalance code: CPP option
3755 ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
3756 o another iteration on solve_*diagonal.F
3757 Make choices independent of AUTODIFF
3758 Default will be the adjoinable vectorized version.
3759 Alternative choices are:
3760 * non-adjoinable original version with low memory footprint:
3761 #define SOLVE_DIAGONAL_LOWMEMORY
3762 * still adjoinable but does not vectorize (k as inner-most loop):
3763 #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
3764 o testreport
3765 - add option to use a home made wrapper around "make"
3766 - remove MITGCM_IEEE env. variable (no longer active)
3767 o pkg/shelfice
3768 - improve computation of friction velocity for velocity dependent
3769 exchange coefficients: include velocities into SHELFICEBoundaryLayer
3770 block to average velocities vertically
3771 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
3772 o Modify diagonal solvers, now three versions (upon request):
3773 #ifndef SOLVE_DIAGONAL_AUTODIFF
3774 1. default version (dating back a while ago)
3775 #else /* def SOLVE_DIAGONAL_AUTODIFF */
3776 # ifdef SOLVE_DIAGONAL_KINNER
3777 2. adjoinable version with k-innermost loop (G. Forget)
3778 # else
3779 3. adjoinable vectorized version of 2.
3780 # endif
3781 #endif /* SOLVE_DIAGONAL_AUTODIFF */
3782 All flags are currently set within routines, but could/should be moved to CPP-options.
3783 Array bounds for 1. are as before, for 2.,3. cover the entire domain
3784 (could be changed for 1. too).
3785 o verification/lab_sea (fwd):
3786 - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
3787 use 7 categories (except hb87), new solve4temp params (except salt_plume),
3788 constant salinity (=4) or variable salinity (salt_plume) done through
3789 SItracer.
3790 o pkg/seaice:
3791 - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
3792 - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
3793 SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
3794 from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
3795 SEAICE_freeze got retired) but already better than previously with
3796 SEAICE_freeze=123456.7 deg.C;
3797 - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
3798 (safer multi-threaded setting); always set SEAICEuseEVP;
3799 - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
3800 SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
3801 stop if multiple specifications for the same coeff; make sure default
3802 SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
3803 o pkg/obcs:
3804 - allow to switch to upwind 1rst order advection scheme for the advective
3805 flux computation at the open-boundary; disabled for adjoint built.
3806 o pkg/ptracers:
3807 - rename PTRACERS_RESTART.h -> PTRACERS_START.h
3808 - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
3809 - add parameter to decide when to start a tracer; use internal flag to
3810 know which tracer to step-forward; switch this internal flag at the top
3811 of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
3812 for adjoint built.
3813 o pkg/seaice:
3814 - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
3815 - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
3816 - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
3817 o pkg/ecco:
3818 - fix writing of output file DiagnosCost_ClimSalt/Theta
3819 and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
3820 o pkg/seaice:
3821 - add missing initialisation of COR_ICE array in dynsolver.F
3822 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
3823 compiled either way, and is tested in all exps (multidim was only tested
3824 in lab_sea ad before).
3825 - cosmetic change to prepare for future addition of ITD. no change to results.
3826 no defaults change.
3827 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
3828 - by lack of adequate verification experiments, I further used custom versions
3829 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
3830 should be correct.
3831 - avoid recomputations in ad.
3832 o array initialisation in adjoint mode:
3833 1) pkg/mom_common/mom_calc_ke.F:
3834 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
3835 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
3836 part this initialisation is gone, resulting in Floating Point Exception
3837 (caught by open64 compiler with debug option).
3838 2) model/src/convective_weights.F
3839 set output convectCount over the full array range (instead of doing
3840 an update): this fix a similar issue when called within recomputation (adjoint)
3841 which could by-pass the initialisation (normally done in the caller S/R).
3842 o pkg/seaice:
3843 - final version of turbulent flux params, as agreed at MIT ice meet:
3844 SEAICE_mcPheePiston (default is ~ 0.000875)
3845 SEAICE_mcPheeTaper (default is 0.)
3846 SEAICE_frazilFrac (defualt is 1.)
3847 SEAICE_mcPheeStepFunc (default is false)
3848 - changes results at trunction error level
3849 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
3850 o added pkg/frazil:
3851 - see frazil_description.tex for details
3852 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
3853 o pkg/shelfice/shelfice_thermodynamics.F
3854 - fix exponents for velocity dependent exchange coefficients: change
3855 from 2/3(=0) to 0.66666666666666667
3856 - move computation of velocity dependent exchange coefficients into
3857 separate loop, so that it applies to both thermodynamics
3858 - move some divisions by constants out of loops
3859
3860 checkpoint63j (2012/02/16)
3861 o pkg/seaice:
3862 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
3863 - SItracer: added run time params, and allow coupling to ocn salinity.
3864 o pkg/seaice: remove (almost) all divisions by constants within loops
3865 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
3866 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
3867 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
3868 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
3869 o pkg/seaice :
3870 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
3871 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
3872 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
3873 - add permanent SItflux diag that corresponds to TFLUX but includes
3874 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
3875 - allow activation/testing of a fix for suspected missing term in
3876 ocn-ice heat budget (to be confirmed). To test this, you want to
3877 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
3878 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
3879 - no change in results, fwd or ad.
3880 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
3881 - switch to variable freezing point.
3882 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
3883 - bug fix : the sublimation term that was missing is now activated.
3884 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
3885 - bug fix : flooding sign term for SIsal0.NE.0.
3886 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
3887 o pkg/seaice:
3888 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
3889 is now the default, and the old default constant freezing point is recovered
3890 with SEAICE_tempFrz0 = -1.96,
3891 SEAICE_dTempFrz_dS = 0.,
3892 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
3893 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
3894 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
3895 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
3896 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
3897 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
3898 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
3899 seaice_growth r149 for legacy branch (no results change).
3900 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
3901 from I. Fenty).
3902 - results did not change except for global_ocean.cs32x15, mostly due to the
3903 switch to variable freezing point (see above item for detail).
3904 o pkg/thsice:
3905 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
3906 seawater freezing in thsice_calc_thickn (not used).
3907 o pkg/seaice: turbulent flux term specification via run time params.
3908 - replace CPP switches with run time switches to facilitate testing
3909 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
3910 GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
3911 - added runtime parameter : SEAICEturbFluxFormula
3912 - move Mcphee constants to SEAICE_PARAMS.h
3913 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
3914 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
3915 remove seaice_summary call (moved to seaice_init_fixed)
3916 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
3917 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
3918 - seaice_summary.F : add missing report of read turbulent flux term set up
3919 and SITRACER.
3920 - seaice_check.F : check range; inform and stop if retired CPPs are used
3921 (incl. SEAICE_AGE).
3922 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
3923 CPP switch, same computation as before for the different options.
3924 - change results at the truncation level.
3925 o pkg/seaice:
3926 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
3927 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
3928 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
3929 - update verification/*/input*/data.seaice:
3930 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
3931 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
3932 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
3933 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
3934 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
3935 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
3936 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
3937 difference in results only due to machine truncation.
3938 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
3939 MaykutPolySatVap; keep MIN_LWDOWN.
3940 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
3941 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
3942 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
3943 o pkg/salt_plume:
3944 - isolate saltPlumeFlux array exch into a specific S/R called from
3945 do_oceanic_phys.F
3946 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
3947 o verification:
3948 - move untested set-up to MITgcm_contrib/verification_other.
3949 o pkg/seaice:
3950 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
3951 o pkg/seaice:
3952 - seaice_solve4temp.F (keeping results unchanged):
3953 * add 2 future run-time params to select which saturation vapor pressure
3954 formula is used and how post-iteration fluxes are set.
3955 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
3956 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
3957 the linearized expression to stay consistent with tsurf finding.
3958 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
3959 can be < 0.
3960 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
3961 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
3962 conductive heat flux F_c , and add it explicitly when updating tsurf as
3963 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
3964 so that now F_ia has a consistent meaning through the entire routine.
3965 This causes differences at truncation level: update output of fwd exp.
3966 global_ocean.cs32x15.seaice.
3967 o pkg/seaice:
3968 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
3969 of arrays, sign/direction of fluxes; no effect on results.
3970 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
3971 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
3972 note: this should have been done before changing celsius2K default.
3973 - to keep results unchanged, add back old value of celsius2K in verification
3974 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
3975 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
3976 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
3977 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
3978 freezing temp is consistent with value in seaice_growth.F ; this causes
3979 differences at machine truncation level: update lab_sea AD output (3/4).
3980 o pkg/seaice:
3981 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
3982 and climsst/sss even when using seaice (to prevent calculation that might
3983 use SST on land); does not affect any verification exp.
3984 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
3985 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
3986 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
3987 over land (non-legacy code)
3988 o vectorize salt_plume package:
3989 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
3990 - this code computes plumebk everywhere (also over land), thus requires
3991 code to avoid divisions by zero and catch the case of kLev=Nr.
3992 - efficiency of salt_plume_frac is still sub-optimal
3993 o tools (genmake2):
3994 - fix makefile NAME specification (option: -makefile NAME) by adding
3995 "-f $MAKEFILE" in few places where it was missing including makedepend
3996 command (contribution from Paul).
3997
3998 checkpoint63i (2012/01/24)
3999 o model/src:
4000 - add factorized versions of some EOS code to find_rho.F,
4001 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
4002 o model/src:
4003 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
4004 - change default celsius2K from 273.16 to 273.15
4005 - to keep results unchanged, add back old value of celsius2K in verification
4006 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
4007 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
4008 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
4009 to make TAF generate vectorizable code
4010 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
4011 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
4012 have flags that do this more efficiently.
4013 o pkg/diagnostics/diagstats_calc.F
4014 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
4015 o pkg/obcs (with exch2):
4016 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
4017 and remove code (in obcs_readparms.F) which was based on EXCH of indices
4018 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
4019 o pkg/exf and seaice exp:
4020 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
4021 so that switching off area & heff advection flags does not affect results.
4022 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
4023 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
4024 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
4025 results of verification experiments: 1D_ocean_ice_column(fwd),
4026 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
4027 and offline_exf_seaice (all 4).
4028 o pkg/seaice:
4029 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
4030 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
4031 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
4032 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
4033 not multi-dim advection;
4034 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
4035 SHORTWAVE_HEATING #undef.
4036 o optim: make Makefile more robust (?)
4037 o pkg/obcs:
4038 * fix treatment of obcs_read_pickup for TAF
4039 o pkg/shelfice:
4040 * add missing initialisation of num_shifwflx
4041 * new adjoint verification exp. for isomip
4042 * change Prandtl and Schmidt numbers from generic formulations
4043 (in terms of model diffus. and visc.) to separate runtime
4044 parameters, with Holland and Jenkins (1999) default values.
4045 o pkg/exf (interpolation):
4046 - extended input field (2 rows) near the N & S poles:
4047 * fill in with the symetric value (when even Nb of data in longitude)
4048 * add average value at the poles only for scalar quantities ; for vector
4049 component interpolation, skip the averaging and keep duplicated values,
4050 unless the 2 components have same location (uvInterp=T) in which case
4051 interpolate the 2 components together using S/R EXF_INTERP_UV.
4052 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
4053 together: this allows to account properly for local orientation when
4054 averaging at N & S pole.
4055 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
4056 exf-interpolation near N & S poles. Undef by default.
4057 - add debug check/print on 1rst iter if debugLevel >=2.
4058 o pkg/exf:
4059 - change masking flags definition (no longer "parameter"), put them in
4060 common block and set them in S/R EXF_INIT_FIXED.
4061 - change recognized masking flag from s,u,v to c,w,s since the mask
4062 to use (maskC,W,S) depends on position on model grid and has little to
4063 do with scalar/vector difference; fix masking if using P-coordinates.
4064 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
4065 and update results of exp. global_with_exf (x2).
4066 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
4067 o pkg/obcs
4068 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
4069 o pkg/exf (interpolation):
4070 - assume periodicity in X only if input field cover full longitude range.
4071 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
4072 and should vectorise).
4073 - fix input lat of the 2 added row (in case we provide N.pole data).
4074
4075 checkpoint63h (2011/12/30)
4076 o pkg/seaice:
4077 - change declaration of UVM from _RL to _RS in order to get B-grid
4078 uIce,vIce monitor when _RS = real*4
4079 o pkg/offline:
4080 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
4081 - compute vertical velocity if not read from file (switch on exactConserv
4082 & staggerTimeStep);
4083 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
4084 o verification:
4085 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
4086 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
4087 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
4088 - update output of exp. global_ocean.cs32x15.viscA4 after changing
4089 grid-file angles (used here for coriolis-3d);
4090 - remove (or gzip) few files not needed to run fizhi-cs experiments.
4091 o pkg/exf (vector interpolation):
4092 - rotate vector component toward local grid-axis orientation using grid-angles
4093 (stored in GRID.h) instead of locally computed rotation angle; keep old code
4094 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
4095 o pkg/seaice:
4096 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
4097 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
4098 o pkg/PKG_OPTIONS.h files:
4099 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
4100 outside of the #ifdef ALLOW_THISPKG / #endif block.
4101 - update verification/*/code/PKG_OPTIONS.h files.
4102 o add a verification experiment (offline_exf_seaice/input.seaice) that test
4103 the B-grid LSOR solver
4104 o pkg/seaice: sort out emissivity and long wave radiation step 2:
4105 - add emissivity for snow and ice as new run-time parameters
4106 (unfortunately) that default to the corresponding exf values; this
4107 changes results in most verification experiments so that for backward
4108 compatibility these parameter have to be set explicitly to inconsistent
4109 values (ugly);
4110 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
4111 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
4112 until we agree how to handle this bug properly
4113 o pkg/exf (interpolation):
4114 - add a set of run-time param ({inputfield}_interpMethod), one for
4115 each interpolated input field, to select the interpolation method
4116 with a value of zero switching off the interpolation;
4117 - print interpolation parameters to standard output;
4118 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
4119 (to use instead runoff_interpMethod=0 in data.exf).
4120 - simplify default setting of interpolation parameters (for all fields,
4121 set position to match model grid cell-center position, leading to trivial
4122 interpolation in case of regular Lat-Lon grid) and fix for the case of
4123 non-uniform delY.
4124 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
4125 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
4126 this factor is absolutely required, because the lw exitance (= out-going
4127 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
4128 where the reflectivity rho = 1-emissivity for conservation reasons. Once
4129 this is established, we can remove the CPP-Flag (if we want to).
4130 o pkg/seaice:
4131 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
4132 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
4133 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
4134 what the name implies (and not emissivity*BoltzmannConstant), this means
4135 the old default value of 5.5e-8 now means
4136 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
4137 S/R exf_readparms
4138 - FV-discretization of the B-grid LSOR solver, turn on with
4139 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
4140 of the calling routine dynsolver, so that B and C-grid code look a
4141 little more alike.
4142 - fix index bugs in ostres.F (B-grid code)
4143 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
4144 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
4145 default for SEAICE_emissivity, if useEXF; requires setting a wrong
4146 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
4147 backward compatiblity
4148 o model/src: use sigmaR in calc_ivdc
4149
4150 checkpoint63g (2011/12/16)
4151 o pkg/seaice/seaice_growth.F:
4152 fix heat conservation of the coupled ocean-seaice system.
4153 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
4154 solid vs liquid water treatment is resolved via QNET.
4155 o pkg/seaice/seaice_growth.F:
4156 add missing term for sublimation in saltFlux, which was breaking conservation.
4157 o pkg/seaice/seaice_model.F:
4158 Remove this patholigical case treatment in evolution branch,
4159 where it is un-necessary and breaks conservation.
4160 Update global_ocean.cs32x15/results accordingly for
4161 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
4162 o model/src:
4163 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
4164 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
4165 o pkg/obcs:
4166 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
4167 tendency for temperature and salinity that is then applied to update
4168 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
4169 horizontal advection and diffusion contributions on the boundary (in
4170 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
4171 removing the mask in S/R timestep_tracer. The advantage of this approach is
4172 that the updated tracer values include contributions from the surface
4173 forcing and vertical diffusion.
4174 This modification changes exp4.stevens because of vertical diffusion.
4175 o model/src:
4176 change non-curvilinear grid setting to also work with exch2 + blank tiles:
4177 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
4178 face dimensions.
4179 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
4180 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
4181 and INI_SPHERICAL_POLAR_GRID.
4182 change test-experiment global_ocean.90x40x15:
4183 - split the domain in many more tiles (9x4 tiles of 10x10 each);
4184 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
4185 - update results of both test (std & dwnslp).
4186 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
4187 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
4188 o model/src:
4189 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
4190 and fix initialisation when using sigma-coords.
4191 o model/src:
4192 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
4193 to their current value at the beginning of forward_step.F": add a new run-time
4194 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
4195 - set doResetHFactors=T in the following test exp:
4196 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
4197 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
4198 and tutorial_global_oce_in_p (nonLinFS in p)
4199 o pkg/ecco
4200 - added IES cost term
4201 o verification/advect_xz
4202 - scale down the depth by 1/100 (from 200 km to just 2.km)
4203 - add secondary test using divergent flow, r-star and implicit vertical advection.
4204 - add note (check_conserve_TS.txt) and matlab script to check global
4205 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
4206 o pkg/rbcs:
4207 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
4208 o pkg/obcs (Stevens BCs):
4209 - fix various problems in the phase speed computations of the Stevens
4210 boundary conditions:
4211 - sign error for western and southern boundaries,
4212 - time tendencies were underestimated by factor of dTracerLev and some just
4213 zero (for multidim advection schemes) -> now estimate time tendencies
4214 from difference between previous (n) time level and the one before (n-1);
4215 this requires storing a field per tracer per boundary, also in the pickup
4216 files.
4217 - replace deltaTmom in cflMer/Zon computation with dTracerLev
4218 - set default phase velocity to cflMer/Zon
4219 - update verification experiment exp4.stevens
4220 o pkg/generic_advdiff (implicit_r):
4221 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
4222 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
4223 - fix implicit vertical diffusion or advection with NonLin FreeSurf
4224 (was using current recip_hFacC instead of future recip_hFacC): set future
4225 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
4226 solver S/R ;
4227 - fill diagnostics of vertical advective fluxes (computed from tendency)
4228 when using implicit vert. advection;
4229 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
4230 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
4231 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
4232 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
4233 o pkg/diagnostics:
4234 - add diags for T & S tendency which goes through Adams-Bashforth.
4235
4236 checkpoint63f (2011/11/30)
4237 o pkg/obcs/obcs_calc_stevens.F:
4238 - join some loops to reduce number of if-statements
4239 - fix a bug in code for northern and southern boundaries.
4240 o pkg/seaice/seaice_init_varia.F
4241 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
4242 caused zero ice-velocities for the B-grid code
4243 o pkg/seaice/seaice_init_fixed.F
4244 - fix a bug in the initialisation of the second metric terms
4245 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
4246 - this affects all seaice configurations with useCurviLinearGrid = .true.
4247 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
4248 = .true. (default)
4249 - the only verification experiment affected is global_ocean.cs32x15:
4250 icedyn, seaice, and seaice_dynmix (AD)
4251 o pkg/thsice/thsice_diagnostics_state.F
4252 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
4253 not contain garbage that can lead to surprises in diagstats_calc.F
4254 o model/src:
4255 - move bi,bj loops inside INTEGR_CONTINUITY ;
4256 - call INTEGR_CONTINUITY directly from forward_step.F
4257 (previously called from momentum_correction_step.F)
4258 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
4259 forward_step.F and pkg/ecco/the_main_loop.F
4260 o model/src/do_oceanic_phys.F:
4261 - reset addMass to zero only if useICEFRONT ;
4262 - separated k-loop for rhoInSitu calculation ;
4263 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
4264 and at constant T,S (= WdRHOdP);
4265 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
4266 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
4267 transport of locally-referenced potential density);
4268 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
4269 o gluemnc:
4270 - replace ncrcat with ncks when adding variables to *.glob.nc
4271 - change the way variables without record dimensions are handled so that
4272 files that have variables with and without record variables can be glued:
4273 add a record dimension with a new unique name to be able to differentiate
4274 between variable with and without a-prior record dimensions. Remove
4275 this record dimension before adding the variable to the *.glob.nc file.
4276 This procedure automatically works also for grid.*.nc files that do not
4277 have any record dimension.
4278 o verification/cpl_aim+ocn:
4279 - generate new reference output on baudelaire (gfortran, mpich2) (previously
4280 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
4281 o pkg/obcs/obcs_calc_stevens.F:
4282 - add code for northern and southern boundaries.
4283 - reorder some loops to save some operations and so that drFBar can be scalar
4284 o model/src:
4285 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
4286 truncation) and add diagnostics for Adams-Bashforth tendency increment.
4287 - update test-exp. AD output:
4288 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
4289 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
4290 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
4291 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
4292 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
4293 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
4294 tutorial_plume_on_slope.
4295 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
4296 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
4297 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
4298 does not even come with an F77 compiler anymore, this should not be
4299 a limitation
4300
4301 checkpoint63e (2011/11/06)
4302 o pkg/seaice adjoint of LSR:
4303 - substantially rework STORE dirs.
4304 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
4305 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
4306 and only perform SOLV_MAX_FIXED adjoint iters.
4307 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
4308 always goes to same record, meaning that the last forward field will be
4309 the one used in the adjoint - an approximation.
4310 - now produces non-zero LSR-related gradients, and acceptable gradients for
4311 An's zonal (x-z) test case (to be checked in)
4312 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
4313 (but these are screwed up by the thermodynamics in the first place);
4314 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
4315 output_adm.txt also reflects changes to seaice_lsr
4316 - global_ocean.cs32x15:
4317 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
4318 (output_adm.seaice.txt was updated)
4319 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
4320 (output_adm.seaice_dynmix.txt)
4321 o test-exp. exp4+stevens:
4322 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
4323 o pkg/seaice (lsr solver):
4324 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
4325 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
4326 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
4327 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
4328 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
4329 - compute (with new S/R) and print initial (+ free-driff sol. if available)
4330 and final residual of linearised system.
4331 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
4332 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
4333 o pkg/obcs: Stevens BCs (still only for east and west)
4334 - fix Stevens BCs by using intermediate velocities of previous
4335 time step as "baroclinic" contribution rather velocity of one grid cell
4336 inside the boundaries; more consistent but makes the entire treatment
4337 more complicated, requires new pickup files and two new S/Rs:
4338 obcs_copy_uv_n and obcs_save_uv_n
4339 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
4340 (undefined by default)
4341 - silently move computation of some grid factors into separate loops to
4342 save some recomputations
4343 - add a hack for non-linear free surface
4344 - add a verification experiment to exp4 that tests this code
4345 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
4346
4347 checkpoint63d (2011/10/25)
4348 o pkg/obcs + seaice-dynamics:
4349 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
4350 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
4351 values (consistent with an implicit method).
4352 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
4353 return to older implementation (same results as before); note that none of
4354 the "experimental" OBCS_SEAICE options are implemented in the new version.
4355 - switch test exp. seaice_obcs to use new version (update output).
4356 o pkg/seaice:
4357 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
4358 - add parenthesis in Water-Ice drag calculations (evp & lsr);
4359 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
4360 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
4361 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
4362 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
4363 o pkg/layers:
4364 - Include potential density as new coordinate (Thanks to David Munday)
4365 o pkg/dic:
4366 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
4367 carbonate computation/output to CALC_PCO2_APPROX
4368 o pkg/generic_advdiff
4369 - make TAF generate code that vectorizes:
4370 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
4371 o model/src:
4372 - improve vectorization also for adjoint code of
4373 solve_tridiagonal and solve_pentadiagonal. As this requires up to
4374 5 new 3D-fields, this code is only turned on for the combination of
4375 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
4376 for singular matrix check (only for TARGET_NEC_SX).
4377 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
4378 ALLOW_AUTODIFF. This flag now needs to be set outside of
4379 solve_tri/pentadiagonal.F
4380 o pkg/exf:
4381 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
4382 optional namelist EXF_NML_OBCS).
4383 - add many debug-print (to trace down where pkg/cal error msg comes from)
4384 o pkg/mom_vecinv/mom_vi_hdissip.F
4385 - rearrange loops so that vectorization is improved and in particular
4386 the adjoint routine vectorizes. The code is a little longer now, but I
4387 think easier to read.
4388 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
4389 o pkg/seaice:
4390 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
4391 o pkg/exch2:
4392 - alternative code (without tile x tile matrix) for cumulated (global) sum;
4393 used as default; keep using matrix version in adjustment.cs-32x32x1.
4394 o tools/build_options:
4395 - after merging some MPI and/or multi-threads specific optfiles so that
4396 the modified default optfile support both built (using genmake2 -mpi
4397 for the MPI built, using genmake2 -omp for OpenMP built),
4398 move now obsolete optfiles to tools/build_options/unsupported/
4399 (add copy of email sent to support list in doc/optfiles_changes.txt)
4400
4401 checkpoint63c (2011/09/28)
4402 o pkg/ebm:
4403 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
4404 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
4405 o pkg/seaice (SItracer pickup)
4406 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
4407 To be done:
4408 - thorough testing of missing fields in S/R seaice_read_pickup
4409 - thorough matching between generic tracers and specific fields used
4410 (e.g. volume-weighted age, area-weighted age, salinity, ...)
4411 o pkg/grdchk:
4412 - all procs calculate and print finite-difference gradient (for testreport)
4413 - change description output used by testreport;
4414 - AD testing: also compare and report Finite-difference gradient;
4415 => update all output_adm*.txt
4416 o test exp. global_ocean_ebm:
4417 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
4418 and turn on exactConserve; update (fwd) output.
4419 o pkg/seaice (LSR):
4420 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
4421 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
4422 * identical results with non-CS topology (but save up to half of EXCH calls)
4423 * no much changes in cs-32 verification tests since no ice at face edges
4424 (differences due to convergence criteria, since nb of iterations changed)
4425 * expect some differences on lat-lon-cap grid.
4426 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
4427 o pkg/exch2:
4428 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
4429 many tiles); until alternative coding is added, just add a stop.
4430 o pkg/kpp:
4431 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
4432 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
4433 o optfiles:
4434 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
4435 into corresponding standard one, which now support different build:
4436 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
4437 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
4438 o pkg/obcs (seaice):
4439 - add missing EXCH for uIce,vIce after applying OBCS;
4440 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
4441 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
4442 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
4443 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
4444 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
4445 and eedata.mth for MPI and mutlti-threaded testing.
4446 o pkg/flt:
4447 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
4448 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
4449 - fix pickup and trajectories + profiles output with multi-threads;
4450 - add parameter to select group of fields to write along trajectory and
4451 profile (default unchanged);
4452 - only call PORT_RAND* function when flt_noise <> 0;
4453 - add multi-threaded test for verification exp. flt_example.
4454 o eesupp/src:
4455 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
4456 - USE_OMP_THREADING: check that number of threads (from eedata) matches
4457 actual number (from env.var. setting).
4458 o pkg/ebm:
4459 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
4460 - add multi-threaded test for verification exp. global_ocean_ebm
4461
4462 checkpoint63b (2011/08/29)
4463 o pkg/ebm:
4464 - fix sign of runoff;
4465 - update directly forcing fields (Qnet,EmPmR) to use standard
4466 external_forcing_surf.F (remove ebm_forcing_surf.F);
4467 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
4468 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
4469 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
4470 - update global_ocean_ebm parameters file data and update output (fwd+ad).
4471 o verification/matrix_example:
4472 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
4473 MPI and mutlti-threaded testing.
4474 o pkg/matrix:
4475 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
4476 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
4477 - fix for multi-threaded (remove DATA statement);
4478 - use standard DIFFERENT_MULTIPLE function;
4479 - add MATRIX_OPTIONS.h
4480 o verification/matrix_example:
4481 To allow to split the domain in several tiles, change the domain size
4482 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
4483 Western side) of land points.
4484 o (*_)write_pickup:
4485 - fix few bugs in mypackage_read/write_pickup.F
4486 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
4487 array of length 1 (was caught by compiler syntax-check).
4488 o pkg/diagnostics (velocity potential solver):
4489 - fix initialisation of main diagonal matrix (for overlap values)
4490 o tools/build_options:
4491 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
4492 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
4493 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
4494 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
4495