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Revision 1.2372 - (show annotations) (download)
Tue Jan 30 14:10:51 2018 UTC (5 years, 1 month ago) by jmc
Branch: MAIN
CVS Tags: checkpoint66o, HEAD
Changes since 1.2371: +4 -1 lines
Final CVS tag: checkpoint66o

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.2371 2018/01/18 14:15:37 jmc Exp $
2 $Name: $
4 Notes on tags used in MITgcmUV
5 ==============================
7 checkpoint66o (2018/01/30)
8 => Final CVS tag ; disable CVS check-in.
10 checkpoint66n (2018/01/18)
11 o pkg/seaice & down_slope:
12 - remove few files from ${pkg}_ad_diff.list (when calling S/R is not in
13 any *_ad_diff.list)
14 o pkg/shelfice:
15 - account for "shelficeLoadAnomaly" in computation of initial pressure
16 that is used in EOS (case selectP_inEOS_Zc >= 2).
17 o pkg/aim_v23:
18 - merge namelist "AIM_PAR_CO2" into "AIM_PARAMS" and replace Aim_CO2_Flag=2
19 option with aim_select_pCO2=2 (using #define ALLOW_AIM_CO2);
20 - add option to derive LW absorption in CO2 band as function of pCO2,
21 using either prescribed pCO2 (aim_select_pCO2=1), or computed pCO2
22 from well-mixed atm-box (aim_select_pCO2=3).
23 o pkg/gchem, changes to enable to use several geo-chemistry pkgs together:
24 - new CPP option GCHEM_ADD2TR_TENDENCY around definition of gchemTendency
25 array (replacing #ifndef GCHEM_SEPARATE_FORCING) ;
26 - in GCHEM_FIELDS.h, change dimension of array "gchemTendency"
27 from PTRACERS_num to GCHEM_tendTr_num ; this later one is set in new header
28 file: GCHEM_SIZE.h, to be included anytime GCHEM_FIELDS.h is included ;
29 - new set of S/R, called from GCHEM_TR_REGISTER, to record rank (in pTracer
30 array) and number of tracers for each geo-chemistry pkg ;
31 - check that GCHEM tracers all fit in pTracer and gchemTendency arrays ;
32 - initialise gchemTendency array in gchem_init_vari.F ;
33 - fix storage directives for gchemTendency ;
34 - add some entry points for new geo-chemistry pkg SPOIL.
35 o verification/isomip:
36 - update secondary test (input.htd): a) drop cd_scheme, useJamartWetPoints=T
37 and increase viscAh ; b) use ivdc_kappa with implicit Diff & Visc ;
38 c) switch off SHELFICEboundaryLayer, turn on pCellMix_select (=20) and
39 use SHELFICEselectDragQuadr=1 ; add new set of pickup files.
40 o pkg/shelfice:
41 - Replace CPP option: SHI_USTAR_WETPOINT with run-time parameter:
42 SHELFICE_oldCalcUStar (default=F <--> #define SHI_USTAR_WETPOINT)
43 but keep only original (old) formula in SHELFICEboundaryLayer code.
45 checkpoint66m (2017/12/12)
46 o add another hook (S/R PDF_FINALIZE) for the Parallel Data Assimilation
47 Framework PDAF (http://pdaf.awi.de/) in the_main_loop.F
48 o pkg/autodiff:
49 - fix pkg/exf AD variable output (mainly ADJprecip), left from pkg/exf modif
50 on Jan 27, 2017. Try also to fix ADJrunoff and TLM output (but less clear).
51 o pkg/obcs:
52 - add simpler setting (single value) of OB indices for the case where
53 indices are uniform over the full section (Bruno Deremble contribution).
54 o pkg/rbcs:
55 - increase size of "relaxMaskFile" to read-in from namelist and save it
56 (+check) into new (renamed) "relaxMaskTrFile" array.
57 o model/src:
58 - option (interViscAr_pCell, interDiffKr_pCell) to account for true vertical
59 distance (including hFac) in vertical viscous flux and diffusive flux ;
60 - add option to increase vertical mixing (for both momentum and tracers)
61 near surface and/or bottom where partial cell is too thin ;
62 - for now, both additions above are within: #ifndef EXCLUDE_PCELL_MIX_CODE ;
64 checkpoint66l (2017/10/24)
65 o pkg/kpp, ggl90 & ebm:
66 - read namelist without IOSTAT=errIO to force to stop if there is an error
67 in the parameter file namelist.
68 o pkg/cheapaml: major changes to relaxation coefficient setting:
69 - rename parameters cheapaml_taurelax & cheapaml_taurelaxocean (in days)
70 to cheap_tauRelax & cheap_tauRelaxOce (now in seconds);
71 - if using cheapMaskFile, set relaxation coeff to: cheapMask/tauRelax
72 (instead of 1/cheapMask over ocean and 1/tauRelax over land);
73 - with cheapMaskFile unset: set relaxation coeff according to land/ocean mask
74 (unchanged) but skip increase near domain edges for periodic domain (in X
75 or Y dir) when cheapamlX/Yperiodic=T ; also fix linear increase (over
76 Cheapaml_mask_width grid points) of coeff towards domain edges (previously
77 was increasing away from edges). Update output of experiment "cheapAML_box".
78 o pkg/cheapaml:
79 - move setting of (fixed in time) relaxation coefficient
80 from cheapaml_init_varia.F to cheapaml_init_fixed.F
81 o pkg/exf:
82 - add specific forcing field for tides to feed model new geopotential anomaly
83 forcing, for now within #ifdef EXF_ALLOW_TIDES.
84 - remove from common block unused params: exf_inscal_sst & exf_inscal_sss.
85 o model:
86 - add new 2-d forcing field for time-dependent geopotential anomaly (e.g.,
87 tidal forcing), in m^2/s^2 ; add run-time param to allow to turn it off.
88 o eesupp/src:
89 - shift standardMessageUnit in eeboot.F and I/O units in mdsfindunit.F
90 for coupling to GEOS AGCM: HACK_FOR_GMAO_CPL option in CPP_EEOPTIONS.h
92 checkpoint66k (2017/09/20)
93 o model/src:
94 - add missing CPP brackets (ALLOW_COST, ALLOW_CTRL in load_fields_driver.F
95 and the_model_main.F)
96 o ctrl:
97 - use zeroRL in place of fc when ALLOW_COST is not compiled (in ctrl_pack.F)
98 - call MDS_READ_FIELD / MDS_WRITE_FIELD instead of deprecated
99 mdsreadfield / mdswritefield (in ctrl_get_gen.F, ctrl_map_ini_gen.F,
100 ctrl_map_ini_genarr.F, and ctrl_map_ini_gentim2d.F )
101 o eesupp:
102 - add CPP option to activate some pieces of code for coupling to GEOS AGCM;
103 - shift commonly used IO unit (in eeboot.F) for coupling to GEOS AGCM.
104 o pkg/bling:
105 - bling_production: Fix typo in calcium carbonate uptake. Also rearranging
106 and cleaning
107 o model/src:
108 - move k loop inside correction_step.F (+ update calling S/R)
109 - collect implicit pressure gradient tendencies in local 2-D array;
110 affect results (at machine truncation level) when using 3-D solver; update
111 output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW,
112 rotating_tank, short_surf_wave,tutorial_deep_convection (x2)
113 & tutorial_plume_on_slope.
115 checkpoint66j (2017/08/15)
116 o pkg/ptracers:
117 - fix surface forcing under ice-shelf (useShelfIce=T).
118 o pkg/atm_phys:
119 - use hFac weighted average when applying A-grid atm-phys momentum tendency
120 to C-grid dynamics; this ensures wind-stress match mom tendency.
121 o eesupp/src:
122 - change default for opening scratch files to avoid STATUS='SCRATCH'
123 - close scratch files with STATUS='DELETE'
124 - changes affect eeset_parms.F and open_copy_data_file.F and many routines
125 that read namelists (because they close the scratch files)
126 - you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES
127 in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad)
128 o pkg/atm_phys:
129 - fix unset arguments in (unused) S/R surface_flux_0d.
130 o eesupp/src:
131 - add argument "procId" to S/R EESET_PARMS to fix scratchFile1 & 2 setting
132 (case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F):
133 called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F
134 o pkg/streamice:
135 - remove blank between _EXCH_XY_RL and "()", which my Apple Xcode
136 preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in
137 streamice_driving_stress_fd.F and streamice_advect_2dtracer.F
138 o pkg/diagnostics:
139 - new option to allow to cumulate thickness-factor (hFac) weighted field
140 (if field permitted); implemented by changing sign of "jdiag" pointer
141 (> 0: cumlulate field, < 0: cumulate hFac weighted field).
142 a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell
143 center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR')
144 b) for now, activated by setting fileFlags 3rd character to 'h'.
146 checkpoint66i (2017/07/18)
147 o pkg/cheapaml:
148 - add parameter "useRelativeWind", default set to False; this change the
149 previous setting which was always using relative wind.
150 o add hooks for the Parallel Data Assimilation Framework PDAF
151 (http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F;
152 to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h
153 o pkg/exf:
154 - interpolation of vector fields (exf_interp_uv.F): fix bug in calculation
155 of South-Pole mean value.
156 - interpolation near the poles, case where second additional row is at the
157 pole (or beyond the pole and moved to the pole): change first addition row
158 value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole)
159 row (instead of just a copy of it).
160 o pkg/seaice:
161 - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
162 - add the option to compute no-slip du/dy, dv/dx (i.e.
163 the offdiagonal strain rate e12) by a second order approximation
164 on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
165 it is too messy to implement for the implicit LSR matrix.
166 SEAICE_2ndOrderBC = .FALSE. by default
168 checkpoint66h (2017/06/02)
169 o pkg/seaice:
170 - add new routines to compute stress tensor components and stress tensor
171 divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
172 - change names of diagnostics SIsigI/II (commonly used for invariants)
173 to SIsig1/sig2 (more common for principal components) to avoid confusion
174 o pkf/exf:
175 - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
176 similarly, stop if rotateStressOnAgrid with constant wind-stress.
177 o pkg/seaice:
178 - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
179 EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
180 - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
181 fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
182 o pkg/diagnostics:
183 - small piece of code to rename (old) diagnostics, when namelist is processed.
184 o model/src:
185 - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
186 originally, set as minimum of adjacent hFacC factor ; now (new default)
187 computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
188 Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
189 o pkg/seaice:
190 - add momemtum advection, off by default, still in test phase
191 most of the momentum advection code is adapted and reused from mom_vecinv
192 o pkg/mom_vecinv:
193 - pass these runtime flags:
194 selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
195 as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
196 so that these routines can also be used in pkg/seaice.
198 checkpoint66g (2017/04/24)
199 o model/src:
200 - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
201 to get same expression (regarding machine truncation) in different places
202 in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
203 Update forward output of experiments: global_ocean.cs32x15 (all 5 except
204 viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
205 o pkg/shelfice:
206 - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
207 to shelfice_init_fixed.F
208 - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
209 ini_masks_etc.F for now) to update ocean upper boundary position according
210 to ice-shelf topography (instead of directly updating hFacC).
211 o model/src:
212 - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
213 packages_init_fixed.F to allow other pkgs to set mask and weight fields.
215 checkpoint66f (2017/04/06)
216 o model/src:
217 - add specific run-time param to select level of printed plot-field-maps,
218 set by default to debugLevel. Remove internal param "printDomain".
219 o pkg/seaice:
220 - add flag to add snow mass to seaiceMassC/U/V, the default is
221 SEAICEaddSnowMass=.FALSE., not to change previous results
222 o pkg/bling
223 - Bug fix in bling_production regarding unit conversion for diagnostics
224 being put in the wrong place
225 o model/src:
226 - add back recomputation of rSurfW & S to ensure consistent column thickness
227 (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
228 when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
229 revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
230 o pkg/autodiff:
231 - clean-up "checkpoint.flow"
232 o pkg/rw (Contribution from Jody Klymak):
233 option to set mds file suffix as function of time in simulation:
234 *) new input parameter "rwSuffixType" (read from PARM03 namelist)
235 to select file suffix format; by default (=0), use iteration number;
236 *) add simple routine to return file suffix according to rwSuffixType;
237 *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
238 use new S/R to get file suffix, except for debug output file (diagFreq)
239 and pkgs offline & rbcs input files.
240 o pkg/rw:
241 - uniform processing of "I10" suffix across writing fld routines; used to
242 simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
243 (similar to cg3d.F, cg3d_ex0.F)
244 o pkg/mom_vecinv:
245 - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
246 vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
247 o pkg/bling:
248 - Many small changes intended to clean the code.
249 Unnecessary ADJOINT_SAFEs removed ;
250 removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
251 diagnostics added.
253 checkpoint66e (2017/03/14)
254 o pkg/exf:
255 - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
256 definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
257 use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
258 avoid any dynamic allocation ;
259 - S/R EXF_CHECK: add new check & stop when file-name is defined but not
260 read-in ; add warning when file is read-in but not used within pkg/exf ;
261 + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
262 - update exf_summary.F (print {FLD}RepCycle).
263 o verification/global_with_exf:
264 - switch on exf interpolation in AD test (just like the forward test)
265 o pkg/mom_vecinv:
266 - add storage directives to avoid recomputations within mom_vecinv.F
267 which were generating seg. fault with gfortran -devel
268 o pkg/ctrl, pkg/smooth:
269 - initialize array halos which were generating seg. fault with
270 gfortran -devel in adjoint mode
271 o pkg/exf:
272 - for each input field, enable to specify a field specific repeat-cycle
273 ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
274 o verification/lab_sea:
275 - update AD results of primary test and noseaicedyn test after switching
276 to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
277 check stays about the same.
278 o pkg/exf:
279 - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
280 - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
281 o pkg/bling, USE_EXFCO2 code:
282 - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
283 - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
284 o pkg/exf:
285 - rename S/R EXF_INIT to EXF_INIT_VARIA ;
286 - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
287 repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
288 and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
289 - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
290 EXF_INIT_FLD) and update calls in exf_init_varia.F
291 - For now, for backward compatibility, keep a simplified version of S/Rs
292 EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
293 - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
294 to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
295 o tools/genmake2:
296 - replace "bc -l" (only used once) by "expr" (already used).
297 o verification/global_ocean.cs32x15:
298 - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
299 Note: exf setting (data.exf) can be compared to other exf secondary exp
300 "seaice" (kept with useCAL=T) which has same time dependent forcing.
302 checkpoint66d (2017/02/13)
303 o pkg/exf:
304 - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
305 early on (in packages_boot.F) to stress this change in pkg setting.
306 - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
307 o model/src:
308 - move call to ecco_phys to end of time step; this may induce minor
309 cost function changes by shifting time averages by one time step
310 for some variables; this revision resulted in changed adjoint results
311 in MITgcm_contrib/verification_other/global_oce_cs32
312 o pkg/exf:
313 - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
314 this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
315 e.g. precip, are not available.
316 o pkg/flt:
317 - flt_init_varia.F: use pickupSuff if specified
318 - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
319 intermediate, step towards completing pkg/exch2 support within pkg/flt;
320 ifdef DEVEL_FLT_EXCH2 then:
321 - flt_init_fixed.F: comment out stop
322 - flt_exch2.F: conserve ipart, jpart (grid coordinates)
323 - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
324 - flt_mapping.F: attempt to fix longitude diagnostic near date-line
325 - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
326 o tools/genmake2 & pkg/pkg_depend:
327 - define new type of pkg dependency rule ("=pkg_x"), less strict than
328 the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
329 (-pkg_x in packages.conf).
330 - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
331 - add "+cal" to dependency list of pkg/ecco (needed to compile).
332 - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
333 o utils/matlab:
334 - adding ocean_basin routines for defining basin masks.
335 o pkg/exf:
336 - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
337 arguments, allowing to check (and stop) if parameter setting of
338 {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
339 useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
340 for backward compatibility.
341 - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
342 exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
343 o pkg/bling (USE_EXFCO2 code):
344 - fix missing setting of apco2StartTime according to apco2startdate1 & date2
345 by adding a call to S/R EXF_GETFFIELD_START.
346 o pkg/exf:
347 - allows to compile without pkg/cal (but disabled by current dependency
348 rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
349 run with useCAL=F ; this involves setting directly {FLD}StartTime instead
350 of {FLD}startdate1 & date2 ; consistency check not yet coded.
351 o verification/global_ocean.cs32x15:
352 - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
353 corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
354 o pkg/exf:
355 - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
356 calculations); change FWD experiment global_ocean.cs32x15
357 (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
358 o pkg/exf:
359 - In preparation for addition to NAMELIST, rename internal (_RL) parameter
360 {FIELD}startdate to {FIELD}StartTime
361 Note: new name also fit better the content, i.e, a start time in second.
362 o eesupp/src:
363 - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
364 o pkg/exf:
365 - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
366 to allow to read-in Sensible & Latent Heat flux ;
367 - simplify pkg/exf main options:
368 1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
369 exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
370 compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
371 2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
372 ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
373 3) improve options documentation in EXF_OPTIONS.h.
374 o pkg/ecco:
375 - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
376 ecco_summary.F: add passive tracer cost functions to gencost;
377 m_ptracer and m_boxmean_ptracer
378 o pkg/ctrl:
379 - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
380 parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
381 of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
382 xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
383 o model/src:
384 - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
385 parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
386 o pkg/exf:
387 - exf_getffields.F: add to list of implemented gentim2d contol parameters:
388 xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
390 checkpoint66c (2017/01/19)
391 o verification:
392 - add new option "-src" to testreport to only produce source code (*.f),
393 including taf output src code (if using '-adm'/'-tlm' option).
394 o pkg/exf:
395 - add saltflx :: Net upward salt flux in psu.kg/m^2/s
396 o pkg/diagnostics:
397 - add run-time variable diagMdsDir to specify a subdirectory for
398 diagnostic output when mds is being used and mdsioLocalDir is not.
399 o pkg/mnc:
400 - mnc_utils.F: edit stop message
401 o pkg/autodiff:
402 - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
403 add HAVE_SYSTEM bracket around system call to mkdir
404 o pkg/profiles:
405 - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
406 profiles_readparms.F: call ALL_PROC_DIE before 'stop'
407 - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
408 add HAVE_SYSTEM bracket around system call to mkdir
409 o pkg/smooth:
410 - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
411 - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
412 - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
413 o pkg/exf:
414 - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
415 issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
416 generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
417 - summary: skip detailed field report if not used (empty file-name).
418 o tools/xmakedepend:
419 - In case line editor "ed" is missing, switch to "sed" command to clean-up
420 Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
421 o pkg/exf:
422 - change definition of "hflux" input file to always include Short-Wave;
423 this is now consistent with hflux computation (if using bulk-formulae)
424 and hflux diagnostic & documentation (in EXF_FIELDS.h).
426 checkpoint66b (2016/12/01)
427 o model & momentum pkgs:
428 - implement fully implicit bottom friction combined with implicit surf.
429 pressure, for now, only in hydrostic formulation:
430 + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
431 and run with selectImplicitDrag=2 ;
432 + currently missing diagnostics of bottom drag and vert. viscosity tendency;
433 - partial implicit time-stepping (bot. friction + vert. visc first, then
434 surf. press) corresponding to selectImplicitDrag=1 should be applicable
435 to NH formulation but not available until we solve for surf. pressure
436 increment (instead of full etaN).
437 - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
438 with implicit vertical viscosity.
439 o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
440 - this is a first version that includes many regularisations that may
441 not all be necessary, to be sorted out,
442 - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
443 - change one verification experiment in seaice_itd to use and test new code
444 - seaice_growth: catch a case where the argument of log can be zero
445 or smaller (important for code stability)
446 o model/src:
447 - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
448 & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
449 similar A.X'=Y' system (with same matrix A) in subsequent calls;
450 switch based on errCode (In/Out) argument value; in calling routines,
451 initialise errCode before first call.
453 checkpoint66a (2016/10/18)
454 o pkg/bling:
455 - BLING package now loads in atmospheric pCO2 file using exf package routines
456 Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
457 o model/src & pkg/ptracers:
458 - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
459 GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
460 implicitDiffusion (respectively) are used (even without momImplVertAdv
461 or temp,salt,PTRACERS_ImplVertAdv).
462 o model/src & generic_advdiff:
463 - add parenthesis in main diagonal calculation of implicit vertical
464 diffusion matrix (impldiff.F & gad_implicit_r.F).
465 This affects results at machine truncation level; update output of many
466 verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
467 o pkg/mom_commom & generic_advdiff:
468 - add deep atmosphere and anelastic scaling factor in implicit vertical
469 advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
470 o model/src:
471 - remove few unnecessary temp array copies in solve_tridiagonal.F
472 & solve_pentadiagonal.F
474 checkpoint65z (2016/09/28)
475 o pkg/seaice: fix multithreading for seaice_fgmres.F
476 - remove unecessary variables from common blocks
477 - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
478 basis, that are stored in commom blocks (including integer variable i1)
479 - clean up code a little by removing commented lines that refer to
480 original code
481 - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
482 o MITgcm manual:
483 - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
484 preliminary documentation for generic controls (8.3; ctrl.tex),
485 a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
486 ecco_costfunction.tex
487 o pkg/ecco:
488 - update and cleanup list of CCP options
489 - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
490 is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
491 - add checks that retired run-time options are not used, and in relation
492 to gencost_mask and gencost_errfile
493 - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
494 gencost_nrecperiod
495 - fix m_eta computation for virtual salt flux case
496 - add m_horflux_vol case (selected via gencost_barfile) that computes
497 transports via cost_gencost_boxmean (gencost_flag=-3)
498 - use gencost_flag more systematically (i.e., avoid using gencost_name)
499 for code switches (aside from physical variable selection)
500 o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
501 attempt appears to be a bit of a hack and my need some repair down the road
502 o pkg/exf:
503 - interpolation near South Pole: fix criteria on input field latitude.
504 o pkg/icefront & pkg/exf:
505 - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
506 from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
507 o pkg/exf:
508 - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
509 "exf_output_interp" (in namelist: EXF_NML_04); change output file name
510 (add suffix "_out" instead of a prefix); keep same record number as in
511 input file but always write record 1 first (to avoid a STOP in I/O S/R).
512 Change output file content by writing interpolated field before applying
513 land-sea mask (helpful for debug).
514 - 2 compon. vector interpolation with rotation: apply scaling factor on
515 each compon. (Eastward and Northward) just before rotation.
516 o pkg/bling:
517 - Cleaned package. Removed not needed code and comments.
518 - adjoint example now works
519 (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
520 o pkg/ptracers:
521 - add Bruno Deremble's code to complete the linear surface correction
522 for tracer conservation;
523 - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
525 checkpoint65y (2016/07/29)
526 o pkg/debug (stats):
527 - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
528 proc/thread mapping);
529 - fix Min & Max for case where 1 thread has only empty tiles;
530 - use RL variable to count number of wet grid points (with big domain,
531 can be too large to fit into integer*4).
532 o pkg/monitor:
533 - use RL variable to count number of wet grid points (but used only for del2)
534 - add new routine to compute Advective CFL within tracer time-stepping with
535 writing delayed until next monitor output.
536 o pkg/obcs:
537 - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
538 o pkg/cal:
539 - calandar-dump: treat case myTime < timePhase in the same way as in
540 eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
541 o pkg/dic & seaice:
542 - fix compilation of ocean component for coupled atm+ocn model with
543 seaice dynamics & dic.
545 checkpoint65x (2016/06/11)
546 o add a license text file in main MITgcm tree.
547 o added pkg/bling:
548 - intermediate complexity biogeochemical model
549 - see bling_description.txt for details
550 - verification experiment is global_oce_biogeo_bling (for now, in
551 Contrib/verification_other/); tested daily on baudelaire with gfortran.
552 - add entry point in pkg/gchem for new pkg "bling".
553 o pkg/seaice: fix tensile stength computation
554 - replace global field tensileStrength by tensileStrFac
555 - tensileStrFac can be computed once in S/R seaice_init_varia
556 - fortunately that does not affect any verification results
558 checkpoint65w (2016/05/12)
559 o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
560 with ECCO_CTRL_DEPRECATED defined
561 o verification/global_ocean.cs32x15:
562 - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
563 with "selectNHfreeSurf=1".
564 o model/src (non-hydrostatic free-surface):
565 - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
566 was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
567 - Calculate surface vertical velocity after 2-D solver adjustment (accounts
568 for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
569 and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
570 This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
571 - Update output (changes at machine truncation level) of verification exp:
572 exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
573 short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
574 o pkg/seaice: ITD code
575 - fix picking up from a single category model by initialising
576 heff/area/hsnowITD = 0. in seaice_itd_pickup.F
577 - split a long warning message in seaice_check_pickup.F into two lines,
578 because NEC SX-ACE cannot deal with the long line.
579 o model/src:
580 - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
581 o pkg/seaice:
582 - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
583 o pkg/seaice:
584 - add basal stress as parameterisation for grounding ice
585 following Lemieux et al. (2015)
586 - turn on by setting new parameter SEAICEbasalDragK2 to a value
587 larger than 0. Lemieux et al. (2015) recommend 15.
588 - The adjoint complains with extra recomputations so there is also a
589 new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
590 order to postpone the problem
591 - compile the new code in lab_sea
592 o verification/halfpipe_streamice:
593 - update both TAF and OpenAD adm output (machine truncation differences)
595 checkpoint65v (2016/04/08)
596 o verification/advect_xz:
597 - increase overlap size from 3 to 4 and add new secondary test for PQM
598 advection scheme (with mono & wino limiter).
599 - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
600 o model/src:
601 - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
602 added phi0Ref) to set vertical axis origin and phiRef origin;
603 keep Ro_SeaLevel for backward compatibility (with a warning).
604 According to coordinate and fluid type:
605 OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
606 ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
607 OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
608 ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
609 - remove Ro_SeaLevel from ATM experiment parameter files;
610 - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
611 complement; update output.txt (changes at machine truncation level).
612 o pkg/seaice/seaice_evp.F
613 - simplify computation of deltaZ and zetaZ to simple averaging following
614 Bouillon et al. (2013). This removes a lot of code, but also changes
615 verification experiment lab_sea.hb87 -> updated
617 checkpoint65u (2016/03/14)
618 o pkg/generic_advdiff:
619 - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
620 with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
621 Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
622 testing and not for actual use.
623 o model/src:
624 - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
625 origin r = rF(1);
626 - add options (parameter selectP_inEOS_Zc) to select which pressure to use
627 in EOS for height coordinate: enable to include NH Pressure or to use
628 more accurate pressure vertical profile; options not linked to EOS type
629 (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
630 - start to implement variable gravity (along vertical): for now, only with
631 z-coords (not even z*).
632 - add Ideal Gas equation of state for height coordinate.
633 - update OpenAD output (affected at machine truncation level) of exp:
634 global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
635 o pkg/exf:
636 - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
637 of exf interpolation (before any rescaling, rotation or interpolation
638 to velocity point) for each field that gets loaded from file. This option
639 identically mimics the input file organization (e.g. record numbers in year
640 by year input files) besides the change in horizontal grid.
641 - add rotateStressOnAgrid run-time switch so that wind stress fields
642 can be provided on the A-grid in zonal/meridional direction and
643 rotated on the fly. This only applies to the case when the exf
644 interpolation is off and rotateStressOnAgrid is false by default.
645 o model/src:
646 - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
647 it's also used with pkg/atm_phys) and add few more parameters (but still
648 inactive, src code yet to come)
650 checkpoint65t (2016/02/10)
651 o pkg/atm_phys:
652 - from Ruth Geen: add optical depth dependence on CO2 concentration.
653 o model/src:
654 - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
655 for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
656 Update output of exp. deep_anelastic (changes at truncation level).
657 o tools:
658 - add a hack in "remove_comments_sed" (used only with TAF) for recent
659 version of OpenMPI (shipped with FC.23): comment out the new header
660 file "mpif-sizeof.h" which causes problems to TAF.
661 o pkg/seaice:
662 - change the termination criterion so that maxits (SEAICElinearIterMax)
663 has an effect
664 - unify iteration parameters for implicit solvers (JFNK and Picard)
665 SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
666 SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
667 SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
668 SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
669 SEAICEnonLinTol replaces JFNKgamma_nonlin
670 - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
671 - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
672 use with SEAICEuseKrylov
673 o pkg/seaice/seaice_lsr.F
674 fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
675 relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
676 an effect.
677 o pkg/seaice: add two new parameters
678 - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
679 parameter is not in any namelist)
680 - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
681 a preconditioner for the non-linear Newton iteration of the JFNK
682 solver
683 o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
684 affects some experiments at truncation level:
685 - global_ocean.cs32x15.icedyn (11 digits),
686 - global_ocean.cs32x15.seaice (11 digits),
687 - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
688 - also update global_ocean.cs32x15 adjoint and tangent-linear results
689 o pkg/salt_plume & pkg/thsice:
690 - for coupled set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
691 connect salt_plume flux to ATM-OCN coupling pkgs interface:
692 a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
693 export to coupler interface) even without compiling pkg/salt_plume ;
694 b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
695 (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
696 o pkg/dic:
697 - use the updated seaice fraction (from seaice pkgs) for DIC forcing
698 instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
699 called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
700 - move also update with values from ATM-OCN Coupler in the same new S/R
701 (previously done in ocn_apply_import.F).
702 o tools/adjoint_options:
703 - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
704 has been changed on Jan 14, 2016.
705 o pkg/ggl90:
706 - add alternative discretisation of vertical shear (off by default), to
707 compute the mean (@ grid-cell center) of vertical shear compon instead of
708 vertical shear of mean flow (@ grid-cell center).
709 - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
710 results on adjacent faces of cubed-sphere grids; this fix the restart.
711 o pkg/atm_compon_interf:
712 - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
713 pass last value, stored directly before export to CPL ;
714 Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
715 - remove atmSLPr from pickup files (no longer needed for restart)
717 checkpoint65s (2016/01/13)
718 o eesupp & genmake2:
719 - first check for Function ETIME and, if it fails, then check for subroutine
720 ETIME and consistent output; use the appropriate version in timers.F
721 o model/src:
722 - to check restart test, add option to apply EXCH to U,V earlier, just before
723 integr_continuity; turned off by default.
724 o pkg/dic:
725 - remove CPP option USE_ATMOSCO2 (not needed)
726 o tools/tst_2+2:
727 - try to ignore difference between +0 and -0 in binary file, causing test
728 to fail for no good reason.
729 o eesupp & genmake2:
730 - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
731 but also check (in genmake2) that test runs and returns meaningful results.
732 o coupler pkgs:
733 Finish implementation of optionally-exchanged variable switches (started on
734 Nov 12) with addition of few more exchanged fields, including 2-way exchange
735 of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
736 advection in OCN component; this requires sequential coupling.
737 coupler (pkg/atm_ocn_coupler):
738 - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
739 routines (useful for debug).
740 - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
741 flux, DIC fields) if corresponding switch is ON.
742 - add option to export RunOff to OCN (to use for DIC river input)
743 - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
744 components (pkg/atm_ & ocn_compon_interf):
745 - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
746 optionally exchanged fields; add a check & stop in cpl_readparms.F.
747 ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
749 - rename: fracIce -> sIceFrac_cpl (<- match coupler var name)
750 + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
751 - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
752 - hold in common block coupler optionally-exchanged variable switch
753 and set default "useImportXXX" accordingly; + check & stop if inconsistent.
754 - add diagnostics for all imported fields from coupler (in both OCN & ATM);
755 this is intended to replace the OCN cplFldtave.* output files (not updated
756 to contain new additional exchanged fields).
757 o pkg/dic:
758 - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
759 o pkg/thsice:
760 - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
761 and writing of thsice pickup files.
762 o pkg/atm_compon_interf:
763 - move all field individual export-call out of cpl_export_import_data.F
764 into new S/R ATM_EXPORT_FIELDS
765 o pkg/atm_compon_interf:
766 - store state variables (for now, only thSIce fields) just before beeing
767 exported (in cpl_export_import_data.F, like on ocean side) instead of from
768 atm_store_my_data.F like all exported fluxes.
769 - new version of pickup_cpl: write field names into meta file and read meta
770 file to find field postion in pickup. Also only write/read fields meeded for
771 restart (same logic as main pickup file ; also using pickupStrictlyMatch)
772 o pkg/dic:
773 - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
774 o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
775 pressure replacement method (=1., default) or original Hibler (1979) (=0.)
776 value can be from domain [0,1] to average between the two methods
777 o pkg/atm_phys:
778 - allow to provide 2-d map of albedo and mixed-layer depth from files (but
779 hold fixed in time).
781 checkpoint65r (2015/12/21)
782 o pkg/seaice:
783 fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
784 solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
785 o pkg/seaice:
786 - fix a bug in computing areaS in (J-J -> J-1) that affects runs
787 when SEAICEscaleSurfStress=.TRUE.,
788 - apply areaW and areaS in S/R seaice_calc_lhs
789 o pkg/atm_phys:
790 - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
791 (shortwave & longwave, net & downward) and diagnostics of temp. tendency
792 for individual contribution (convection, LSC cond, radiation)
793 - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
794 information); activated with: solar_exponent=0. and wv_exponent=-1.
795 o pkg/ggl90:
796 - within IDEMIX add upper limit for horizontal group velocity to
797 avoid instability problems in the explicit horizontal diffusion term for
798 long time steps or high resolution
799 o pkg/diagnostics:
800 - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
801 (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
802 o testreport:
803 - remove "-v" (verbose option) in default mpirun command.
804 o pkg/seaice/seaice_growth:
805 - catch potential division by zero in ITD code, does not change
806 verification results
807 o pkg/ecco:
808 - retire old codes to the Attic. The calls to retired functions are
809 left in a commented form in case they ever need to be re-activated.
810 - ecco_check.F: issue warning if any old CPP option is
811 defined that corresponds to retired codes -- then stop.
812 o pkg/atm_compon_interf:
813 - change seaice fraction (use for OCN dic surf.flux) stored and sent to
814 coupler: use last time-step value instead of average over cplSendFrq_iter
815 time-step, similar to what is done for seaIceMass.
816 This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
817 o eesupp & genmake2:
818 - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
819 <= remove until a fix is found for some ifort version on ia32 machine.
820 o pkg/seaice/seaice_evp:
821 - refine residual computation
823 checkpoint65q (2015/11/18)
824 o pkg/seaice/seaice_evp:
825 - fix residual computations so that they no longer affect the actual
826 simulation code
827 - fix seaice_readparams to be able to actually set new parameters
828 SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
829 o model/src:
830 - fix wrong truncation (single prec) from "FLOAT" function in expressions
831 like: deltaT*FLOAT(myIter) when myIter is large:
832 a) replaced by DFLOAT (if not seen by TAF);
833 b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
834 o pkg/aim_v23:
835 - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
836 when pickupSuff is set ; do write rolling pickups + at the end of the run.
837 o pkg/atm_ocn_coupler + ocn_compon_interf:
838 - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
839 coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
840 add corresponding call in DO_OCEANIC_PHYS.
841 o coupler pkgs:
842 Start a new way to set-up optionally-exchanged variables (previously, only
843 there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
844 data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
845 send switch to ATM & OCN compon before reading their own "data.cpl" (so that
846 compononent param default can be set accordingly).
847 Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
848 but rather applies to a group a fields (going both ways like for DIC)
849 and corresponds to an option of coupling config.
850 coupler (pkg/atm_ocn_coupler):
851 - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
852 and read namelist directly (without eessup S/R calls) instead of
853 in the very un-flexible old way, 1 param per line, in fixed order;
854 - add error-counter to track errors (e.g., missing "data.cpl") and to stop
855 cleanly in CPL_CHECK_CPLCONFIG
856 - add new coupling-exchange selectors (some not yet active) including
857 cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
858 and ocnCpl_exchange_DIC=T in OCNIDS.h);
859 - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
860 component ; called directly from coupler.F, after comp. registrations;
861 - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
862 atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
863 -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
864 components (pkg/atm_ & ocn_compon_interf):
865 - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
866 CPP header file in all pkg source files.
867 - move checking of comp. configs out of cpl_exch_configs.F into new S/R
869 - add error-counter to track errors (e.g., in "data.cpl") and to stop
871 - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
872 from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
874 verification/cpl_aim+ocn/:
875 - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
876 "data.cpl" for coupler (in input_cpl).
877 o eesupp/inc:
878 - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
879 #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
880 to always cumulate tile local-sum in the same order (still uses
881 MPI_Allreduce like standard code).
882 - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
883 that are now identical to standard version (in eesupp/inc).
884 o pkg/shelfice:
885 - add SHELFICETransCoeffTFile for initializing spatially varying
886 heat and salt transfer coefficients
887 o pkg/atm_compon_interf & ocn_compon_interf:
888 - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
890 - move bi,bj loops inside S/R OCN_STORE_MY_DATA
891 o pkg/atm_ocn_coupler:
892 - initialise to zero ATMVARS.h & OCNVARS.h arrays.
893 o pkg/rbcs:
894 - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
895 to compile with maskLEN=1 when all tracers use the same RBCS-mask.
896 - add a short report (to STDOUT) about RBCS-mask settings.
898 checkpoint65p (2015/10/23)
899 o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
900 there is no adjoint test for EVP, we don't know what it does to the adjoint
901 solution, but at least there are no more recomputation warnings left
902 o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
903 a chance of giving the same results as a fully converged VP (JFNK) solver
904 o tools/adjoint_options/adjoint_diva:
905 - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
906 o pkg/streamice:
907 - spotted bug in streamice_driving_stress using dyG where should have been dxG
908 o pkg/exf:
909 - remove STOP statement that prevented to use wind or (wind-)stress
910 interpolation for constant-in-time forcing fields (wind/stress period = 0).
911 o pkg/seaice:
912 - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
913 5 additionals 2D fields and 6 new store directives
914 - change logic in seaice_readparms.F: EVP code can now be turned on in
915 various ways, setting SEAICE_deltaTev is no longer required,
916 alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
917 or SEAICEaEVPcoeff
918 o pkg/shelfice/shelfice_thermodynamics.F
919 - redefining uLoc/vLoc to u/v, instead of 2u/v
920 o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
921 - this is an intermediate state of a truely converging EVP that has
922 the potential of outperforming implicit VP methods, I do not recommend
923 using it yet.
924 - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
925 and all parameters are hardwired
926 - for convergence it still requires very smooth regularisations, that means,
927 if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
928 different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
929 specific averaging appears to be required, still subject to tuning
930 - still needs cleaning and I need to turn parameter into runtime parameters
931 - add code to compute and print residuals of iteration, compile with
932 defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
933 o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
934 that entered with r1.54 on Sep04, 2015, -> update results
936 checkpoint65o (2015/09/14)
937 o pkg/mom_vecinv & mom_common:
938 - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
939 called from there.
940 - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
941 allows to use Vector-Invariant form in deep atmos and anelastic formulation
942 o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
943 and Koenig-Beatty+Holland (2012)
944 - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
945 - global 2D field tensileStrength, computed in seaice_calc_ice_strength
946 - requires an extra input argument for S/R seaice_calc_viscosities
947 - tensileStrength's depth dependence is different from Itkin et al. (2015)
948 (to be changed and played with, for now exponential)
949 o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
950 - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
951 by AREA according to Connelly et al. (2004), JPO.
952 - For EVP and the LSR solver, the implicit part of the drag term is
953 the only non-zero term in the denominator when there is no ice (which
954 prevented running the model with zero ice-ocean drag). If
955 SEAICEscaleSurfStress = .TRUE., this results in a division by zero
956 (or zero main diagonals BU/BV) which need to be caught. A practical
957 consequence is that for open water, the momentum equation reduce
958 to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
959 they happen to be zero, often leading to a non-zero solution over
960 open water.
961 o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
962 efficient EVP method.
963 - introduce area-weighted averages for e12 (analogously to
964 seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
965 remain, but also changing the order of terms in the previous average
966 changed the results as much) -> update experiment
968 - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
969 TEM-code
970 - adjust loop bounds so that only required fields are computed
971 - add new averaging code for zetaZ/deltaZ (again similar to
972 seaice_calc_viscosities.F), inactive by default for now (will change
973 results again), but will replace old code eventually
974 o eesupp/src:
975 - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
976 to always cumulate tile local-sum in the same order
977 (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
978 Still uses MPI_Allreduce (like standard code) but on array of tiles
979 and should be faster than GLOBAL_SUM_SEND_RECV code.
980 - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
981 (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
982 - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
983 aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
984 fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
985 natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
986 tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
988 checkpoint65n (2015/07/29)
989 o pkg/thsice:
990 - add a warning when used with pkg/aim but without updating SST
991 (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
992 o pkg/offline:
993 - change where Offline-Fields are loaded, from load_fields_driver.F to
994 directly within FORWARD_STEP, just after updating iter number and time;
995 - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
996 S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
997 These changes allow:
998 a) to recover exactly on-line results using deltaToffline=deltaTClock,
999 tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
1000 both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
1001 time-step, both with GM & KPP files and with recomputing these fields;
1002 b) no needs to switch on staggerTimeStep anymore;
1003 c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
1004 - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
1005 o pkg/offline:
1006 - change (rarely used) offset-iteration parameter to an offset time (in s):
1007 can easily recover previous offset-iter effect by setting offset-time
1008 (offlineTimeOffset) to offset-iter x deltaToffline;
1009 - do not turn-off Temp & Salinity surface relaxation when using KPP (used
1010 in KPP as part of surface buoyancy forcing) in offline run.
1011 - fix ptracers KPP non-local term in the case where KPP is re-computed.
1012 o OpenAD
1013 - Adding preliminary ggl90 test to OpenAD verification.
1014 Config. with ggl90 currently diverges after 64 time steps
1015 so will need more work to become more stable
1016 - Adding preliminary kpp test to OpenAD verification.
1017 required small tweakes in kpp_routines.F
1018 - Merge and update from Krishna Narayanan's contrib area:
1019 * Add one variable for preliminary OpenAD DIVA
1020 * Add replacement time-stepping for OpenAD DIVA
1021 * genmake2 flag -diva (but only for OpenAD; preliminary)
1022 * required modifs for OAD_support
1023 successful preliminary test for tutorial_global_oce_biogeo/
1024 o pkg/seaice:
1025 - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
1026 - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
1027 delta with a smooth function in s/r seaice_calc_viscosity
1028 (no effect on EVP)
1029 - rename local suffix "sqr" into "sq" for more consistent variable names
1030 o pkg/seaice:
1031 add new parameter SEAICE_deltaMin that is used ***only***
1032 for regularizing Delta (and nothing else, like the parameter
1033 which is also used for all sorts of things SEAICE_EPS).
1034 Defaults to SEAICE_EPS for backward compatibility only.
1035 o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
1036 the wrong key by inialising it before use -> fixes a recomputation
1037 problem but does not fix the gradient
1038 o pkg/layers:
1039 - move resetting of flux arrays to outside the iLa loop
1040 (this caused layers_diapycnal to not work with more than one layer coord.)
1041 - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
1042 o pkg/layers:
1043 - remove from common block 3D layers fields (used to diagnose transport
1044 in tracer coords) and declare them as local arrays in layers_calc.F
1045 o pkg/seaice:
1047 in lab_sea forward experiment (changes results -> updated)
1048 - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
1049 o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
1050 computations; for SEAICE_VECTORIZE_LSR
1051 - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
1052 sweep to the outside,
1053 - remove store directives and add "CADJ loop sequential" directives
1054 in analogy to model/src/solve_tridiagonal.F
1055 - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
1056 boundaries to yield more readable code. This has also the charming side
1057 effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
1058 SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
1059 seaice_lsr_tridiagu/v now requires either of these flags, vectorization
1061 an additional option)
1062 The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
1063 but the adjoint gradients (which are affected by this change) still explode.
1064 o coupler (atm & ocn _compon_interf):
1065 - avoid using Exch2 IO mapping if not suitable.
1067 checkpoint65m (2015/06/15)
1068 o pkg/layers:
1069 - clean-up old parameters setting (from Sep 2012):
1070 + remove old parameters setting from common block (declared locally);
1071 + stop if any old parameter is mixed with new parameters;
1072 + check for valid or consistent parameter setting (e.g., layers_name)
1073 - check that layers_bounds for Pot.Density are in the right range;
1074 this is supposed to catch un-updated setting after recently shifting
1075 potential density field "prho" by -1000 (now in "sigma" scale).
1076 o pkg/layers:
1077 - Added missing call to layers_fill for keeping track of tottend in
1078 pkg/diagnostics/diagnostics_fill_state.F
1079 o pkg/layers:
1080 - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
1081 of diapycnal fluxes
1082 o pkg/layers:
1083 - reverted changes to interpolation to previous treatment; there
1084 was never actually a problem
1085 o pkg/layers:
1086 - fix interpolation of layers tracers in the presence of partial cells
1087 - add lots of new functionality to compute water mass transformation
1088 (enabled by CPP flag LAYERS_THERMODYNAMICS)
1089 - add new calls from main code (diags_oceanic_surf_flux.F,
1090 thermodynamics.F, impldiff.F) and gad to save the necessary fields
1091 for layers_thermodynamics calculations
1092 o pkg/ptracers:
1093 - add capability of stepping a passive tracer forward without advection
1094 by setting PTRACERS_advScheme to 0.
1095 o pkg/diagnostics:
1096 - add few (threads) _BARRIER around any update of "diag_pkgStatus".
1097 o pkg/layers:
1098 - shift potential density field "prho" by -1000 for density layer averaging so
1099 that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
1100 Note that density bin boundaries (layers_bounds in data.layers) have
1101 to be set accordingly (i.e., shifted, in sigma scale).
1102 o pkg/layers:
1103 - fix snap-shot output of layer thickness @ V.pt and output of pot.density
1104 - fix calculation of layer non-weighted velocity and layer probability
1105 - add diagnostics for pot.density used for layer averaging
1106 o pkg/seaice:
1107 - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
1108 positiveness, modify a few comments and improve variable names,
1109 - the changed computation of deltaC affects most seaice-related
1110 experiments at the truncation level.
1111 seaice_itd.thermo is affected by far the most, with
1112 only 7 digits of agreement remaining; update experiments.
1114 checkpoint65l (2015/05/04)
1115 o pkg/shelfice:
1116 - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
1117 factor drKp1 to zero where it is negative (ie. do not use
1118 SHELFICEBoundaryLayer if hFacC>1)
1119 - the same for factor drLoc in shelfice_forcing.F
1120 o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
1121 with modules in ptracers, when using testreport option "-small_f"
1122 o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
1123 - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
1124 o verification/testreport
1125 - add new option -small_f
1126 with this option testreport first makes the target small_f (*.f files)
1127 before running make (all). This is useful for explicit inlining when
1128 all sources need to be full available.
1129 o pkg/exf/exf_interp.F:
1130 remove previous changes related to reverse (decreasing) input grids latitude
1132 checkpoint65k (2015/04/01)
1133 o pkg/ecco:
1134 fix missing cosphi initialization; use eccoiter in place of optimcycle;
1135 if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
1136 instead of active read/write
1137 o pkg/ctrl:
1138 if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
1139 instead of active read/write.
1140 o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
1141 return if .NOT.useAUTODIFF
1142 o pkg/seaice: add CPP brackets (cost function related).
1143 o model/src:
1144 add useAUTODIFF run time switch.
1145 o pkg/exf/exf_interp.F:
1146 add code to allow input grids with latitude starting in the north (i.e. when
1147 j=1 corresponds to northern edge of field); modify global_with_exf to test
1148 this feature.
1149 o verification/testreport:
1150 - replace "grep -A3" with POSIX conformal sed command, because there are
1151 implementations of grep that cannot do contextual searches
1152 - replace "cat -n" by "nl" (two occurrences), because not all implementations
1153 of "cat" have the option "-n"
1154 o model/src:
1155 add new file gsw_teos10.F that contains 3 functions, more or less a copy
1156 of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
1157 convert from conservative to potential temperature. For now they are not
1158 called anywhere.
1159 o pkg/ggl90: make "useIDEMIX" useful
1160 - re-organize code in s/r ggl90_calc a little to move computations that
1161 are different for idemix into separate loops (changes verification
1162 experiment idemix at truncation level, 12 digits remain -> updated)
1163 - requires 2 new 2D fields KappaM, verticalShear
1164 - make hFacI and recip_hFacI local 3D variables that are passed to
1165 s/r ggl90_idemix
1166 - fix and improve some comments
1168 checkpoint65j (2015/02/25)
1169 o pkg/openad
1170 - synchronize seawater.F with version in model/src: replace routine
1171 body of sw_temp by calling sw_ptmp and fix/add a few comments.
1172 o pkg/mnc:
1173 - change default value of pickup_read/write_mnc params to FALSE
1174 (since few features are missing in reading MNC pickup files).
1175 o model/src:
1176 - change default (background) vertical diffusivity for salt to be the
1177 temperature (background) vertical diffusivity.
1178 - change background vertical diffusivity in vertical mixing pkgs ggl90,
1179 kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
1180 This makes ptracers default diffusivity (that uses salt diffKr) more
1181 consistent with vertical mixing schemes.
1182 o verification/testreport:
1183 - fix typo in "-pcls" option ;
1184 - put temp files in /tmp (instead of in local dir)
1185 - add option "-ncad" to use genmake2 new option "-nocat4ad"
1186 - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
1187 o pkg/ggl90 (idemix code):
1188 - apply few fixes ; add some missing "_d 0" ; update output of exp.
1189 global_ocean.90x40x15.idemix
1190 o OpenAD
1191 - enable active file I/O and begin removal of work-around code
1192 for OpenAD for handling control variables (memory vs. active files)
1193 - new CPP options file OPENAD_OPTIONS.h
1194 - revert to genarr2d gradient check for hs94.1x64x5
1195 - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
1196 - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
1197 o tools/genmake2:
1198 - add option for an alternative Makefile (from Martin) where multiple
1199 source files are sent to TAF (instead of all in one file).
1200 o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
1201 - code provided by Carsten Eden as an extension of ggl90
1202 - so far the code is turned on within ggl90 by setting a CPP-flag at
1203 compile time; a runtime flag implementation is not yet complete
1204 - tested in new verification experiment global_ocean.90x40x15.idemix
1205 o verification:
1206 - reduce length of the AD test run by half for experiments
1207 global_ocean.cs32x15 (std + thsice) and isomip
1208 - enable active file I/O for OpenAD, adjust verifications accordingly
1209 - halfpipe_streamice: change gradient check from genarr2d to gentim2d
1210 o verification/testreport:
1211 - fix two non-POSIX sed statements so that there are no error messages
1212 on Mac OS X
1213 - replace hostname -s with hostname | sed 's/\..*$//'
1214 o model/src/seawater.F:
1215 - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
1216 (following the matlab code), which would have avoided the bug caught
1217 by Matt (see below) in the first place
1218 o pkg/shelfice:
1219 - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
1220 and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
1221 - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
1222 ice-shelf case (i.e., within surface level).
1223 - add config summary in shelfice_check.F
1224 - remove global variable recip_SHELFICElatentHeat and replace by a local
1225 variable recip_latentHeat
1226 - introduce diagnostics for friction velocity uStar (in case of
1227 SHELFICEuseGammaFrict)
1228 - change verification experiment isomip.htd:
1229 + start from pickup (as input_ad at nIter0=8640)
1230 + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
1231 + test SHELFICEuseGammaFrict = .TRUE.
1232 + test SHELFICEadvDiffHeatFlux = .TRUE.
1233 o model/src:
1234 - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
1235 in-situ Temp) and in routine SW_TEMP (in pkg/openad);
1236 update output of experiments global_with_exf.yearly and isomip (all 6).
1237 o pkg/shelfice:
1238 - change setting of kTopC to also be zero where there is no ice-shelf.
1239 - zero out surface forcing arrays (for now, for T & S + EmPmR) where
1240 ice-shelf is.
1241 - first attempt to get RealFreshWaterFlux effects: for now, only without
1242 SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
1243 o pkg/seaice: add the option to prescribe a fixed thickness PDF
1244 for thermodynamic calculations
1245 - because of divisions of the type 7/7 not exactly equal to 1, this change
1246 affects results of some verification experiments by up to 4 digits:
1247 global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
1248 seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
1249 adjoint: lab_sea, lab_sea.noseaicedyn
1250 -> updated
1252 checkpoint65i (2015/01/23)
1253 o model/src:
1254 - change units of frictionHeating field from W to W/m^2
1255 - fix bug in frictional heating from stratospheric drag in
1257 - with synchronous time-stepping: move resetting to zero of frictionHeating
1258 field from load_fields_driver.F to thermodynamics.F ;
1259 - add diagnostics for frictional heating.
1260 o model/src & gmredi K3D:
1261 - add frictionHeating field to pickup-files (for synchronous time-stepping)
1262 - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
1263 - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
1264 and name in pickup file).
1265 - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
1266 o model/src:
1267 - move (from ini_forcing.F) initialisation of all arrays in header file
1268 FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
1269 (since Nov 2012) with option selectAddFluid=1.
1270 o pkg/shelfice:
1271 - change units (+ document) of newly added field "shelfIceMassDynTendency"
1272 - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
1273 o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
1274 o pkg/seaice: two new runtime parameters:
1275 - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
1276 long overdue
1277 - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
1278 parameterization of tensil stress for fast ice (does not do anything yet)
1279 o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
1280 for LSR: move checking overlaps out of JFNK-if-block
1281 o pkg/atm_phys:
1282 - move copy of grid and dynamical fields out of atm_phys_driver.F into
1284 - fix level height for Linear Free-Surf case (to be consistent with
1285 fixed-in-time pressure levels).
1286 o pkg/mom_common (bottomdrag):
1287 - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
1288 to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
1289 update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
1290 o pkg/shelfice (u/v_drag):
1291 - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
1292 - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
1293 (now similar to shelfice_u_drag.F)
1294 - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
1295 from mom_vecinv.F (similar to mom_fluxform calls).
1296 o pkg/mom_common (bottomdrag):
1297 - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
1298 - add options for alternative discretisation of velocity norm in quadratic
1299 bottom drag: averaging of grid-cell-center KE to U.point and V.point
1300 (selectBotDragQuadr=0, original code) can produce noisy patterns; this
1301 improves when averaging only the other component (e.g. vVel for U bottom
1302 drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
1303 - add options (bottomVisc_pCell) to account for partial-cell in bottom
1304 friction (no-slip BC) thus getting the true distance from the bottom;
1305 off by default since this also reduces model stability (explicit bottom
1306 friction). Changes produce different machine truncation with linear-drag
1307 + no-slip BC: update output of experiments exp4.stevens (10 digits) and
1308 front_relax (bvp & mxl, 10 & 11 digits).
1309 o model/src & mom pkgs:
1310 - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
1311 since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
1312 - for now and until vertical mixing scheme are updated to fill up level Nr+1,
1313 just copy level Nr value to level Nr+1.
1314 o doc:
1315 - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
1316 o pkg/shelfice:
1317 - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
1318 SHELFICE.h: move array shelficemass to init_varia, initialise
1319 from array shelficemassinit, which is set in init_fixed and
1320 has option to be set from file; introduce array
1321 shelficeMassDynTend array, set thru file in init_fixed
1322 - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
1323 shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
1324 pkg/streamice
1325 - shelfice_thermodynamics.F: call shelfice_step_icemass if
1326 SHELFICEMassStepping = .true.
1327 - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
1329 checkpoint65h (2014/12/17)
1330 o verification/global_ocean.90x40x15, global_ocean_ebm:
1331 - update to generic controls.
1332 o pkg/ctrl:
1333 - ctrl_map_ini_genarr.F: test for igen>0
1334 - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
1335 - move gentim2d part of ctrl_map_ini_genarr.F to
1336 new separate routine : ctrl_map_ini_gentim2d.F
1337 - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
1338 add time variable weights and cyclic controls (time mean,
1339 seasonal cycle, etc) capabilities to gentim2d
1340 o pkg/ecco:
1341 - move reading of error, conversion to weights from
1342 ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
1343 o global_oce_llc90, cs32:
1344 - activte sbo.
1345 - CTRL_SIZE.h : add maxCtrlProc.
1346 - activate the new genctrl capabilities.
1347 - update following reorganization of global_oce_input_fields.tar.gz
1348 o pkg/ctrl/ctrl_ad_diff.list:
1349 - add missing ctrl_init_rec.f
1350 o tools/OAD_support/keepOriginal:
1351 - add ctrl_init_rec.F
1352 o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
1353 - avoid recomputations of xx_gentim2d_dummy.
1354 o momentum diagnostics:
1355 - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
1356 mom_vecinv.F to timestep.F (to include Smag-3D contribution).
1357 o pkg/seaice/seaice_lsr.F:
1358 - fix computation of BU/BV, make sure they are non-zero, only necessary
1359 for cubed sphere exchanges and SEAICE_OLx/y>0.
1360 This makes calling s/r fill_cs_corner_rl obsolete (removed).
1361 o verification/global_ocean.cs32x15/input.seaice
1362 - add test for strong implicit coupling and restricted addtive Schwarz
1363 methods for LSR
1364 - update results/output.seaice.txt
1365 o verification/tutorial_global_oce_biogeo:
1366 - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
1367 and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
1368 update output_adm,_oadm,_tlm.txt
1369 o pkg/dic:
1370 - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
1371 - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
1372 for tracer 1 & 2 is set (to avoid double counting of dilution effect).
1373 o verification/tutorial_global_oce_biogeo:
1374 - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
1375 dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
1376 update output_adm,_oadm,_tlm.txt
1377 o eesupp/src:
1378 - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
1379 and call it in seaice_lsr when using nonzero SEAICE_OLx/y
1380 o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
1381 LSR (following Hutchings et al. 2004)
1382 - introduce zetaZ as a global variable (requires adjustments in
1383 seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
1384 in seaice_calc_viscosities.F
1385 - new flag SEAICEuseStrImpCpl (default off)
1386 - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
1387 momentum equations
1388 - JFNK-solver (preconditioner) adjusted to allow using this method
1389 (where it does not have any positive effect)
1390 o pkg/seaice
1391 - add overlap for restrictive additive Schwartz method also to LSR, but
1392 turn it off by default (because it only seems to work for non-cubed
1393 sphere/llc topologies)
1394 o pkg/autodiff
1395 - add extra exchanges in addummy_in_steppging also for mnc output
1396 o pkg/seaice:
1397 - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
1398 to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
1399 o pkg/obcs:
1400 - add option to specify domain-connected piece Id along OB though files
1401 (for now, only used to diagnose PhiVel; default =1 -> global correction)
1402 - modify obcs_diag_balance.F to process each connected-part separately;
1403 exclude OB where Id = 0 but keep the full divergence there (-> constant
1404 Psi along this portion of OB and all inflow derived from grad(Phi))
1405 - add example of OB-conect files in verification/so_box_biogeo/input.
1406 o pkg/diagnostics:
1407 - improve treatment of Open-Boundaries in Velocity-Potential calculation:
1408 a) use non zero matrix element across OB and solve for Phi 1 grid point
1409 outside OB (i.e, where tracer OBCS are applied).
1410 b) global imbalance of inFlow/outFlow across OB: instead of modifying
1411 velocity across OB, spread it uniformly along the OB in the RHS.
1413 checkpoint65g (2014/11/19)
1414 o pkg/diagnostcis:
1415 - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
1416 o pkg/my82,pp81,kl10:
1417 - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
1418 field diffKr as background diffusivity to set minimum diffusivity value.
1419 o pkg/seaice:
1420 - add new parameter SEAICEuseEVPrev (for revisited EVP by
1421 Bouillon et al 2013)
1422 - add SEAICE_evpAlpha/Beta to namelist
1423 - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
1424 involve trivial re-ordering of divisions/multiplications that should not
1425 have any effects, but ... they do change the results of lab_sea.hb87 so
1426 that only 2 digits of agreement remain, in line with the general
1427 instability/fragility of the evp-code. For now, I do not care and just
1428 update the verification experiment
1429 o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
1430 - remove xx_genarr2d_numsmooth etc
1431 - use xx_genarr2d_preproc etc instead
1432 - carry out smooth_correl2D at initialization stage rather than during
1433 time stepping.
1434 - get smoothOpNb from xx_gentim2d_preproc
1435 o global_oce_cs32 :
1436 - add test of generic ecco capabilities.
1437 o pkg/exf/exf_getsurfacefluxes.F :
1438 - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
1439 o pkg/ctrl,ecco :
1440 - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
1441 is defined.
1442 o pkg/seaice: add diagnostics for Delta (deformation parameter)
1443 o model/src:
1444 - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
1445 diffusivity (background) is specified but ignored.
1446 o verification:
1447 - in testreport, convert hostname to lower case for default output dir name
1448 o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
1449 o pkg/dic: add modifications from Hajoon:
1450 - add iron sedimentation flux function of the flux of PO4 out of bottom layer
1451 - light attenuation: add self-shading effect by climatological Chlorophyll
1452 (read from file).
1453 o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
1454 compiles when SEAICE_ALLOW_DYNAMICS is undefined
1455 o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
1457 ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
1458 approach where CPP_OPTIONS.h includes an omnipotent
1459 ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
1460 o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
1461 ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
1462 o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
1463 to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
1464 (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
1465 o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
1467 - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
1468 - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
1469 - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
1470 o pkg/ctrl,ecco,exf :
1471 - remove variables associated with NON-generic costs,
1472 unless ECCO_CTRL_DEPRECATED is defined.
1473 - remove NON-generic NON-obcs controls,
1474 unless ECCO_CTRL_DEPRECATED is defined.
1475 o pkg/ctrl : added ctrl_local_params.h
1476 o pkg/ecco : added ecco_local_params.h
1477 o verification : added ECCO_CTRL_DEPRECATED to most as and oad
1478 experiments, which will progressively be removed once the
1479 experiments are revised to use only generic controls/costs.
1481 checkpoint65f (2014/10/13)
1482 o pkg/ctrl, ecco, seaice : minor changes in headers
1483 o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
1484 cost function and control capabilities added since checkpoint65c.
1485 o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
1486 o pkg/ecco: increase modularity and improve logic
1487 - ecco_toolbox.F (new) : basic operations that are often used,
1488 including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
1489 ecco_addcost, ecco_add, ecco_div, ecco_readbar.
1490 - cost_gencal.F (new) : determine filnames and records.
1491 - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
1492 - cost_generic.F : use spzeroloc rather than hard-coded -9999,
1493 and exploit the above functions leading to more compact code.
1494 - cost_genread.F : rm un-necessary arguments, re-arrange args order.
1495 - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
1496 using_ers, using_gfo, using_mdt is now only defined within gencost)
1497 o pkg/ecco: extend generic cost capabilities
1498 - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
1499 capabilities via gencost_preproc (+ _c,_i,_r related params),
1500 gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
1501 gencost_outputlevel arguments to cost_generic
1502 - pkg/ecco/cost_genread.F (new) : interface between cost_generic
1503 and active_read, making room for gencost_preproc to take effect.
1504 Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
1505 - pkg/ecco/cost_generic.F :
1506 compute and store misfit maks*(model-data) in localdif that is
1507 then used in cost and for output, output misfit if outlev.GT.0
1508 - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
1509 rather gencost_barfile for deciding whether to write barfile
1510 - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
1511 - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
1512 ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
1513 - pkg/ecco/ecco_summary.F : report gencost variables
1514 - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
1516 o pkg/ecco: internal re-organization
1517 - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
1518 (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
1519 mv relevant variables definition from ecco_cost.h to ecco.h,
1520 make sure gencost routines only include ecco.h)
1521 - throughout : add missing CCP switches, rm unused variables,
1522 and rm un-necessary CPP switches
1523 - throughout gencost routines : replace modelstartdate with
1524 gencost_startdate when needed
1525 - cost_bp_read.F : use arguments, instead of common blocs
1526 so that it can be used also by (new) cost_gencost_bpv4.F
1527 - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
1528 - ecco_phys.F : compute etanFull
1529 - ecco_readparms.F : rename using_topex as using_tpj, add
1530 bpv4-grace to gencost list, initialize added parameters
1531 - ecco_summary.F : include SIZE.h needed for augmented ecco.h
1533 checkpoint65e (2014/09/28)
1534 o pkg/obcs:
1535 - replaced the just-added CPP options with run-time variables
1536 (see pkg/obcs/OBCS_PARAMS.h for details)
1537 o pkg/obcs:
1538 - add additional CPP options for sponge boundary layers
1539 (see pkg/obcs/OBCS_OPTIONS.h for details)
1540 o pkg/atm_phys:
1541 - implement simple (obliquity only, assuming circular planet orbit)
1542 seasonal cycle for incoming insolation ; used when run-time parameter
1543 "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
1544 o pkg/exf, pkg/ecco, pkg/ctrl:
1545 - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
1546 - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
1547 - implement gentim2d for xx_tauu, xx_tauv
1548 o pkg/ctrl, pkg/ecco :
1549 - fix and complement the generic controls implementation
1550 o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
1551 pkg/shelfice/shelfice_thermodynamics.F,
1552 verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
1553 verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
1554 - add weight in CTRL_GET_GEN calls
1555 o pkg/ctrl :
1556 - ctrl_get_gen.F : add weight as input parameter, and apply
1557 it directly rather than using smooth_correl2Dw (to be retired).
1558 - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
1559 o pkg/ctrl :
1560 - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
1561 ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
1562 - re-activate ctrl_summary (call in ctrl_init.F)
1563 o pkg/ctrl/ctrl_cost_gen.F :
1564 - fix CCP brackets, remove un-necessary myiter, mytime
1565 o pkg/ecco, pkg/ctrl :
1566 - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
1567 - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
1568 - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
1569 - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
1571 checkpoint65d (2014/09/15)
1572 o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
1573 - add xx_genarr2d_bounds,xx_genarr3d_bounds,
1574 xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
1575 o pkg/ctrl/ctrl_map_ini_genarr.F :
1576 - remove compilation failure
1577 - replace hard coded example
1578 - use ctrl_map_ini_gen2D, 3D
1579 o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
1580 - on/off switch based upon xx_genarr2d_weight,3d
1581 o src/packages_init_variables.F :
1582 - regroup pkg/estimation calls
1584 (moved to ctrl_init_variables)
1585 o cost/cost_init_varia.F :
1586 - remove ecco_cost_init_varia
1587 (moved to ecco_init_varia)
1588 o ctrl/ctrl_init_variables.F :
1591 o ctrl/ctrl_map_ini.F :
1592 - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
1593 (moved to ctrl_init_variables)
1594 o ctrl/ctrl_map_ini_ecco.F :
1595 - remove ECCO_PHYS (mv to ecco_init_varia)
1596 - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
1597 o ecco/ecco_ad_diff.list :
1598 - add ecco_init_varia.f
1599 o ecco/ecco_init_varia.F
1600 - new routine
1601 o pkg/streamice:
1602 - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
1603 to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
1604 - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
1605 o pkg/generic_advdiff:
1606 - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
1607 o pkg/exf:
1608 - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
1609 xxg_precip capability
1610 - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
1611 o pkg/ctrl:
1612 - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
1613 o model/src/load_fields_driver.F :
1615 so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
1616 o OpenAD verification experiments:
1617 - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
1618 in src files (to enable to skip the ECCO_CPPOPTIONS.h);
1619 for now, only in pkgs used in OpenAD verification experiments.
1620 - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
1621 specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
1622 instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
1623 This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
1624 o OpenAD verification tests:
1625 - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
1626 - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
1627 tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
1628 - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
1629 and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
1630 o model/src & generic_advdiff:
1631 - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
1632 forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
1633 dynamics requires valid tracer forcing only over tile interior but, for
1634 some diagnostics, may need to extend it over 1 point in tile halo region.
1635 - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
1636 tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
1637 setting in temp/salt/ptracer_integrate.F
1638 o pkg/dic:
1639 - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
1640 gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
1641 in gchem_forcing_sep.F
1642 o pkg/autodiff & obcs:
1643 - add storage of current OB values for U & V (was already done for T & S).
1645 checkpoint65c (2014/08/30)
1646 o pkg/dic:
1647 - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
1648 and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
1649 AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
1650 o verification:
1651 - new experiment testing OBCS and DIC pkgs, using params & output from
1652 tutorial_global_oce_biogeo but limited to a sub-domain around Drake
1653 passage: take OBCS from the last year of a 2 yrs simulation and initial
1654 conditions from t=1.yr while keeping the same forcing.
1655 o model/src:
1656 - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
1657 (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
1658 o pkg/diagnostics (Stats-Diags):
1659 - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
1660 a) refine region where stats are computed, excluding where arrhFac=0 ;
1661 b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
1662 c) extend regional stats over the region edges (for U or V pt location).
1663 o pkg/gchem:
1664 - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
1665 pkg/dic is currently changing/updating ptracers values beyond the OB).
1666 o verification (hs94):
1667 - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
1668 bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
1669 hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
1670 apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1671 o pkg/ptracers:
1672 - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
1673 switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
1674 - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
1675 with AB-2 code (so that it get tested).
1676 o model/src:
1677 - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
1678 with AB-2 code (previously only available with AB-3 code).
1679 Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
1680 to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
1681 there, by calling CYCLE_AB_TRACER).
1682 o pkg/generic_advdiff:
1683 - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
1685 + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
1686 S/R temp/salt/ptracers_integrate.F
1687 o model/src & pkg/ptracers:
1688 - remove common block variables gT,gS (in DYNVARS.h), except when
1689 USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
1690 - remove common block variable gPtr.
1691 o model/src & pkgs:
1692 - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
1696 + change accordingly all calling S/R.
1697 - use local temperature/salinity/ptracer tendency array (without bi,bj)
1698 in S/R temp/salt/ptracers_integrate.F
1699 o pkg/seaice:
1700 - move computation of stress contributions to rhsU/V in s/r seaice_lsr
1701 to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
1702 - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
1703 in seaice_lsr
1704 - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
1705 in s/r seaice_lsr_calc_coeffs
1706 o pkg/mdsio:
1707 - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
1708 (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
1709 too long (e.g., > MAX_LEN_FNAM/2 )
1711 checkpoint65b (2014/08/12)
1712 o pkg/matrix:
1713 - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1714 o model/src:
1715 - fix initialisation of geothermalFile; compile geothermal-flux code in
1716 natl_box verification experiment.
1717 o model/src & pkg/down_slope:
1718 - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1719 - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1720 field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1721 results at machine truncation level: update output of experiments
1722 global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1723 o pkg/diagnostics (Stats-Diags):
1724 - do not cumulate the full volume when DIAGNOSTICS_FILL is
1725 called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1726 This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1727 times (but Min,Max and StD are still wrong).
1728 o model/src:
1729 - add geothermal flux forcing: read in ini_forcing.F as time-constant
1730 field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1731 o model/src:
1732 - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1733 _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1734 arrays are already updated while adjustments (filters, conv.adjustment) are
1735 still applied later, in S/R TRACERS_CORRECTION_STEP.
1736 o model/src:
1737 - store in common bloc array "rhoInSitu" the virtual potential temperature
1738 anomaly that is used to compute geopotential: this make the atmos code
1739 more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1740 o pkg/seaice/seaice_lsr.F
1741 - rename integer variable ilcall to ipass (that's what it is called
1742 in the residual diagnostics
1743 - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1744 default) for improved non-linear convergence of the first few steps
1745 - adjust a few comments and add new ones to explain some of the store
1746 directives
1747 o pkg/generic_advdiff (& ptracers):
1748 - re-work the code to check for valid advection scheme and for minimum
1749 size of overlap (now stored in local common bloc in gad_advscheme.F)
1750 o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1751 - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1752 - add an auxilliary variable "bet" and fix store directives and keys in
1753 seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1754 less exact gradients in my tests); but there are still
1755 recomputation warning (although gradients are sort of OK), when
1756 SEAICE_LSR_VECTORIZE is not defined, so this flag and
1757 SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1758 - update verification experiments lab_sea.
1759 - change some comments in S/R seaice_calc_viscosities
1760 o model/src:
1761 - if staggerTimeStep=T, always apply exchange to velocity field in
1762 do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1763 (independent of using multi-dim advection or not); no effect on FWD run
1764 but affects AD results (at machine truncation level): update output of
1765 experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1766 and isomip (oad: 12.d).
1767 o pkg/generic_advdiff:
1768 - stop if doAB_onGtGs is set to FALSE but ignored
1769 - refine warning related to stability of tracer time-stepping
1770 regarding internal wave dynamics.
1771 - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1772 on staggerTimeStep & implicitIntGravWave (will now get a warning
1773 if potentially unstable).
1774 o pkg/kl10:
1775 - add new pkg "kl10" for mixing due to internal wave breaking, from
1776 http://www.sciencedirect.com/science/article/pii/S1463500310000144
1777 (contribution from Jody Klymak), tested in verification experiment
1778 verification/internal_wave/input.kl10/
1779 o isomip experiment:
1780 - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1781 (input.htd) and update the output.
1782 o cd_code experiments:
1783 - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1784 #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1785 global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1786 update the corresponding output.
1787 o pkg/seaice:
1788 - reduce the number of include files and store directives in
1789 S/R seaice_lsr_tridiagu/v
1790 - change the order of loops in one case in S/R seaice_lsr_tridiagv
1791 (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1792 get rid off one store directive (a TAF bug?)
1793 - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1794 S/R seaice_lsr_tridiagv to change the loop range for consistency
1795 - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1796 - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1797 S/R seaice_lsr_tridiagu/v (requires update of
1798 offline_exf_seaice/input.dyn_jfnk)
1800 checkpoint65a (2014/07/27)
1801 o model/src:
1802 - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1803 surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1804 (topo in p-coords, ice-shelf in z-coords); update output of experiments
1805 tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1806 o model/src:
1807 - collect momentum forcing tendency into local 2-D array (passed as argument
1808 to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1809 parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1810 affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1811 - collect T & S forcing tendency into local 2-D array (passed as argument to
1812 apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1813 affects results at machine truncation level (e.g., ocean: if using
1814 SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1815 correction due to vertical advection).
1816 - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1817 global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1818 seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1819 obcs_ctrl (ad & fwd grd @ 12 & 7).
1820 o pkg/ptracers & diagnostics:
1821 - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1822 title (to avoid some unexpected truncation); sort out ptracers diags units.
1823 - collect ptracer forcing tendency into local 2-D array (passed as argument
1824 to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1826 checkpoint65 (2014/07/18)
1827 o pkg/fizhi:
1828 - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1829 affects results at machine truncation level. Update output of experiments
1830 fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1831 o pkg/seaice: more clean up
1832 - rename TAF common block tapes to be more consistent and remove
1833 unnecessary duplicates
1834 - add store directives to remove more recomputations, but use smaller
1835 tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1836 The idea behind this flag is to reduce the memory footprint when the
1837 adjoint of the LSR is not required. As of now, defining the flag
1838 SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1839 a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1840 For experiment offline_exf_seaice, this means on a linux box with gfortran
1841 nearly a factor of 10 (but keep in mind there is mostly seaice code in
1842 this experiment):
1843 > size mitgcmuv_ad
1844 text data bss dec hex
1845 5100659 1216 220458952 225560827 d71c8fb
1846 5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1847 but only a moderate increase of 36% for global_ocean.cs32x15:
1848 text data bss dec hex
1849 6695027 1648 1014578664 1021275339 3cdf6ccb
1850 6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1851 - note: there are still recomputations in global_ocean.cs32x15 and
1852 offline_exf_seaice and the gradient agreement changes (gets a
1853 little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1854 - in general, the AD gradients still are wrong
1855 o OpenAD
1856 - clean up code_oad/ directories somewhat by moving files
1857 dontCompile, dontTransform, keepOriginal to OAD_support/
1858 o model/src:
1859 - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1860 (not currently tested): add dissipation terms before NLFS rescaling of
1861 tendencies (previously done after).
1862 o pkg/diagnostics:
1863 - write stats-diags in ascii file with more digits (same as in monitor).
1864 o pkg/down_slope:
1865 - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1866 NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1867 o model/src:
1868 - new file "apply_forcing.F" containing all the code previously in
1869 external_forcing.F, but with new argument list: pass, as new argument,
1870 the current level tendency array to update (instead of a direct update
1871 of the common bloc array). Change the corresponding calls.
1872 - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1873 EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1874 o pkg/seaice/seaice_lsr, a little bit of clean up
1875 - rearrange some code blocks, so that now all calculations for
1876 setting up the right-hand-sides done within one single block
1877 (I find that easier to read and understand)
1878 - rearrange freedrift-code to reduce the number of ifdefs
1879 - adjust some indentations and comments
1881 checkpoint64z (2014/07/10)
1882 o model/src and several pkgs:
1883 - change argument list of all S/R called from external_forcing.F and
1884 called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1885 to pass, as argument, the current level tendency array to update
1886 (instead of a direct update of the common bloc array).
1887 - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1888 - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1889 o pkg/seaice/seaice_lsr.F
1890 - always initialize local arrays in seaice_lsr_tridiagu/v
1891 - add more local tapes to seaice_lsr_tridiagu/v
1892 - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1893 keep it in bi/bj loop; this seems to be essential
1894 - gradients are still wrong but only by 4-7 orders of magnitude
1895 instead of 15 orders of magnitude, lab_sea improves a little
1896 o pkg/seaice
1897 - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1898 generates unnecessary code in seaice_lsr_ad
1899 - add more store directives in seaice_lsr to avoid unnecessary code
1900 in seaice_lsr_ad
1901 - exclude some residual computations in seaice_lsr when
1902 ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1903 in seaice_lsr_ad
1904 - add more storing, a new tape (model/src/the_main_loop.F) and
1905 another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1906 and klockey should be checked by a specialist)
1908 and update lab_sea after previous changes in pkg/seaice below
1909 o pkg/autodiff:
1910 - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1911 viscFacInAd : run time parameters allowing for adjoint switches
1912 note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1913 o pkg/ecco:
1914 - introduce cost_gencost_boxmean.F that computes a box mean
1915 temperature (for use in adjoint sensitivity studies).
1916 o model/src/set_defaults.F : initialize viscFacAdj to 1.
1917 o pkg/mom_common/mom_calc_visc.F:
1918 - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1919 o pkg/seaice/seaice_summary.F:
1920 - statement for SEAICEadjMODE now in autodiff_readparms.F
1921 o pkg/seaice:
1922 - remove some store directives and add new ones in an effort to get
1923 finally rid off the recomputation warnings. This is successful
1925 defined (i.e. no extensive recomputation warnings left), but there
1926 are still too many recomputations on the solver iteration level
1927 - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1928 - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1930 - add a store directive in S/R seaice_calc_viscosities
1931 o pkg/seaice (ITD code):
1932 - fix definition of Hlimit for multi-threaded case
1933 - use double precision arithmetic to compute Hlimit: this affects results;
1934 update output of experiment seaice_itd.
1935 o replace content of verification/seaice_itd
1936 - instead of a 1D column use the configuration of offline_exf_seaice
1937 to test the ice thickness distribution code with ridging
1938 - this is a first shot at this experiment
1939 - change of some defaults of ridging parameters SEAICEhStar (from
1940 100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1941 and lot of new comments.
1943 checkpoint64y (2014/06/20)
1944 o pkg/seaice/seaice_reg_ridge.F:
1945 - modify the regularization of very small volumes of ice; only check
1946 total volume HEFF, and do not apply correction to individual ice
1947 classes because that leads to funny patterns in the heat and fw-fluxes
1948 into the ocean. Adjust seaice_itd/results/output.txt
1949 - replace nITD by SEAICE_multDim in loop-ranges
1950 o pkg/exf:
1951 - add code to process the case field period = -12. with UV interpolation.
1952 - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1953 into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1954 o verification/global_with_exf:
1955 - switch all fields period to -12. (was previously untested) in input/data.exf
1956 (but keep secondary test ".yearly" unchanged); update the reference output.
1957 o pkg/cal:
1958 - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1959 o pkg/exf:
1960 - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1961 to replace logical switch "exf_verbose"
1962 - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1963 o pkg/sbo:
1964 - update from Katherine Quinn: evaluate mass directly from density and SSH
1965 (budget using Finite Volume method) instead of from bottom pressure.
1966 - allow testreport to collect few selected SBO output ; tested in exp.
1967 global_ocean.90x40x15 (after updating the results, to include SBO output).
1968 - fix some multi-threading issues (in output part).
1969 o model/src & most packages:
1970 - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1971 - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1972 PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1973 "data.{pkg}" exist ; and leave the S/R (return) just after.
1974 - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1975 + call LAND_READPARMS from packages_readparms.F
1976 o pkg/seaice:
1977 - remove code that resets useThSice in S/R seaice_readparms and
1978 replace it by a warning in S/R seaice_check
1979 - remove parameter MULTDIM, replace with nITD and runtime
1980 parameter SEAICE_multDim (still hard-wired to nITD if
1981 SEAICE_ITD is defined)
1983 checkpoint64x (2014/05/24)
1984 o verification/lab_sea:
1985 - update adjoint and TLM output following changes to pkg/salt_plume
1986 - un-do the update after putting back local recip_Cp in few places.
1987 o pkg/salt_plume: modifications by An Nguyen:
1988 - add capability to do brine rejection (salt-plume) as function of
1989 volume+tracers (instead of only salinity tracer).
1990 - conserve volume by exchanging volume from each kLev to above to
1991 accommodate in-coming brine volume
1992 - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1993 - switch KPP surf buoyancy due to brine forcing to 3-d
1994 (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1995 - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1996 - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1997 in East/West Arctic.
1998 o pkg/sbo:
1999 - incorporate modifications from Katherine Quinn to enable the use of sbo
2000 pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
2001 output for future testreport verification (unfinished).
2002 o pkg/atm_phys:
2003 - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
2004 skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
2005 output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
2006 o pkg/seaice
2007 seaice_calc_ice_strength.F: modify expression to avoid divisions
2008 (affects truncation)
2009 seaice_do_ridging.F: clean up the insectarium
2010 - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
2011 - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
2012 - set closing/openingRate to zero where no extra iteration is need (3rd bug)
2013 - add some debugging information and error messages (warnings)
2014 o model/src: modifications relatd to atmosphere p*:
2015 - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
2016 - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
2017 of vertical profile tRef in geopotential background and anomaly.
2018 - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
2019 and pkg/atm_phys.
2020 - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
2021 fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
2022 o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
2023 o pkg/ptracers: compute ptracer source/sink due to linear free surface.
2024 not used right now, but can be used in BGC packages to fix conservation.
2025 o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
2026 other packages too.
2027 o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
2028 SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
2029 o model/src:
2030 - since we have several heat capacity (even in model/src), define "recip_Cp"
2031 as local variable (no longer in common block) to avoid any confusion.
2032 - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
2033 o pkg/exf:
2034 - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
2035 air density as function of air Temp, Humidity and atm pressure.
2037 checkpoint64w (2014/05/02)
2038 o verification:
2039 - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
2040 seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
2041 code from seaice_growth.F & seaice_advdiff.F to new ridging routines
2042 seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
2043 (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
2044 o model/src: for atmosphere in p* coords:
2045 - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
2046 - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
2047 but not yet activated.
2048 o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
2049 - move computation of opnWtrFrac = 1-AREA to before computing ice strength
2050 - this changes the results (but not for any verification experiment, because
2051 none tests this), but avoids having an extra field in the restart files
2052 o pkg/seaice: remove global variable TICE (not needed)
2053 - replace by TICES or local variable where necessary (cost_seaice_test,
2054 seaice_diagnostics_state)
2055 - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
2056 - use specific read/write routines for reading and writing individual leves
2057 of a multilevel field
2058 o pkg/ctrl & model/inc:
2059 - move additional anomaly fields of control vars (related to options:
2061 from DYNVARS.h into new header file: CTRL_FIELDS.h
2062 o pkg/seaice: some small modifications to the ridging code
2063 - make fw2ObyRidge a global variable and add the freshwater flux to
2064 seaice_growth
2065 - pass actual thickness from seaice_prepare_ridging, so that it is
2066 computed only in one place and compute it in the same way as in
2067 seaice_growth
2068 - initialise more fields in seaice_do_ridging that where cause floating
2069 point exceptions over land
2070 o pkg/seaice: preparations for ridging code and first real ridging code
2071 - move most of "PART 1" of S/R seaice_growth into a new and separate
2072 S/R seaice_reg_ridge that will both regularize the state variable after
2073 advection call the actual ridging routine;
2074 - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
2075 d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
2076 - remove ridging code from seaice_advdiff
2077 - clean up remaining part 1 of seaice_growth in an attempt to make it
2078 more readable (this is probably subjective)
2079 - call seaice_itd_redist once in the initialisation phase to have the initial
2080 conditions in the correct category
2081 - finally: add new ridging routine for ITD code
2083 checkpoint64v (2014/04/11)
2084 o pkg/ecco:
2085 - add runtime parameters mdt[start,end]date[1,2]
2086 - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
2087 o pkg/seaice:
2088 - make deltaC a global variable, so that it can be used in ridging code
2089 - first step towards ridging: introduce new routines that compute
2090 ice strength based on ridging parameters
2091 - add diagnostic for HSNOWITD
2092 - add opnWtrFrac as a global variable (required for ridging scheme)
2093 o pkg/salt_plume + pkg/seaice/seaice_growth.F
2094 - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
2095 AREA exceeds a threshold (code contributed by I.Fenty in 2011)
2096 o verification/hs94.1x64x5:
2097 - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
2098 - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
2099 o autodiff:
2100 - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
2101 and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
2102 For now, only in pkgs used in verification/hs94.1x64x5.
2103 - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
2104 which are specific to TAF/TAMC).
2106 since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
2107 is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
2108 - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
2109 building mitgcmuv_ad (make adAll).
2110 o pkg/ecco:
2111 - cost_gencost_seaicev4.F:
2112 reformulate proxy cost as function of sst and local param SEAICE_freeze
2113 change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
2114 - add stop statement if old names siv4-[sst,vol] are used
2115 - add snapshots + cost reports for atmospheric longwave
2116 - remove factor 0.1 in front of wtau[u,v]
2117 - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
2119 o pkg/atm_phys:
2120 - add some diagnostics for Short-wave and for convection S/R.
2121 o pkg/seaice/seaice_growth:
2122 - fix a bug in the lateral melt parameterization for SEAICE_ITD
2123 in seaice_growth; tempFrz needs to be computed inside the i/j-loop
2124 - rearrange loop order for better vector code in the same code block
2125 - rewrite the floeDiameter formula to have fewer divisions
2126 - (miraculously) none of this changes the results of seaice_itd
2127 o pkg/smooth:
2128 - move param smooth2Ddiffnbt to pkg/ecco
2129 o pkg/salt_plume:
2130 - salt_plume_frac.F:
2131 clean up local param names
2132 reformulate (1-frac) to frac; original 1-frac was based on swfrac code
2133 o pkg/rw:
2134 - add RS version of S/R READ_MFLDS_LEV.
2135 o pkg/streamice:
2136 - fix the restart test by writing/reading pickup_streamice files.
2137 o pkg/seaice:
2138 - refine checks for jfnk-related parameters
2139 - comment out if statement with SEAICEuseIMEX parameter as long as there
2140 is no IMEX code to avoid confusion and surprises
2142 checkpoint64u (2014/03/07)
2143 o verification/MLAdjust:
2144 - rename secondary test suffix:
2145 1.leith -> A4FlxF + switch to flux-form & add side-drag
2146 0.leithD -> AhFlxF + switch to flux-form
2147 0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag
2148 0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag
2149 o pkg/mom_vecinv:
2150 - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
2151 to be before mom_calc_visc.F)
2152 - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
2153 - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
2154 this is simpler for the adjoint and for diagnostics.
2155 o model/src + pkg/momentum:
2156 - add input files for 2-D additional Western and Southern cell-edge wall
2157 (e.g., to add "thin-wall" where it is =1).
2158 - fix sideDrag option for thin-walls with Non-Lin Free-Surf
2159 using 2nd hFacZ that is computed from initial (fix domain) hFac
2160 - known limitations of thin wall implementation: not yet coded for sigma
2161 coords; not working with CD-scheme neither.
2162 o pkg/seaice:
2163 - rename recently introduced parameters from (wrong name) AB to
2164 BDF (backward difference time discretisation)
2165 - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
2166 o tools/adjoint_options:
2167 - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
2169 checkpoint64t (2014/02/01)
2170 o pkg/ecco
2171 - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
2172 runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
2173 - replace hard-coded record number and period which only work for monthly
2174 with read-in runtime param that works for other periods (month,day,year)
2175 o pkg/thsice
2176 - corrected store directive fixes thsice adjoint gradient checks
2177 o genmake2 & testreport:
2178 - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
2179 in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
2180 Update testreport accordingly. No need to set "export OPENAD=true"
2181 in adjoint_options/adjoint_oad anymore (will be removed later).
2182 o pkg/shelfice:
2183 - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
2184 only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
2185 so that surface forcing applies to k=kSurf if using pkg/shelfice.
2186 o pkg/ctrl, pkg/grdchk, pkg/ecco:
2187 - Changes to make GENARR more modular (i.e. invisible if not used)
2188 o model/src/temp_integrate.F and salt_integrate.F
2189 - re-include store directives that were removed on Dec 27th.
2190 o model/src/external_forcing_surf.F
2191 - add storage directives for EmPmR and PmEpR to avoid recomputation of
2192 seaice_model in the adjoint that is problematic when seaice_model is
2193 turned off in the adjoint. The resolved issue dated back to July when
2194 EXTERNAL_FORCING_SURF call was moved.
2195 Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
2196 o pkg/exf/exf_check.F
2197 - fix a small bug again (originally found by Wentao Liu, now found again)
2198 - streamline error output
2199 o pkg/streamice and aim_v23:
2200 - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
2201 Apple's /usr/bin/cpp knows what to do:
2202 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
2203 Target: x86_64-apple-darwin13.0.0
2205 checkpoint64s (2014/01/05)
2206 o tools/adjoint_options:
2207 - switch to fastopt.net TAF server (instead of default fastopt.de) for
2208 AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
2209 o model/src:
2210 - remove some unnecessary TAF storage directives in forward_step.F and
2211 in dynamics.F (note: not always removed by TAF, e.g., double storage
2212 of kappaRU,kappaRV in former version of dynamics.F).
2213 o model/src & pkg/ptracers:
2214 - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
2215 salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
2216 and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
2217 - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
2218 - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
2219 - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
2220 o useSingleCpuInput separates single-CPU input from single-CPU output;
2221 for now only implemented for in exf_interp_read.F
2222 o verification/advect_xy:
2223 - fix missing EXCH call in local version of ini_salt.F and update output.
2224 o momentum diagnostics:
2225 - fix which deltaT is used in Total-Tendency diagnostics.
2226 - fix typo in diagnostics for momentum tendency from AB.
2227 o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
2228 SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
2230 checkpoint64r (2013/12/08)
2231 o verification/*/results:
2232 - Update reference output of experiments that were passing with just 13 digits
2233 (make it easier to detect future changes in results)
2234 o model/src & pkg/ptracers:
2235 - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
2236 inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
2237 to inside ptracers_integrate.F ; remove ptracers_advection.F
2238 o coupling interface pkgs:
2239 [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
2240 - change the config check to test the agreement of Ocean Depth
2241 with ATM land/sea mask (instead of ATM orography);
2242 - send to coupler the number of coupler time-steps to do for this run:
2243 this allows to check for consistency and don't need anymore to be
2244 specified in parameter file "data";
2245 in coupler:
2246 - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
2247 - improve report to log-file of config setting (pass log-file unit to few S/R)
2248 o pkg/compon_communic:
2249 - add coupling send/receive for non-tiled integer vector;
2250 - add S/R to check and stop if any proc has an error (similar to
2251 eesupp/src/stop_if_error.F but single thread and across Comm_World).
2252 o pkg/exch2:
2253 - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
2254 through list of all tiles my proc owns.
2255 o model/src:
2256 - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
2257 from rTrans) to simplify dependencies (no need to store rTrans anymore in
2258 calling S/R); this affects AD results at machine truncation level:
2259 update AD-output (TAF) of experiments: 1D_ocean_ice_column,
2260 bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
2261 o tools/build_options:
2262 - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
2263 o coupling interface pkgs:
2264 [compon_communic, atm_compon_interf & ocn_compon_interf]
2265 - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
2266 to each S/R that needs it; remove un-used variables.
2267 - change component tile registration (cpl_register.F in both compon_interf
2268 and mitcomponent_tile_register.F) to pass the full list of tiles
2269 information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
2270 - with pkg/exch2: adopt the same convention used for I/O to define mapping
2271 towards coupler global array (unless W2_useE2ioLayOut=F):
2272 a) can now use different tiling between atm & ocn comp.
2273 b) no needs to modify the run-Off map when changing tiling (was needed
2274 even if using the same tiling between atm & ocn).
2275 c) will allow to run with blank-tiles in 1 component (e.g., for ocean
2276 full land tiles); not yet tested.
2277 - check for valid mapping from comp. tile to coupler global array
2278 - improve report of tile registration results to log file.
2279 o pkg/exch2:
2280 - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
2281 tile-registration (CPL_REGISTER);
2282 - activate (un-comment) definition and setting of "W2_tileIndex" list to
2283 store the local bi,bj indices of each tile;
2284 - also print bi,bj in local report to log file;
2285 - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
2286 Jun 2009 modif of pkg/exch2).
2287 o testing on baudelaire:
2288 - run 2 tests at a time: no significant slow down (since enough cpu) and
2289 get the full set of test done earlier
2290 - switch the ifort test to "-devel" ; run the OpenAD test everyday.
2291 o model/src/thermodynamics.F and routines called from it:
2292 - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
2293 gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
2294 velocity (outp) by adding bolus velocity.
2295 - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
2296 mass transport from velocity + lateral grid cell area
2297 - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
2298 - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
2299 in thermodynamics.F
2300 - remove k from thermodynamics.F and move it to temp_integrate.F
2301 salt_integrate.F and ptracers_integrate.F (now done inside the tracer
2302 loop).
2303 - compute locally (in thermodynamics.F) 3-D velocity field that is used to
2304 advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
2307 - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
2308 global_ocean.90x40x15, tutorial_global_oce_biogeo and
2309 tutorial_tracer_adjsens (+ TLM output).
2310 o tools/OAD_support and (verification/*/) code_oad:
2311 - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
2312 module conversion ; remove unneeded CPP_EEOPTIONS.h.
2313 - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
2314 version (closer to model/inc/CPP_OPTIONS.h).
2315 o model/src:
2316 - remove parameter "useOldFreezing" from PARAMS.h and push it to the
2317 retired list of parameters (routine FREEZE has been replace by surface
2318 freezing (10.yrs ago) and by pkg/frazil (interior freezing).
2319 o pkg/gmredi:
2320 - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
2321 velocity (same scheme but affects machine truncation) for GM_AdvForm.
2322 - update output of FWD experiments: front_relax.bvp,
2323 global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
2325 checkpoint64q (2013/11/17)
2326 o verification:
2327 - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
2328 tutorial_global_oce_biogeo and global_ocean.90x40x15.
2329 - generate new output (growth & melt) for seaice_itd experiment after
2330 updating the input pickup_seaice files (previously wrong).
2331 o pkg/cost:
2332 - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
2333 (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
2334 o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
2335 cannot be applied to var in common block).
2336 o allows to get results independent of tile-per-proc setting (if using
2337 slower GLOBAL_SUM_SEND_RECV option).
2338 - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
2339 thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
2340 forward gradients: update output).
2341 - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
2342 S/R and, for most exp., also comment out GLOBAL_SUM_R8.
2343 o pkg/mom_common:
2344 - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
2345 code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
2346 viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
2347 ensure that all field value that are used are set.
2348 o tutorial_deep_convection (smag3d):
2349 - add missing scaling in mom_calc_smag_3d.F;
2350 - set smag3D_coeff in input.smag3d such that results do not change.
2351 o pkg/dic:
2352 - change dic_cost.F to compute cost on each tile first and then apply
2353 GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
2354 tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
2355 - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
2356 o eesupp/src & pkg/mdsio:
2357 - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
2358 (from pkg/mdsio) since they are no longer used for tape IO.
2359 - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
2360 (+ keep a copy in pkg/atm_ocn_coupler).
2361 o verification/isomip:
2362 - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
2363 o tools/build_options:
2364 - optfile linux_amd64_ifort11, fast (no ieee) case:
2365 to get a working restart for all experiments, add "-fp-model source"
2366 to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
2368 checkpoint64p (2013/10/20)
2369 o pkg/autodiff:
2370 - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
2371 criteria, return to simple (default) tape IO format.
2372 o pkg/mdsio (+ eesupp/src):
2373 - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
2374 previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
2375 - fix globalFile and singleCpuIO options using simpler global mapping.
2376 - new pairs of scatter/gather vector S/R (one for each type, generated from
2377 template) corresponding to simpler global mapping.
2378 - adread_write.F: switch to new S/R (but leave old calls commented) and write
2379 to globalFile when parameter globalFiles is set to True.
2380 - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
2381 o pkg/autodiff:
2382 - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
2383 with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
2384 missing, just add a STOP if array type do not match.
2385 o pkg/exf:
2386 - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
2388 and rename array obsSIce to exf_iceFraction.
2389 o tutorial_deep_convection:
2390 - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
2391 for now all in this exp. code dir.
2392 - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
2393 testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
2394 o eesupp/src:
2395 - added SINGLE_DISK_IO option because reading of parameter files on
2396 very large number of processors did not work with existing set-up
2398 checkpoint64o (2013/09/25)
2399 o pkg/atm_phys & atm_compon_interf:
2400 - allows for coupling of gray-atmosphere (atm_phys) with ocean.
2401 o tools/build_options:
2402 - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
2403 & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
2404 remove CPP setting (was identical to genmake2 default).
2405 o pkg/gmredi & model/src: Some updating and work done on the residual model.
2406 - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
2407 - fixed up the calculation of the eddy stress and how it is added to the
2408 external forcing via taueddy_external_forcing.F
2409 - at the moment, it is very experimental and only works with the variable eddy
2410 diffusivity calculated in gmredi_k3d.F
2411 o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
2412 lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
2413 o testreport (& tools/do_tst_2+2):
2414 - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
2415 o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
2416 - remove CPP='cpp -traditional -P' (this is genmake2 default)
2417 - add switch (for big setups) to use 'medium' memory-model (but leave it
2418 commented out for now). Note: needed with FC 19 to compile big setups.
2419 o pkg/atm_compon_interf:
2420 - regroup per field origin (model & pkgs) the coupling storage routines
2421 (which accumalate in time each coupling field)
2422 - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
2423 update accordingly + simplify aim_do_physics.F
2425 checkpoint64n (2013/08/26)
2426 o pkg/bbl:
2427 - update formulation to reduce dispersion of tracer properties in bbl
2428 - replaced horizontal and vertical transport parameters with velocities
2429 - changes results for verification/global_with_exf.yearly
2430 o verification/halfpipe_streamice:
2431 - change to matrix construction; update both Fwd & AD output.
2432 o verification/tutorial_tracer_adjsens:
2433 - OpenAD test: switch to vector-invariant momentum since fluxform with
2434 rStar causes problems with OpenAD; update output.
2435 o tools:
2436 - genmake2: define a common prefix for all temp-file names ; move them
2437 to local /tmp disk (but would be easy to move them back);
2438 - xmakedepend: apply the same switch for temp-files.
2439 o pkg/offline:
2440 - changes for use with rStar (NLFS): assume that we continue to provide
2441 UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
2442 output files) and apply r* scaling at each time-step (function of the time
2443 varying Eta field); use normal pickup files (needed for restart with NLFS).
2444 o adjoint with OpenAD:
2445 - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
2446 package openad. This package has to be compiled for all runs with OpenAD
2447 instead of specifying code_oad_all as a modification directory.
2448 - link the fortran templates from tools/OAD_support to the build directory
2449 for preprocessing to avoid conflicts between different setups compiled
2450 simultaneously and simplify cleanup.
2451 o pkg/exf:
2452 - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
2453 main model or other pkgs are exchanged in EXF_MAPFIELDS).
2454 o model/src:
2455 - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
2456 (similar to do_fields_blocking_exchanges.F).
2457 o tools/genmake2:
2458 - remove TAF output src code just before calling staf (when not doing a fresh
2459 built, will stop if things go wrong with staf).
2460 - fix target "adobj" (left from TAF version-2 transition)
2461 o pkg/diagnostics:
2462 - add a parameter to track the status of pkg/diagnostics activation;
2463 this replace/extend the use of logical param "settingDiags" (to check
2464 when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
2465 New S/R to print error message and stop when pkgStatus is not right.
2466 - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
2468 checkpoint64m (2013/08/13)
2469 o model/inc:
2470 - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
2471 8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
2472 o pkg/kpp & aim_v23:
2473 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
2474 o pkg/seaice:
2475 - restore (last time on 2011/12/24) ability to compile pkg/seaice with
2476 undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
2477 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
2478 o eesupp/src:
2479 - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
2480 in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
2481 o switch to TAF version-2:
2482 - add flow directives to "freeze" naming convention for ad-routines that
2483 are used in I/O routines of adjoint state and associated common blocks
2484 that are used in adcommon.h (backward compatible with version-1)
2485 - update all ad-optfiles (in tools/adjoint_options + few local to some
2486 verification exp) to switch to latest TAF version (currently 2.5.5);
2487 merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
2488 out except for diva).
2489 - the major change with TAF version-2 is that both the differentiated
2490 routines and the forward routines (new) are returned as part of the TAF
2491 output source code. Update genmake2 accordingly.
2492 - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
2493 with version-2 when compared to TLM or FWD gradient); other experiments
2494 output show minor changes (machine truncation level); update the few AD &
2495 TLM output with 12 matching digits only (some prior to version-2 switch).
2497 checkpoint64l (2013/08/05)
2498 o model/src:
2499 - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
2500 - main_do_loop.F: no longer includes additional (AUTODIFF) header files
2501 when using TAF but only if using OpenAD.
2502 o pkg/mom_common+fluxform+vecinv:
2503 - always set horiz. viscosity arrays to background value before calling
2505 only when using variable horiz. viscosity (useVariableVisc=T);
2506 - simplify mom_vecinv.F (only 1 block for momViscosity).
2507 o pkg/mom_common: variable horiz. viscosity in NH code
2508 - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
2509 from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
2510 - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
2511 useBiharmonicVisc & useVariableVisc.
2512 - fix old bug (already in 1rst implementation of variable horizontal viscosity
2513 in calc_gw.F, version 1.27, 2006/06/20):
2514 horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
2515 even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
2516 - change background horiz viscosity in vertical momentum (gW) to always be
2517 viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
2518 any type of variable viscosity, e.g., viscAh/4Grid)
2519 - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
2520 viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing
2521 horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
2522 default viscAh,viscA4 is zero).
2523 o model/src:
2524 - extend length of drC & recip_drC from Nr to Nr+1.
2525 o Divided Adjoint (DIVA) with MPI:
2526 - genmake2: do not create local ./mpi_headers dir when no file to copy into.
2528 and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
2530 checkpoint64k (2013/07/23)
2531 o tools/OAD_support:
2532 - avoid the need for file "oadtempflile" in insertTemplateDir.bash
2533 and remove it from genmake2.
2534 o tools/build_options:
2535 - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
2536 MPI_HEADER_FILES list (let genmake2 find the missing headers)
2537 o verification/halfpipe_streamice:
2538 - change to driving stress formulation; update both Fwd & AD output.
2539 o tools/genmake2 and Divided Adjoint with MPI:
2540 - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
2541 - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
2542 - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
2543 Makefile, which is set by genmake2, and check which mpi-headers are needed.
2544 Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
2545 - update target "CLEAN" (to also remove ./mpi_headers/ dir).
2546 o testreport:
2547 - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
2548 perform additional runs (number of additional runs is "add_DIVA_runs" taken
2549 from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
2550 o verification/lab_sea (AD test):
2551 - change to test Divided Adjoint Run in this set-up (both standard AD test
2552 and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
2553 o pkg atm_ & ocn_compon_interf:
2554 - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
2555 staggerTimeStep implementation) and disable (retired) corresponding
2556 parameter.
2557 o pkg/offline:
2558 - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
2559 - add S/R OFFLINE_CHECK to print offline parameter summary
2560 and stop if loading a file that is not used;
2561 - enable to calculate GMRedi tensor, KPP mixing and convective index
2562 when the corresponding file(s) is/are not specified (but pkg is used).
2563 - comment out resetting of monitorFreq (to endTime) since it still useful
2564 for monitoring CFL numbers and checking offline fields.
2565 o OpenAD:
2566 - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
2567 smaller standard output) and generate new (smaller) output (on baudelaire
2568 using gfortran with -ieee) for exp. tutorial_tracer_adjsens
2569 o model/src:
2570 - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
2571 (where external_forcing_adjust was called) and change list of arguments;
2572 - merge external_forcing_adjust.F into external_forcing_surf.F
2573 - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
2574 which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
2575 previously in file "balance_relax.F", now removed); remove corresponding
2576 arrays in FFIELDS.h.
2577 - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
2578 a hack for getting back surfaceForcingS (loaded from file) when using
2579 ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
2580 - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
2581 (was getting only 11 digits for AD-grad, due to different truncation
2582 error in AD code).
2584 checkpoint64j (2013/07/04)
2585 o pkg/offline:
2586 - to enable the use of other features with pkg offline (e.g., obcs),
2587 also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
2588 - comment out "allowFreezing" (now active) in 2 offline testing exp.
2589 o pkg/exf ALLOW_RUNOFTEMP
2590 - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
2591 - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
2592 - changes verification/global_ocean.cs32x15/results/output.seaice.txt
2593 o pkg/atm_phys:
2594 - allows to add some damping on uVel,vVel (strength only function of k).
2595 o verification, ad-tests:
2596 - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
2597 global_ocean_ebm and offline_exf_seaice.thsice.
2598 o verification/halfpipe_streamice:
2599 - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
2600 flux input boundary conditions to be ignored; a fix for this bug changed
2601 verification results for forward test.
2602 - add adjoint test.
2603 o pkg/ptracers:
2604 - allow to restart without SOM pickup (resetting SOM to zero).
2605 o pkg/gmredi:
2606 - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
2607 - It uses mixing length theory and suppression by steering level effects to
2608 calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
2609 to JPO, for more details).
2610 - It also uses the diffusivity to calculate an eddy induced streamfunction
2611 based on a PV closure (rather than a buoyancy closure as in GM).
2612 - New files added to pkg/gmredi:
2613 gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
2614 induced overturning streamfunction (called from gmredi_calc_tensor)
2615 gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
2616 for use in gmredi_k3d
2617 gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
2618 the eddy diffusivity
2620 checkpoint64i (2013/06/18)
2621 o pkg/cheapaml:
2622 - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
2623 that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
2624 with pkg/cheapaml.
2625 o utils/python: add subpackage for cubed sphere function, first example is
2626 simple cs.pcol to plot 2D fields on a map
2627 o pkg/streamice:
2628 - This is a new package in MITgcm, which solves dynamic equations for ice
2629 sheets and ice streams
2630 - At the moment it is independent of atmosphere/ocean dynamics, or any
2631 other physical packages in MITgcm, even ShelfIce (although it is anticipat-
2632 ed that this will change)
2633 - There is a new verification exercise that tests it, halfpipe_streamice,
2634 evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
2635 rectangular embayment
2636 - halfpipe_streamice is forward-only for now, will have TAF test soon
2637 - for questions, email dgoldber@mit.edu
2638 o pkg/thsice:
2639 - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
2640 of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
2641 - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
2642 call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
2643 - allow precip from pkg/cheapaml to make snow over seaice.
2644 o pkg/cfc:
2645 - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
2646 - remove atmos CFC 2-D arrays from common bloc (now local variables)
2647 - change some hard-coded constant to run time parameter for reading and
2648 and interpolating atmospheric CFC ; keep same default as previously.
2649 - more flexible reading of Atmos CFC (number of records no longer hard-coded)
2650 - put arguments in standard order: myTime, myIter, myThid
2651 - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
2652 atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
2653 - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
2654 - new routine to print summary of CFC params and check for consistency.
2655 o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
2656 similar to thsice_advdiff.
2657 Note that for the B-grid case the routine parameters uc/vc are overwritten.
2658 o pkg/cfc:
2659 - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
2660 update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
2661 - fix interpolation of atmphspheric CFC between Sorthern and Northern
2662 hemisphere value.
2663 o pkg/seaice:
2664 - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
2665 o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
2666 so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
2667 - requires an additional time level that is stored in the pickup
2668 - you can start with AB2 from a pickup without this time level with
2669 pickupStrictlyMatch = .false.
2671 checkpoint64h (2013/05/26)
2672 o pkg/cheapaml:
2673 - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
2674 affect machine truncation (but exp cheapAML_box still pass with 13 digits).
2675 - consistent treatment of uWind,vWind location: assume everywhere in
2676 pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
2677 (Note: was already the case for Tair,Qair advection);
2678 add option (INCONSISTENT_WIND_LOCATION) to recover old results.
2679 - compute diabatic forcing only in the interior (excluding overlap regions)
2680 - fill in array "Qsw" (for short-wave heating);
2681 - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
2682 before any update (consistent with MITgcm state var diagnostics);
2683 - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
2684 non periodic ; + adjusted for uWind,vWind (C-grid).
2685 o pkg/seaice:
2686 - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
2687 add explicitly pkg/exf in experiments that currently use pkg/seaice.
2688 - allows to compile pkg/seaice without pkg/exf.
2689 o tools/OAD_support:
2690 - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
2691 of array "ourStepOf" in function rvNextAction (revolve.F90).
2692 o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
2693 - change pkg name (to be used with other atmospheric physics pkg)
2694 but by-pass CVS when making the new pkg so that we keep the CVS history.
2695 o pkg/offline:
2696 - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
2697 (previously called from pkg/dic_surfforcing_init.F)
2698 o model/src:
2699 - re-order sequence of calls within packages_init_variables.F, using
2700 standard order, except for:
2702 CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
2703 o new pkg: atm_phys
2704 - add entry point and source code (previously in contrib
2705 verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
2706 (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
2707 - re-order sequence of calls within packages_readparms.F,
2708 packages_init_fixed.F and packages_write_pickup.F
2709 (but skip packages_init_variables.F because of TAF issues).
2710 - update contrib/*/atm_gray/ experiment.
2711 o pkg/seaice (ITD code):
2712 - simplify and fix the writing of pickup-files for ITD case
2713 o pkg/seaice (ITD code):
2714 - introduce floe size dependent lateral melt for ITD case;
2715 - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
2716 - update seaice_itd experiment main output.
2717 o pkg/thsice:
2718 - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
2719 declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
2720 changed accordingly pkg/atm2d.
2722 checkpoint64g (2013/05/01)
2723 o pkg/exf ALLOW_RUNOFTEMP
2724 - if defined, river and glacier runoff temperature can be read-in from
2725 runoftempfile; runoftempfile needs to have same format as runofffile
2726 o pkg/thsice (& pkg/bulk_force):
2727 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
2728 for energy content of Precip + RunOff & Evap (like with pkg/exf).
2729 - change computation domain to always be the interior (without overlap).
2730 - fix bug (wrong overlap) when using EXF and stressReduction > 0.
2731 o verification/tutorial_global_oce_biogeo:
2732 - add preliminary OpenAD setup (still has problems)
2733 o pkg/seaice:
2734 - turn some parameters for choosing the convergence criterion of
2735 the inexact Newton method (JFNK) into runtime parameters for convenience
2736 - clean up seaice_calc_viscosities.F: remove/retire two options for
2737 SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
2738 the results of lab_sea/input because a division has been replaced by
2739 a multiplication with the reciprocal (sumNorm)
2740 - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
2741 convergence of solver (changes results, of course), and to test some
2742 new features
2743 o model/src:
2744 - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
2745 - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
2746 - move forcing adjustment (balancing surface forcing) in specific S/R
2747 where might also be applied exchanges (if needed) to forcing arrays.
2748 o pkg/shelfice:
2749 - allow to specify the Ice-Shelf mass per unit area (instead of
2750 shelficeLoadAnomaly) and do the conversion from one to the other
2751 - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
2752 to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
2753 (b) will be loaded in time (before calling INI_PRESSURE) in case it is
2754 needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
2755 - update isomip experiment forward output (get machine truncation error
2756 from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
2757 o verification/offline_exf_seaice:
2758 revise data.seaice in input.thermo and input_ad and update results accordingly
2759 HO = 0.2, SEAICE_areaLossFormula = 2,
2760 SEAICE_growMeltByConv = .TRUE.,
2761 SEAICE_doOpenWaterMelt = .TRUE.,
2762 Improve consistency with input.thsice and fix the spurious 500m ice corners
2763 o verification/global_ocean.cs32x15:
2764 - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
2765 in icedyn (thsice+seaice-dyn) test and update output.
2766 o verification/offline_exf_seaice:
2767 - adjust list of tested variables (with testreport) and update
2768 standard test output with better slection of monitored fields.
2769 o pkg/cd_code:
2770 - swtich off Adams-Bashforth on the 1rst iteration. Update output of
2771 experiment lab_sea.hb87
2772 o tools/genmake2:
2773 - change default makedepend from the system default to tools/xmakedepend:
2774 When no makedepend is specified, select tools/xmakedepend it the test pass,
2775 otherwise select the system default (if exist and pass the test) or
2776 try to build cyrus-makedepend ; stop if none of the 3 works.
2777 o pkg/exf & pkg/thsice:
2778 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
2779 for energy content of Precip + RunOff & Evap. Assumes:
2780 1) Rain has same temp as Air.
2781 2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
2782 3) Run-Off comes at the temp of surface water (with same Cp)
2783 4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
2784 put directly into Latent Heat flux & should use water-vapor heat capacity.
2785 5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
2786 with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
2787 o pkg/seaice: simplify the use of CPP flags in JFNK-related files
2788 (compile when SEAICE_ALLOW_JFNK is defined)
2789 o pkg/thsice:
2790 - fix oceanic flux diagnostics & timeave (left from new sequence of calls
2791 implementation): move THSICE_AVE call after the advection (called directly
2792 from thsice_do_advect.F).
2793 o verification/global_ocean.90x40x15 and OpenAD:
2794 New experiment for OpenAD is identical to the one in input_ad except that
2795 multiDimAdvection=.FALSE.,
2796 There is still an issue with this.
2797 o pkg/thsice:
2798 - account for ice velocity (ocean relative velocity) in turbulent heat flux
2799 at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
2800 and offline_exf_seaice (main test).
2802 checkpoint64f (2013/03/31)
2803 o verification/OpenAD:
2804 - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
2805 o verification/isomip, pkg/shelfice and OpenAD:
2806 - add OpenAD setup to this exp and make shelfice package work with OpenAD
2807 o verification/tutorial_global_oce_biogeo:
2808 - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
2809 o verification/offline_exf_seaice:
2810 - replace adjoint experiment (now similar to fwd input.thermo/ setup).
2811 o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
2812 - add OpenAD setup to this exp and make ptracers package work with OpenAD
2813 o pkg/seaice/seaice_evp.F:
2814 mask the asymmetric contribution of the ice-ocean stress (when
2815 the turningAngle is non-zero) over open water to avoid stripes
2816 in the EVP-solutions after many EVP-substeps. This does not change
2817 the verification experiment (because turningAngle=0 in that experiment),
2818 but will affect other EVP solutions with turningAngle.ne.0
2819 o verification, AD & TLM output:
2820 - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
2821 additions and multiplications which affect results at machine truncation
2822 level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
2823 lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
2824 (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
2825 digits of matching.
2826 o pkg/seaice:
2827 modify lsr-algorithm so that it vectorizes AND converges by using a
2828 "zebra" method: split vector loop into two with step size 2; this
2829 solves a general convergence problem for the JFNK solver on a vector
2830 computer. It has the potential to even improve convergence for
2831 non-vector machines, but it does change the results so it is turned
2832 off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
2835 checkpoint64e (2013/03/05)
2836 o pkg/ecco and several verification experiments:
2837 Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
2838 from ecco package, and revert to unified routine in model/src/
2839 Adjust verification experiments accordingly, especially gloal_oce_llc90
2840 Should conclude long-standing work by Gael to reconsile the_main_loop with
2841 ECCO and will enable OpenAD's revolve loop in ECCO setup.
2842 o pkg/generic_advdiff:
2843 - implement compressible flow method for multi-dim advection (similar to
2844 gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
2845 TAF generates many recomputations) to use it; no yet coded with implicit
2846 vertical advection.
2847 - change experiment advect_cs (new output) and advect_xy (same output)
2848 to test compressible flow multi-dim advection.
2849 o pkg/generic_advdiff:
2850 - fix SOM advection for unusual cases (linear Free-Surf in r*, other
2851 cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
2852 o pkg/seaice:
2853 - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
2854 bug affects two verification experiments (lab_sea and lab_sea.hb87),
2855 recover old (wrong) results by setting noSlipFac = 2. in
2856 seaice_calc_strainrates.F;
2857 - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
2858 - add runtime parameter SEAICE_JFNKepsilon for that finite difference
2859 gradient in the Jacobian times vector operation (s/r seaice_jacvec)
2860 - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
2861 o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
2862 - new subroutines seaice_lsr_tridiagu/v
2863 - introduce loop bounds i/jmin/max to be able to use a restricted
2864 additive Schwarz method, but not used for now.
2866 - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
2867 o OpenAD support
2868 Reorganize S/R call for overall time-stepping loop to facilitate
2869 OpenAD revolve loop replacement
2870 (new S/R main_do_loop.F)
2871 o model/src:
2872 - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
2873 - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
2875 o pkg/cheapaml:
2876 - add new parameter (default=F, same as before) to disable full domain
2877 (including land) periodicity in X & Y dir.
2878 - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
2879 prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
2880 into single S/R CHEAPAML_TIMESTEP.
2882 checkpoint64d (2013/02/17)
2883 o pkg/monitor (angular momentum):
2884 - do not add Eta contribution to the total AM if using rigid-lid;
2885 - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
2886 - horizontal discretisation: compute Zonal wind contribution separately for
2887 each component (instead of from cell centered averaged) and use the 4
2888 grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
2889 - Check that AM is conserved with linear dynamics (momAdvection=F and linear
2890 FreeSurf) if using vectorInvariant momentum.
2891 o model/src (horizontal grid):
2892 - move initialisation of all horizontal grid arrays to null value
2893 from specific horizontal grid S/R to main S/R INI_GRID;
2894 - add 2 new arrays to project model C-grid velocity on to zonal direction
2895 (similar to AngleCosC & -AngleSinC but at U and V point location) and
2896 compute them in S/R CALC_GRID_ANGLES.
2897 o pkg/seaice: replace a hard coded parameter by a runtime parameter
2898 SEAICE_JFNK_tolIter
2899 o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
2900 preconditioner for JFNK (run LSR into the overlaps as far as possible,
2901 i.e OLx/y-2, but overwrite the solution in the overlaps)
2902 - extend loop range in seaice_calc_viscosity
2903 - add new parameters SEAICE_OLx/y (default = OLx/y-2)
2904 - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
2905 - slightly modify loops in tridiagonal solver lsr-preconditioner
2906 - by default remove the extra exchange in seaice_preconditioner with a
2907 replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
2908 - modify offline_exf_seaice so that old results without RAS are reproduced
2909 for output.dyn_jfnk.txt
2910 in seaice_fgmres.F (unrelated to RAS)
2911 - add a cpp-flag option for a re-ordered mapping (potentially more
2912 efficient), but because this changes the results, turn it off by
2913 default
2914 - replace the save statement by local common blocks
2915 o utils/matlab:
2916 - fix tile-offset in rdmnc.m when output was produced using EXCH2.
2917 - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
2918 instead of local script "load_cs.m".
2919 o pkg/seaice:
2920 - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
2921 to the scalarProductMetric and the unrolling. By chance this does not
2922 change the verification experiment, because of the particular domain
2923 decomposition
2924 o pkg/diagnostics:
2925 - change default missing_value from UNSET_RL to -999.
2926 o pkg/layers: improve vectorization of layers_fluxcalc.F
2927 - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
2928 time spent in this routine by more than a factor of 3 on an NEC-SX8
2929 - step 2: replace search algorithm by a bisection algorithm found in
2930 Press et al. Numerical Recipes in Fortran. This algorithm can be
2931 vectorized and finds the correct bin in approx. log2(Nlayers) steps.
2932 For now, use this algorithm only for TARGET_NEC_SX defined.
2933 - moved the search algorithm into a separate subroutine, that is kept
2934 within the same file for automatic inlining.
2935 - modified catching potential errors
2936 o pkg/ecco:
2938 o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
2939 - modifications for ALLOW_GENTIM2D_CONTROL
2940 -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
2941 -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
2942 -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
2943 -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
2944 o model/src:
2945 - account for moist thermodynamics in (dry) potential temperature equation;
2946 update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
2947 and cpl_aim+ocn.
2948 - also switch to standard compiler (gfortran, was using ifort previously)
2949 for fizhi-cs experiments reference output.
2950 o pkg/ctrl:
2951 - 1st step toward generic time-varying control variable (2D) via CPP option
2953 - note new namelist ctrl_nml_genarr in data.ctrl
2954 o verification/global_ocean.cs32x15:
2955 - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
2956 thsice calling sequence and update "output.icedyn.txt" output file.
2957 o pkg/ptracers:
2958 - from Ryan A.: code to allow to restart a tracer at regular time interval
2959 specifying a reset frequency and a reset-phase (for each tracers).
2960 o pkg/thsice:
2961 - implement new sequence of calls for thsice+seaice:
2962 previously: ice-Dyn,ice-Advect,ice-Thermo(thsice)
2963 new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
2964 - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
2965 in CPP_OPTIONS.h) to recover old sequence;
2966 - update diagnostics for Intermediate State thsice diagnostics: now filled
2967 just before advection (instead of just after advection in old sequence);
2968 - update output of experiment offline_exf_seaice (standard test);
2969 - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
2970 by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
2971 o pkg/aim_v23:
2972 - use tiled array for aim_CO2 and surface wind speed for export to coupler;
2973 - use standard pkg/mdsio routines to read & write CO2 pickup file;
2974 - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
2975 - Implement new sequence of calls for seaice advection (with thsice and
2976 seaice diffusion): do ice advection after ice-Thermodynamic (previously
2977 was done before); change aim_do_physics.F (split the bi,bj loops block);
2978 - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
2979 o pkg/thsice:
2980 - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
2981 where just seaice diffusion is used without seaice-dynamics.
2983 checkpoint64c (2013/01/18)
2984 o pkg/seaice:
2985 - add a parameter JFNKres_tFac that can replace JFNKres_t
2986 (= JFNKres_tFac*JFNKresidual before JFNK solver)
2987 - add a line search option to the JFNK solver
2988 - move update of u/vIce and computation of initial residual into a separate
2989 routine (same file); makes the code a little easier to read (?)
2990 - the line search requires computation of the residual and for some reason
2991 I cannot do the update of u/vIce at the beginning of the Newton loop
2992 without changing the results, so we move computation of the new residual
2993 also to the end of the Newton loop, even without the line search
2994 o pkg/mdsio:
2995 - write missing value (corresponding to undefined array value) to meta files;
2996 skip this if missing value is one (UNSET_RL would be a better value for the
2997 case of undefined missing value but it's current the default missing-value);
2998 Also update mdsio_read_meta.F (reading timeInterval & missing-value).
2999 o pkg/exf & thsice:
3000 - for diagnostics purpose, fill-up and update Qsw array (+ fill the
3001 diagnostics) even when SHORTWAVE_HEATING is #undef;
3002 o verification/cfc_example:
3003 - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
3004 illustrate how to use it).
3005 o verification/offline_exf_seaice:
3006 in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
3007 files to only one time-record.
3008 in input.thermo: narrow the 2 bands of low initial ice-concentration near
3009 N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
3010 snapshot output; same mcPheePiston value as in thsice with
3011 surf-current=0.2m/s.
3012 in input.thsice: similar set-up as in input.thermo (channel with same seaice
3013 initial conditions).
3014 o verification/cfc_example:
3015 - update file "data" with more standard choice (default rotationPeriod,
3016 exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
3017 set deltaTFreeSurf to deltaTtracer) and update the output.
3018 o pkg/layers:
3019 - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
3020 - ensure that "layers_bolus" is switched to False when useGMRedi=False.
3021 o verification/offline_exf_seaice:
3022 - set all {field}period to zero for constant-in-time forcing (not tested
3023 anywhere else).
3024 o verification/offline_exf_seaice:
3025 - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
3026 - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
3027 o model/src:
3028 - implement Finite-Volume method for (hydrostatic) presure gradient
3029 from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
3030 o pkg/seaice: implement EVP* by Lemieux et al. (2012).
3031 - In order to be compatible with the default EVP code, this requires changing
3032 the EVP code around a little; and because any small change immediately
3033 breaks the lab_sea.hb87 verification experiment, the reference output is
3034 updated two times (each time the remaining aggrement was only 2 digits):
3035 - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
3036 - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
3037 The adjoint test lab_sea.evp also needed to be updated.
3038 - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
3039 SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
3040 a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
3041 explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
3042 INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
3043 kept obscure, because I need to test it a little more.
3044 o pkg/cheapaml:
3045 - fix few incorrect type (_RL/_RS) in subroutine calls.
3046 o pkg/seaice:
3047 - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
3048 to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
3049 o model/src:
3050 - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
3051 change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
3052 experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
3053 o pkg/cheapaml:
3054 - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
3055 update output of experiment cheapAML_box.
3056 - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
3057 and set them only in one place (cheapaml_readparms.F).
3058 - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
3059 - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
3060 and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
3061 o model/src/the_main_loop.F:
3062 - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
3063 o pkg/seaice:
3064 - remove legacy branch code.
3065 - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
3066 o verification/*/code*/SEAICE_OPTIONS.h:
3067 - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
3069 o pkg/cheapaml:
3070 - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
3071 to load new forcing fields.
3072 - add missing "_d 0" where it's needed; + some editing (improve indentation).
3073 - remove switch to "-r8" compiler option (no longer needed) in verification
3074 cheapAML_box, keep same output (small trucation error differences).
3075 o verification/offline_exf_seaice:
3076 - add thermodynamics only test.
3077 o verification/cheapAML_box:
3078 - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
3079 keep same output (same 14 digits for cg2d).
3080 - switch on "-r8" compiler option (some numerical values are missing
3081 the "_d 0") and update output (only 6 digits for cg2d were preserved).
3083 checkpoint64b (2012/12/24)
3084 o pkg/cheapaml:
3085 - remove un-used variables (Qnet,EmPmR) from pickup files.
3086 - store tendency of advected variables into cheapaml pickup file
3087 and fix the AB-2 restart.
3088 o verification/offline_exf_seaice and lab_sea adjoint:
3089 - switch to new code (#undef SEAICE_GROWTH_LEGACY).
3090 - switch to 4 time steps in offline, consistent with lab_sea.
3091 - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
3092 - update results after change of experiment seaice.
3093 o pkg/seaice:
3094 - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
3095 parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
3096 still defined since SEAICE_multDim needs to be set to MULTDIM value (from
3097 SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
3098 o model/src:
3099 - add run-time parameter to select CG2D solver minimum-residual solution
3100 (in case of a poor convergence).
3101 o pkg/seaice/seaice_lsr.F
3102 - move calculation of matrix coefficients into new
3103 S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
3104 file; the main purpose of this change is to be able to reuse the code
3106 - modify the computation of the residual so that the mass of sea-ice
3107 is not used twice; this simplifies the calculations, but since
3108 the residual is never used except when LSR_mixIniGuess.ge.4---and this is
3109 not tested in testreport---this does not affect the testreport results.
3110 o verification/seaice_obcs:
3111 - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
3112 verification/lab_sea/input.salt_plume; changes results/output.txt*
3113 o model/src:
3114 - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
3115 o pkg/seaice:
3116 - improve description of parameters in seaice_fgmres.F and start
3117 cleaning up the code
3118 - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
3119 second argument
3120 - add a metric based on grid cell area to SEAICE_SCALPROD; update
3121 results of offline_exf_seaice.dyn_jfnk
3122 - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
3123 o pkg/aim_v23:
3124 - fix an other bug in dissipation heating (grid-cell area was missing).
3125 o model/src + pkg/seaice:
3126 - add global (multi-tile) linear solver for pair of tri-diagonal system
3127 along X and Y lines, respectively for U and V component.
3128 Note: 1) MPI and cube-exchange not yet coded.
3129 2) probably not accurate for poorly conditioned / large size problem.
3130 - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
3131 default: not compiled and not used.
3132 o pkg/seaice:
3133 - first attempt at a multi-threaded fgmres solver for the JFNK solver:
3134 introduce bi/bj loops and use global_sum_tile_rl instead of
3135 mpi_allreduce in seaice_fgmres.F
3136 - improve diagnostics output for fgmres solver (seaice_fgmres.F)
3137 - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
3138 - add a verification experiment for JFNK in offline_exf_seaice
3139 o verification:
3140 - change (for now, only fwd test) offline_exf_seaice experiment:
3141 use a re-entrant channel with idealized coastline (trapezoidal shape)
3142 at southern boundary to explore seaice dynamics and thermodynamics
3143 with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
3144 secondary test (input.thsice) use thermodynamics only with SST relaxation.
3145 - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
3146 o pkg/exf:
3147 - disable "sstExtrapol" when Nr=1
3148 o verification:
3149 - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
3150 to test pkg/cheapaml.
3151 o pkg/aim_v23 & pkg/shap_filt:
3152 - fix dissipation heating (erroneous gravity multiplication factor).
3153 o pkg/seaice:
3154 - remove unused field pressPre from jfnk solver
3155 - rename two subroutines in seaice_preconditioner.F
3156 o eesupp/src:
3157 - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
3158 o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
3159 - remove wrong parts of the rhs and the lhs (were in there
3160 because I did not understand the concept of this preconditioner)
3161 - add an exchange between u- and v-sweep. This increases communication
3162 by a factor of two but improves the convergence of jfnk. Ideally,
3163 one would like the u- and v-sweep to be independent. So far within
3164 undocumented ifdefs
3165 - reorganize the extra computations for printing the residuals
3166 o tools/genmake2:
3167 - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
3168 since it's not necessary (and was preventing to use MNC in some cases).
3170 checkpoint64a (2012/11/16)
3171 o pkg/autodiff:
3172 - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
3173 autodiff_readparms.F no longer depends on calling order (within
3174 packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
3175 rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
3176 and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
3177 o pkg/obcs:
3178 - adding tidal velocity forcing capability to obcs
3179 for usage example, see verification/seaice_obcs/input.tides
3180 o pkg/seaice:
3181 - turn the LSR-relaxation parameters WFAU/V into runtime parameters
3182 SEAICE_LSRrelaxU/V
3183 - introduce runtime parameter SEAICEetaZmethod (=0 by default)
3184 o pkg/aim_v23:
3185 - implement heating from friction (bottom friction and stratospheric drag).
3186 o pkg/shap_filt:
3187 - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
3188 dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
3189 o model/src:
3190 - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
3191 time-constant addMass field from file (addMassFile);
3192 - support for heating due to friction (and Kinetic Energy dissipation):
3193 add option, run-time switch and 3-D field array + support code ; each pkg
3194 or S/R can add heating contribution (if there is a sink of KE); the sum is
3195 accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
3196 o pkg/seaice:
3197 - complete merge of ITD code into seaice_growth.F
3198 from MITgcm_contrib/torge/itd/code/
3199 no verification so far, but Torge Martin tested
3200 "1-D test case and Beaufort set up;
3201 deliver okay results after 1 model year."
3202 - complete merge of SEAICE_SIZE.h into all relevant routines
3203 - move computation of eta at Z-points into calc_viscosities
3204 + introduce global field etaZ
3205 + add different methods for computing etaZ, for now the old
3206 method (simple averages of eta to Z-points) is hardwired
3207 + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
3208 seaice_preconditioner
3209 - simplify computations for SEAICE_ZETA_SMOOTHREG
3210 - seaice_preconditioner:
3211 + replace one remaining press by pressLoc (mistake)
3212 + adjust printing of residuals
3213 - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
3214 + add (SEAICE.h) and rename some counters (initiliased in
3215 seaice_init_fixed.F)
3216 + add _BEGIN/END_MASTER (myThid) around print statements
3217 + print total number of iterations and failures over SEAICE_monFreq
3218 interval to STDOUT
3219 - move control over output-messages by fgmres to seaice_jfnk to save
3220 some operations
3221 - move resetting initial guess for fgmres outside of seaice_fgmres_driver
3222 in order to make restarts with sol .ne. zero (fgmres with restarts)
3223 (seaice_jfnk.F, seaice_fgmres.F)
3224 - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
3225 a serious convergence problem when open boundaries are involved
3226 o pkg/ggl90: fix computation of control volumes for the case of
3227 ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
3228 up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
3229 o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
3230 o pkg/autodiff
3231 - Add inAdMode switch for SEAICEuseDYNAMICS:
3233 (extend logic in ADAUTODIFF_INADMODE_SET)
3234 o pkg/seaice
3235 - Step 1 of merging ice-thickness distribution (ITD) code from
3236 MITgcm_contrib/torge/itd/ (author: Torge Martin)
3237 The code implements concept laid out in Thorndike et al. (1975);
3238 code is enabled via CPP flag SEAICE_ITD
3239 nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
3240 code is not complete yet!!
3241 - SEAICE_SIZE.h now included in almost all seaice routines
3242 o verification (using seaice):
3243 - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
3244 global_ocean.cs32x15.seaice ; update results.
3245 - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
3246 - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
3247 offline_exf_seaice (previously compiling B-grid).
3248 o pkg/exf:
3249 - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
3250 to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
3251 forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
3252 o pkg/layers (adjust changes from Sept 19):
3253 - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
3254 this allows to remove "layers_maxNum" dimension from all layers arrays.
3255 o pkg/layers (adjust changes from Sept 19):
3256 - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
3257 - snap-shot extended to all type of layers (not just the 1rst type);
3258 - remove layers variables when corresponding CPP option is undef.
3259 o pkg/layers:
3260 - rename pkg/layers variable and add new output (layer exist & un-weighted
3261 velocity in layer)
3262 o pkg/seaice:
3263 - simplify (?) ocean-drag coefficent computations by using
3264 the same routine in all three solvers (saves some code lines)
3265 - remove global fields DRAGA and DRAGS from C-grid code and
3266 declare them locally in lsr.F (the only place where they are
3267 still used)
3268 - update AD output of lab_sea.evp (very sensitive anyway).
3269 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
3270 (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
3271 and SEAICEuseJFNK=.true. A few things to note:
3272 - involves a FGMRES, that is parallel but very inefficient,
3273 because of many scalar products (global sums) in the Gram-Schmidt
3274 orthogonalization method. Needs to be replaced. Original code
3275 from J.-F. Lemieux
3276 - preconditioner for FGMRES is a stripped down version of LSOR
3277 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
3278 preconditioner. For the preconditioner, the default is set to 10.
3279 - Jacobian times vector is computed with finite differences
3280 - marginally related to JFNK-solver: add a smooth regularization for
3281 zeta with tanh that will improve convergence (Lemieux and Tremblay,
3282 2009) for any implicit solver (not implemented for EVP because EVP
3283 does not need this regularization in the first place). Define
3285 o eesupp/src:
3286 - check in genmake2 that intrinsic S/R flush is available.
3287 - add S/R to flush IO unit (if intrinsic S/R flush is available)
3288 - flush standard & error msg unit before MPI termination
3289 - if debugMode, flush IO unit after printing msg
3290 o pkg/ctrl:
3291 - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
3292 to ctrl_set_unpack_xyz.
3294 checkpoint64 (2012/10/09)
3295 o pkg/shelfice
3296 - in mom_fluxform.F, mom_vecinv.F:
3297 CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
3298 Bug fix KappaRU -> KappaRV
3299 does not change verification/isomip but may change other setups
3300 (presumably constant KappaRU=KappaRV)
3301 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
3302 o pkg/obcs:
3303 - fixed some indexing bugs in obcs_seaice_sponge.F
3304 - added obcs relaxation subroutines for HSALT and HSNOW
3305 - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
3306 o pkg/seaice:
3307 - add "multicategory" parameterization for snow in analogy to ice,
3308 default is off for now.
3309 o pkg/obcs:
3310 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
3311 see verification/seaice_obcs/input.seaiceSponge for example application.
3312 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
3313 index setting by master-thread. This fix multi-threads Pb in previous modifs.
3314 o pkg/layers :
3315 - add diagnostics to pkg/layers
3316 - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
3317 (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
3318 o pkg/generic_advdiff/gad_implicit_r.F :
3319 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
3320 o pkg/seaice/seaice_growth.F:
3321 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
3322 o pkg/obcs:
3323 - change default setting of OBCS_UVICE_OLD from defined to undef;
3324 - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
3325 in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
3326 - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
3327 - change OB null index value (OB_indexNone) to -99 ; this fix the problem
3328 with Southern & Western OB at a tile edge (at least in a simple set-up).
3329 o pkg/obcs:
3330 - change settings of OB index in case OB coincides with tile edge (shared by
3331 2 tiles), so that common OB location is registered by both tiles (instead of
3332 only 1). However, for Southern and Western OB, index value = 0 is not
3333 recognized as valid OB index (=default null value) and needs to be fixed.
3334 - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
3335 - new parameter "OB_indexNone" for null index value (for now, still zero)
3336 to replace hard-coded null index value of zero.
3337 o pkg/exch2:
3338 - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
3339 always check buffer-size (but outside the loop); move checking for valid
3340 index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
3341 print each tile and point connection only if |W2_printMsg|>= 2 and 3.
3342 o pkg/ctrl (pack & unpack):
3343 - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
3344 (locally defined) for different variables (+ remove the variable-specific
3345 file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
3346 (to be extended to other local file names in ctrl.h).
3347 o pkg/flt:
3348 - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
3349 o pkg/mdsio:
3350 - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
3351 o tools/genmake2:
3352 - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
3353 (added by Alistair in version 1.51 for building without make depend);
3354 - remove Header files list (H_SRC_FILES) from the dependence of targets
3355 ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
3356 place in version 1.23): this save going through staf when unrelated header
3357 file has been modified.
3358 Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
3359 "make depend" step, still need to do "make links" before "make adtaf".
3360 o eesupp/src (+ few pkg src files) & genmake2:
3361 - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
3362 - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
3363 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
3364 upper/lower case ; account for space between "#" and undef/define)
3365 o pkg/flt (with exch2):
3366 - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
3367 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
3369 checkpoint63s (2012/09/05)
3370 o pkg/ecco:
3371 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
3372 - add more relevant #ifdef ALLOW_SMOOTH ones.
3373 - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
3374 o pkg/ctrl:
3375 - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
3377 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
3378 doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
3379 ctrlSmoothCorrel3D (new).
3380 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
3381 - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
3382 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
3383 controls when useAtmWind, and vice versa.
3384 - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
3385 - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
3386 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
3387 - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
3388 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
3389 - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
3390 replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
3391 o pkg/smooth:
3392 - remove un-necessary includes.
3393 - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
3394 Those CPP options were never defined, and not necessary.
3395 o model/src:
3396 - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
3397 - standard treatment of useSMOOTH.
3398 o pkg/autodiff:
3399 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
3400 useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
3401 o pkg/exch2:
3402 - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
3403 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
3404 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
3405 and tiles to process mapping.
3406 - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
3408 rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
3409 from w2_eeboot.F to w2_readparms.F.
3410 o eesupp/src:
3411 - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
3412 ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
3413 also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
3414 - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
3415 is defined (remove condition on usingMPI) to match cases where MPI_INIT
3416 has been called.
3417 - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
3418 - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
3419 (so that on 1 proc, get same myPid independently of usingMPI)
3420 - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
3421 useCubedSphereExchange with EXCH-1 (safer).
3422 - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
3423 o pkg/ggl90:
3424 - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
3425 used in ALLOW_GGL90_SMOOTH code.
3426 o pkg/flt:
3427 - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
3428 floats at the Southern end of the domain).
3429 o eesupp/inc:
3430 - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
3431 but not used (and not to be used) anywhere, just for documentation.
3432 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
3433 - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
3434 a) can damage previously written records in any other multi-record files.
3435 b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
3436 o tools/genmake2:
3437 - define variable MAKE within Makefile and use it in place of 'make';
3438 - update AD_CONFIG.h (if needed) before building any of the executable
3439 (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
3440 and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
3441 - always print usual warning comment 'this file is automatically generated'
3442 from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
3443 o pkg/cheapaml:
3444 - updated to correspond to the code used in accepted paper (Nico Wienders).
3445 o pkg/exf:
3446 added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
3447 ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
3448 and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
3449 o pkg/exf, autodiff, ctrl, ecco and seaice:
3450 remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
3451 o pkg/ctrl, ecco:
3452 allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
3453 Depending on useAtmWind, one is inactive, and the other is active (see
3454 exf_getffields.F/exf_getsurfacefluxes.F).
3455 o tools/genmake2:
3456 - improve error msg when failing in 2nd test of check_for_broken_Ff
3457 - fix option '-makefile' short-name (-mf according to genmake2 -help)
3458 - source local config file "genmake_local" just after processing the genmake2
3459 command arguments (previously done before processing arg).
3460 o pkg/grdchk:
3461 - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
3462 to this routine from cost_final has been dropped in g_cost_final)
3463 - improve printed information (more explicit msg, no longer using "print *,"
3464 fix fcpertminus printed value).
3465 o model/src:
3466 - move call to COST_INIT_VARIA out of packages_init_variables.F directly
3467 into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
3468 this prevents getting cost-funct reset in adinitialise_varia recomputations.
3469 o pkg/dic:
3470 - move initialisation of "freefe" array from from dic_biotic_forcing.F to
3471 fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
3472 o pkg/grdchk:
3473 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
3474 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
3475 o pkg/autodiff/ctrl/grdchk :
3476 - attempt to sort out what works and what does not,
3477 with regard to I/O, and to warn/stop accordingly.
3478 o pkg/grdchk:
3479 - attempt to fix grdchk in the case of useSingleCpuIO.
3480 - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
3481 statements were moved from grdchk_main.F and into
3482 grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
3483 - a global sum is applied to record numbers icvrec/layer
3484 out of grdchk_loc so that they be passed to I/O routines.
3485 o pkg/smooth:
3486 - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
3487 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
3488 o verification/testreport:
3489 - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
3490 - can also use compressed (gzip) reference output file;
3491 - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
3492 to be easier to collect by testreport.
3493 - update existing TLM output (half out-of-date by more than 3 yrs).
3494 - report NETCDF & LAPACK settings (from genmake2) in output dir.
3495 - report run-time in each individual summary (previously only for AD test);
3496 for TLM test, add also TAF version.
3497 - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
3499 checkpoint63r (2012/08/15)
3500 o tools/genmake2:
3501 - fix Makefile for target ftlall (+ update files to clean after make ftlall)
3502 o pkg/ecco/ecco_cost_final.F :
3503 - fix fc print statements (to stdout and costfunction0000) so
3504 that the printed value is always after the global sum.
3505 o pkg/seaice/seaice_dynsolver.F :
3506 - fix ice strength assymptote at SEAICE_area_max<1
3507 (no change for the standard case of SEAICE_area_max=1)
3508 o some cleaning:
3509 - pkg source files: ensure that all *.F files from each pkg included the
3510 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
3511 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
3512 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
3513 includes;
3514 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
3516 is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
3517 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
3518 - update option-file CPP_OPTIONS.h of all AD experiments:
3519 * no longer include PACKAGES_CONFIG.h ;
3520 * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
3521 * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
3522 including ECCO_CPPOPTIONS.h).
3523 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
3524 - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
3525 separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
3526 not necessary accurate).
3527 - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
3528 pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
3529 deliberately break compilation (a remainder that it needs to be customized)
3530 - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
3533 o tools/genamke2:
3534 - check for lapack.
3535 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
3536 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
3537 jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
3538 from both packages.
3539 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
3540 - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
3541 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
3542 of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
3543 o pkg/cost : add comments to explain special and/or untested setups.
3544 o pkg/exf:
3545 - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
3546 (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
3547 o verification/*/code_ad:
3548 mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
3549 - reccord when this file is included (define ECCO_CPPOPTIONS_H)
3550 - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
3551 allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
3552 o pkg/seaice :
3553 - added possibility to change ice strength/PRESS0 relationship to
3554 HEFF, according to the following run time parameters
3555 SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
3556 SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
3557 SEAICEpresH0 :: HEFF threshold for ice strength (m)
3558 o pkg/ggl90 :
3559 - added run time flag mxlSurfFlag to include the code that ensure
3560 mixing between first and second level (previously included as a comment)
3561 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
3562 - add test of newly added dumpAdByRec=T option where
3563 we write all records to one file per variable.
3564 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
3566 to check that this code is ok with taf and compiles in adjoint.
3567 o pkg/autodiff :
3568 - added run time param dumpAdByRec : ad dump format switch.
3569 If true then write all records to one file per variable.
3570 Else write one file per record (remains the default).
3571 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
3572 o pkg/seaice:
3573 - Added SEAICEuseTILT run time switch : if set to
3574 false then omit the tilt term in seaice dynamics.
3575 - Fix free drift calculation.
3576 o pkg/shelfice:
3577 When initializing SHELFICEDragQuadratic, set default to be
3578 consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
3579 but retain option to set it independently
3580 (inconsistenty spotted by Veronique Dansereau)
3581 o eesupp/inc:
3582 - in EEPARAMS.h, add real-type constant for some frequently used simple number
3583 (0,1,2,1/2), with name explicitly referring to RS/RL type.
3584 o model/src:
3585 - move balancing of relaxation terms to new S/R balance_relax.F.
3586 o pkg/autodiff:
3587 re-write active I/O high-level (control) S/R:
3589 - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
3590 - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
3591 MDS_READ/WRITE_FIELD); change loops to multi-threads.
3592 - update and merge active_file_control_slice.flow into active_file_control.flow
3593 - update the calls in lower level S/R (active_file.F, active_file_g.F and
3594 active_file_ad.F) keeping the argument list and function unchanged.
3595 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
3596 =.TRUE.") and remove high-level (control) _loc version (not called anymore).
3597 - new low-level active I/O routines, one for each type (RL/RS), for active var
3598 of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
3599 fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
3600 right type.
3601 o autodiff and RS=real*4:
3602 - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
3603 ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
3604 - change argument type of 3-D mask argument to _RS to match type in the call
3605 (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
3606 o pkg/thsice:
3607 - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
3608 - option to correct ocean fresh-water flux for imbalance of Atmos+Land
3609 fresh-water flux: uniform correction or proportional to local precip.
3610 o pkg/ctrl:
3611 - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
3612 - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
3614 - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
3616 checkpoint63q (2012/07/30)
3617 o pkg/autodiff:
3618 note about monitor and snap-shot of ad-variables:
3619 a) need to apply ADEXCH before monitor or output of ad-vars to include
3620 overlap contributions (was done for adjDump but missing for monitor).
3621 b) since ADEXCH implies adding overlap values to interior array, machine
3622 truncation error is expected when adding an ADEXCH call in the middle of
3623 the time-stepping (although mathematically identical).
3624 modifs:
3625 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
3626 declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
3627 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
3628 apply ADEXCH before monitor or snap-shot of ad-variables:
3629 =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
3630 - implement new method (copy+adexch) for snap-shot and monitor of main model
3631 ad-vars (initially not used by default -> output unchanged).
3632 - change default (set to 2) to use new method and update few output_adm.txt
3633 with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
3634 and both tutorial_tracer_adjsens tests).
3635 - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
3636 and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
3637 o pkg/ctrl:
3638 enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
3639 generic control variables via
3641 Only required customization should be S/R ctrl_map_ini_genarr.F
3642 (routine in repository contains example)
3643 o pkg/exf:
3644 - fix and refine checking of surface-relaxation setting when using EXF
3645 o verification (adjoint exp):
3646 - reduce length of simulation by half for experiment global_ocean.cs32x15
3647 (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
3648 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
3649 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
3650 of KE that can occur with aggressive optimization
3651 + put quadratic bottom drag calculation in separated loops (only done if
3652 using bottomDragQuadratic)
3653 o model/src: CG2D_NSA
3654 - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
3655 and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
3656 - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
3657 change cg2d residual target to be expressed in Wunits (=> do not normalise
3658 RHS ; this fix global_max Pb with TAF); update output.
3659 o verification/tutorial_tracer_adjsens:
3660 improve parameter consistency (and get rid of warnings):
3661 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
3662 - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
3663 - use staggerTimeStep (for stability) in som81; use default rotation period.
3664 o pkg/exch2:
3665 - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
3666 reset to 0 = 1 long line in X)
3667 o pkg/mdsio:
3668 - fix reading of dimensions from meta file for large-size domain
3669 o model/src:
3670 - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
3671 - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
3672 Cubed-Sphere Exch with CS-corners inside the domain;
3673 make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
3674 globalArea and to set hasWetCSCorners.
3675 - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
3676 metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
3677 - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
3678 useCDscheme and useCubedSphereExchange).
3679 o pkg/seaice/seaice_growth.F :
3680 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
3681 for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
3682 when the previous code was not correct.
3683 - in all cases diagnoze the boundary condition mismatch to SIaaflux
3684 - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
3685 that term to QNET (essentially to set the melt/freeze water to 0degC).
3686 when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
3687 o verification/global_ocean.cs32x15/input.seaice :
3688 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
3689 - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
3690 - update results (output.seaice.txt) accordingly.
3691 o verification/lab_sea/input/data.seaice :
3692 - remove SEAICEheatConsFix, which is now be tested
3693 in global_ocean.cs32x15. The presently coded fix
3694 is only consistent with real fresh water + nlfs.
3695 - update results (output.txt) accordingly.
3696 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
3697 o AD_CONFIG.h file:
3698 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
3699 - remove #include "AD_CONFIG.h" from all included OPTIONS files and
3700 add it explicitly in each fortran src file where it is needed.
3701 motivation: header file AD_CONFIG.h is generated/modified after "make depend"
3702 thus introducing potentially wrong dependency; therefore, better to include
3703 it only where it's really needed, and after any other included OPTIONS file
3704 (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
3707 checkpoint63p (2012/07/06)
3708 o pkg/autodiff:
3710 - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
3711 which are now read from new parameter file "data.autodiff" (inAdExact
3712 previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
3713 - add file "data.autodiff" in all verification/*/input_ad/ directories.
3714 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
3715 mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
3716 o verification/tutorial_tracer_adjsens/
3717 - add extra sub-verification which uses "SOM" advection scheme
3718 (2nd Order-Moment Advection Scheme, Prather Limiter) with
3720 and in data:
3721 multiDimAdvection=.TRUE.,
3722 tempAdvScheme=81,
3723 saltAdvScheme=81,
3724 o model/src:
3725 - introduce ALLOW_BALANCE_RELAX which allow the removal
3726 of the global mean of relaxation terms by setting
3727 balanceThetaClimRelax and balanceSaltClimRelax
3728 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
3729 This case is now treated appropriately in seaice_growth.F
3730 o pkg/seaice:
3731 - do balanceEmPmR and balanceQnet based on the net fluxes
3732 (SItflux) that enter the ocean+ice system rather than QNET
3733 and EMPMR. Works best in real fresh water.
3734 - SIatmFW, SIatmQnet, and SItflux computations had to be moved
3735 out of the diagnotics bloc, and stored in global arrays.
3737 checkpoint63o (2012/06/29)
3738 o vertical mixing schemes:
3739 - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
3740 - replace computation of density (in Function STATE1, opps_calc.F) by a call
3742 - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
3743 and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
3744 affects output (vermix.ggl90) at truncation level.
3745 o testreport:
3746 - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
3747 (nSx,nSy) for the number of threads (from eedata.mth)
3748 o model/src:
3749 - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
3750 related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
3751 o verification/tutorial_tracer_adjsens/
3752 - compile with ALLOW_CG2D_NSA
3753 - run with nonlinFreeSurf=3
3754 - update reference output_adm.txt
3755 o tools/genmake2:
3756 - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
3757 refine usePROFILES switching off (only when NetCDF is not available).
3758 o verification (atmospheric set-up):
3759 - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
3760 o pkg/profiles : refine profiles and files handling.
3761 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
3762 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
3763 - changes to use model/src/the_main_loop.F rather than the ecco version
3764 in ecco type adjoint runs.
3765 o model/src:
3766 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
3767 - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
3768 - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
3769 o model/src:
3770 - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
3771 update output of test experiment bottom_ctrl_5x5.
3772 o pkg/generic_advdiff:
3773 - implement vertical bi-harmonic diffusion (for now, only for T & S and
3774 only explicitly).
3775 o verification/bottom_ctrl_5x5/
3776 update reference output (results changed quite some time ago,
3777 not sure when; but new reference results look ok in terms of grdchk)
3778 o verification/1D_ocean_ice_column/
3779 For verification purposes, the exact adjoint rather than an approx.
3780 should be used (e.g., to comare against F.D. or TLM).
3781 removed autodiff_inadmode*_ad.F routines in code_ad/
3782 Update results/ accordingly.
3783 o pkg/cal:
3784 - change cal_getdate.F so that output date is function of input time only
3785 (less ambiguous, not mixed up with input iteration number).
3786 - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
3787 o pkg/diagnostics:
3788 - implement calendarDumps also for stats-diags
3789 - implement calendarDumps also for snap-shot output (negative freq)
3790 - for now, ignores calendarDumps if non-zero phase-lag.
3792 checkpoint63n (2012/06/04)
3793 o model/src:
3794 - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
3795 between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
3796 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
3797 similar to calc_r_star.F); update results of experiment internal_wave and
3798 tutorial_global_oce_in_p (affected @ truncation level).
3799 o pkg/shelfice:
3800 - add parameterisation of advective-diffusive flux into the ice shelf
3801 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
3802 - simply eps3/3a computation
3803 o eesupp:
3804 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
3805 between tiles, just fill-in edges assuming locally periodic subdomain) and
3806 add corresponding exchange subroutines (EXCH0);
3807 - new CG-solver version (_EX0) for disconnected-tiles special case.
3808 o model/src (CG-solvers):
3809 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
3810 (similar final residual output and max-Iter number as with standard version);
3811 - allows to store and use lowest-residual solution (standard & _SR versions);
3812 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
3813 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
3814 o eesup/src:
3815 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
3816 ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
3817 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
3819 checkpoint63m (2012/04/27)
3820 o pkg/shelfice:
3821 - account for partical cells in surface level below ice-shelf for hydrostatic
3822 pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
3823 o ad test experiments:
3824 - update and rename to "ad_optfile.local" local AD-optfile specific to a
3825 particular adjoint verification experiment (in verification/*/code_ad/)
3826 o pkg/seaice & pkg/exf:
3827 - Part two of ECCO-CLIVAR code merges.
3828 Completes merge of seaice area relax. code.
3829 Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
3830 to be set in EXF_OPTIONS.h since this pkg controls its I/O
3831 (and avoids second CPP option in SEAICE_OPTIONS.h)
3832 - change default value of costIceStart & costIceEnd to a valid date.
3833 - add snowPrecip to HSNOW in seaice_growth
3834 o pkg/ptracers:
3835 - move ptracers summary and setup check into separated S/R ; add a check for
3836 valid PTRACERS_Iter0 value (error+stop or just warning).
3837 o pkg/cal (+ pkg/ecco):
3838 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
3839 as input; and for AD, unless both are not differentiable (e.g., k index)).
3840 o model/src:
3841 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
3842 is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
3843 temporary set to usingZCoords value (to be changed to F when using shelfice).
3844 - hydrostatic pressure: implement partial cell near the surface also for
3845 Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
3846 usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
3847 o pkg/ctrl/ctrl_init.F:
3848 - add a formal parameter to s/r ctrl_init_rec to print
3849 xx_$(ctrl_valiable)_file for easier debugging
3850 - move call of cal_* routines into the if-block where they are really
3851 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
3852 to specify a startdate
3853 o pkg/seaice:
3854 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
3855 global_ocean.cs32x15/code versions).
3856 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
3857 verification experiment global_ocean.cs32x15.seaice and update results.
3858 o pkg/exf:
3859 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
3860 (according to useExfYearlyFields).
3861 o pkg/cal:
3862 - move calendar setting & summary (previously in cal_readparams.F) into new
3863 S/R CAL_INIT_FIXED to be called later in the initialisation process, once
3864 length of the simulation is set (after SET_PARMS call); This is an attempt
3865 to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
3866 - For safety: keep a record of pkg/cal parameter settings status
3867 to allow to STOP if one pkg/cal S/R is called too early.
3868 - add a stop in all basic pkg/cal subroutines if called before setting is done.
3869 - modify cal_getdate.F: stop when nothing was returned;
3870 if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
3871 this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
3873 checkpoint63l (2012/04/04)
3874 o pkg/bbl:
3875 - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
3876 update global_with_exf output.yearly.txt file.
3877 o pkg/cal:
3878 - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
3879 - remove 2 unsused and very short (1 line only) functions ;
3880 - remove unsused subroutines from AD-Diff list.
3881 o model/src:
3882 - start to implement clean wait to stop in initialization S/R (config_check.F,
3883 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
3884 o folowing PRINT_MESSAGE changes:
3885 - remove reminder multiple print to the same file (STDOUT) when multi-threads.
3886 o pkg/bbl:
3887 - modification so it can work with z*
3888 - replace deltaT with dTtracerLev(k) for asynchronous time stepping
3889 - global_with_exf/input.yearly verification; changes output.yearly.txt
3890 o eesupp/src:
3891 - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
3892 writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
3893 - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
3894 # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
3895 - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
3896 - when using MPI, always set usingMPI=T ; set default accordingly and stop
3897 if not consistent.
3898 - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
3899 argument is zero (in case called within single-thread section).
3900 o pkg/fizhi:
3901 clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
3902 in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
3903 o pkg/exch2:
3904 - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
3905 activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
3906 - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
3907 but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
3908 with bad ones coming from a not-yet-updated halo.
3909 This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
3910 o pkg/frazil:
3911 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
3912 http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
3913 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
3914 o verification/lab_sea
3917 * nTimeSteps 3 -> 4
3918 * changed reference output accordingly
3919 o pkg/ctrl:
3920 * fix ctrl_get_gen for xx_sst, xx_sss
3921 o pkg/fizhi:
3922 - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
3923 update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
3924 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
3925 fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
3926 clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
3927 o pkg/gmredi:
3928 - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
3929 o pkg/fizhi:
3930 - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
3931 (old)aces open64 tuv test.
3932 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
3933 o pkg/mom_vecinv:
3934 - fix 1 loop range in mom_vecinv.F to be like all the other loops which
3935 set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
3936 with non-lin free-surf).
3937 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
3938 in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
3939 some compilers (gfortran 4.6.0 on MacOS)
3940 o momentum:
3941 - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
3942 & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
3943 fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
3945 checkpoint63k (2012/03/17)
3946 o model/src:
3947 - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
3948 flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
3949 - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
3950 (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
3951 o model/src: solve_*diagonal.F
3952 - replace division with multiplication by inverse (similar to original version)
3953 update output of AD exp. global_ocean.90x40x15.
3954 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
3955 to enable the use of the vectorized & differentiable solve_tridiagonal.F
3956 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
3957 vertical advection (to get solve_tridiagonal tested in AD mode).
3958 o pkg/seaice: ECCO-CLIVAR merge:
3959 1. seaice AREA relaxation
3961 * runtime flag: SEAICE_tauAreaObsRelax
3962 2. modified global mean cost imbalance code: CPP option
3964 o another iteration on solve_*diagonal.F
3965 Make choices independent of AUTODIFF
3966 Default will be the adjoinable vectorized version.
3967 Alternative choices are:
3968 * non-adjoinable original version with low memory footprint:
3970 * still adjoinable but does not vectorize (k as inner-most loop):
3972 o testreport
3973 - add option to use a home made wrapper around "make"
3974 - remove MITGCM_IEEE env. variable (no longer active)
3975 o pkg/shelfice
3976 - improve computation of friction velocity for velocity dependent
3977 exchange coefficients: include velocities into SHELFICEBoundaryLayer
3978 block to average velocities vertically
3979 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
3980 o Modify diagonal solvers, now three versions (upon request):
3982 1. default version (dating back a while ago)
3983 #else /* def SOLVE_DIAGONAL_AUTODIFF */
3985 2. adjoinable version with k-innermost loop (G. Forget)
3986 # else
3987 3. adjoinable vectorized version of 2.
3988 # endif
3990 All flags are currently set within routines, but could/should be moved to CPP-options.
3991 Array bounds for 1. are as before, for 2.,3. cover the entire domain
3992 (could be changed for 1. too).
3993 o verification/lab_sea (fwd):
3994 - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
3995 use 7 categories (except hb87), new solve4temp params (except salt_plume),
3996 constant salinity (=4) or variable salinity (salt_plume) done through
3997 SItracer.
3998 o pkg/seaice:
3999 - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
4000 - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
4001 SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
4002 from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
4003 SEAICE_freeze got retired) but already better than previously with
4004 SEAICE_freeze=123456.7 deg.C;
4005 - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
4006 (safer multi-threaded setting); always set SEAICEuseEVP;
4007 - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
4008 SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
4009 stop if multiple specifications for the same coeff; make sure default
4010 SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
4011 o pkg/obcs:
4012 - allow to switch to upwind 1rst order advection scheme for the advective
4013 flux computation at the open-boundary; disabled for adjoint built.
4014 o pkg/ptracers:
4016 - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
4017 - add parameter to decide when to start a tracer; use internal flag to
4018 know which tracer to step-forward; switch this internal flag at the top
4019 of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
4020 for adjoint built.
4021 o pkg/seaice:
4022 - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
4023 - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
4024 - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
4025 o pkg/ecco:
4026 - fix writing of output file DiagnosCost_ClimSalt/Theta
4027 and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
4028 o pkg/seaice:
4029 - add missing initialisation of COR_ICE array in dynsolver.F
4030 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
4031 compiled either way, and is tested in all exps (multidim was only tested
4032 in lab_sea ad before).
4033 - cosmetic change to prepare for future addition of ITD. no change to results.
4034 no defaults change.
4035 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
4036 - by lack of adequate verification experiments, I further used custom versions
4037 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
4038 should be correct.
4039 - avoid recomputations in ad.
4040 o array initialisation in adjoint mode:
4041 1) pkg/mom_common/mom_calc_ke.F:
4042 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
4043 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
4044 part this initialisation is gone, resulting in Floating Point Exception
4045 (caught by open64 compiler with debug option).
4046 2) model/src/convective_weights.F
4047 set output convectCount over the full array range (instead of doing
4048 an update): this fix a similar issue when called within recomputation (adjoint)
4049 which could by-pass the initialisation (normally done in the caller S/R).
4050 o pkg/seaice:
4051 - final version of turbulent flux params, as agreed at MIT ice meet:
4052 SEAICE_mcPheePiston (default is ~ 0.000875)
4053 SEAICE_mcPheeTaper (default is 0.)
4054 SEAICE_frazilFrac (defualt is 1.)
4055 SEAICE_mcPheeStepFunc (default is false)
4056 - changes results at trunction error level
4057 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
4058 o added pkg/frazil:
4059 - see frazil_description.tex for details
4060 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
4061 o pkg/shelfice/shelfice_thermodynamics.F
4062 - fix exponents for velocity dependent exchange coefficients: change
4063 from 2/3(=0) to 0.66666666666666667
4064 - move computation of velocity dependent exchange coefficients into
4065 separate loop, so that it applies to both thermodynamics
4066 - move some divisions by constants out of loops
4068 checkpoint63j (2012/02/16)
4069 o pkg/seaice:
4070 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
4071 - SItracer: added run time params, and allow coupling to ocn salinity.
4072 o pkg/seaice: remove (almost) all divisions by constants within loops
4073 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
4074 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
4075 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
4076 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
4077 o pkg/seaice :
4078 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
4079 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
4080 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
4081 - add permanent SItflux diag that corresponds to TFLUX but includes
4082 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
4083 - allow activation/testing of a fix for suspected missing term in
4084 ocn-ice heat budget (to be confirmed). To test this, you want to
4085 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
4086 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
4087 - no change in results, fwd or ad.
4088 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
4089 - switch to variable freezing point.
4090 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
4091 - bug fix : the sublimation term that was missing is now activated.
4092 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
4093 - bug fix : flooding sign term for SIsal0.NE.0.
4094 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
4095 o pkg/seaice:
4096 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
4097 is now the default, and the old default constant freezing point is recovered
4098 with SEAICE_tempFrz0 = -1.96,
4099 SEAICE_dTempFrz_dS = 0.,
4100 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
4101 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
4102 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
4103 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
4104 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
4105 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
4106 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
4107 seaice_growth r149 for legacy branch (no results change).
4108 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
4109 from I. Fenty).
4110 - results did not change except for global_ocean.cs32x15, mostly due to the
4111 switch to variable freezing point (see above item for detail).
4112 o pkg/thsice:
4113 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
4114 seawater freezing in thsice_calc_thickn (not used).
4115 o pkg/seaice: turbulent flux term specification via run time params.
4116 - replace CPP switches with run time switches to facilitate testing
4119 - added runtime parameter : SEAICEturbFluxFormula
4120 - move Mcphee constants to SEAICE_PARAMS.h
4121 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
4122 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
4123 remove seaice_summary call (moved to seaice_init_fixed)
4124 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
4125 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
4126 - seaice_summary.F : add missing report of read turbulent flux term set up
4127 and SITRACER.
4128 - seaice_check.F : check range; inform and stop if retired CPPs are used
4129 (incl. SEAICE_AGE).
4130 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
4131 CPP switch, same computation as before for the different options.
4132 - change results at the truncation level.
4133 o pkg/seaice:
4134 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
4135 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
4136 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
4137 - update verification/*/input*/data.seaice:
4138 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
4139 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
4140 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
4141 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
4142 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
4143 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
4144 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
4145 difference in results only due to machine truncation.
4146 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
4147 MaykutPolySatVap; keep MIN_LWDOWN.
4148 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
4149 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
4150 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
4151 o pkg/salt_plume:
4152 - isolate saltPlumeFlux array exch into a specific S/R called from
4153 do_oceanic_phys.F
4154 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
4155 o verification:
4156 - move untested set-up to MITgcm_contrib/verification_other.
4157 o pkg/seaice:
4158 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
4159 o pkg/seaice:
4160 - seaice_solve4temp.F (keeping results unchanged):
4161 * add 2 future run-time params to select which saturation vapor pressure
4162 formula is used and how post-iteration fluxes are set.
4163 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
4164 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
4165 the linearized expression to stay consistent with tsurf finding.
4166 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
4167 can be < 0.
4168 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
4169 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
4170 conductive heat flux F_c , and add it explicitly when updating tsurf as
4171 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
4172 so that now F_ia has a consistent meaning through the entire routine.
4173 This causes differences at truncation level: update output of fwd exp.
4174 global_ocean.cs32x15.seaice.
4175 o pkg/seaice:
4176 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
4177 of arrays, sign/direction of fluxes; no effect on results.
4178 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
4179 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
4180 note: this should have been done before changing celsius2K default.
4181 - to keep results unchanged, add back old value of celsius2K in verification
4182 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
4183 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
4184 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
4185 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
4186 freezing temp is consistent with value in seaice_growth.F ; this causes
4187 differences at machine truncation level: update lab_sea AD output (3/4).
4188 o pkg/seaice:
4189 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
4190 and climsst/sss even when using seaice (to prevent calculation that might
4191 use SST on land); does not affect any verification exp.
4192 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
4193 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
4194 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
4195 over land (non-legacy code)
4196 o vectorize salt_plume package:
4197 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
4198 - this code computes plumebk everywhere (also over land), thus requires
4199 code to avoid divisions by zero and catch the case of kLev=Nr.
4200 - efficiency of salt_plume_frac is still sub-optimal
4201 o tools (genmake2):
4202 - fix makefile NAME specification (option: -makefile NAME) by adding
4203 "-f $MAKEFILE" in few places where it was missing including makedepend
4204 command (contribution from Paul).
4206 checkpoint63i (2012/01/24)
4207 o model/src:
4208 - add factorized versions of some EOS code to find_rho.F,
4209 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
4210 o model/src:
4211 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
4212 - change default celsius2K from 273.16 to 273.15
4213 - to keep results unchanged, add back old value of celsius2K in verification
4214 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
4215 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
4216 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
4217 to make TAF generate vectorizable code
4218 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
4219 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
4220 have flags that do this more efficiently.
4221 o pkg/diagnostics/diagstats_calc.F
4222 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
4223 o pkg/obcs (with exch2):
4224 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
4225 and remove code (in obcs_readparms.F) which was based on EXCH of indices
4226 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
4227 o pkg/exf and seaice exp:
4228 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
4229 so that switching off area & heff advection flags does not affect results.
4230 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
4231 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
4232 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
4233 results of verification experiments: 1D_ocean_ice_column(fwd),
4234 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
4235 and offline_exf_seaice (all 4).
4236 o pkg/seaice:
4237 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
4238 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
4239 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
4240 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
4241 not multi-dim advection;
4242 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
4244 o optim: make Makefile more robust (?)
4245 o pkg/obcs:
4246 * fix treatment of obcs_read_pickup for TAF
4247 o pkg/shelfice:
4248 * add missing initialisation of num_shifwflx
4249 * new adjoint verification exp. for isomip
4250 * change Prandtl and Schmidt numbers from generic formulations
4251 (in terms of model diffus. and visc.) to separate runtime
4252 parameters, with Holland and Jenkins (1999) default values.
4253 o pkg/exf (interpolation):
4254 - extended input field (2 rows) near the N & S poles:
4255 * fill in with the symetric value (when even Nb of data in longitude)
4256 * add average value at the poles only for scalar quantities ; for vector
4257 component interpolation, skip the averaging and keep duplicated values,
4258 unless the 2 components have same location (uvInterp=T) in which case
4259 interpolate the 2 components together using S/R EXF_INTERP_UV.
4260 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
4261 together: this allows to account properly for local orientation when
4262 averaging at N & S pole.
4263 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
4264 exf-interpolation near N & S poles. Undef by default.
4265 - add debug check/print on 1rst iter if debugLevel >=2.
4266 o pkg/exf:
4267 - change masking flags definition (no longer "parameter"), put them in
4268 common block and set them in S/R EXF_INIT_FIXED.
4269 - change recognized masking flag from s,u,v to c,w,s since the mask
4270 to use (maskC,W,S) depends on position on model grid and has little to
4271 do with scalar/vector difference; fix masking if using P-coordinates.
4272 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
4273 and update results of exp. global_with_exf (x2).
4274 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
4275 o pkg/obcs
4276 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
4277 o pkg/exf (interpolation):
4278 - assume periodicity in X only if input field cover full longitude range.
4279 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
4280 and should vectorise).
4281 - fix input lat of the 2 added row (in case we provide N.pole data).
4283 checkpoint63h (2011/12/30)
4284 o pkg/seaice:
4285 - change declaration of UVM from _RL to _RS in order to get B-grid
4286 uIce,vIce monitor when _RS = real*4
4287 o pkg/offline:
4288 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
4289 - compute vertical velocity if not read from file (switch on exactConserv
4290 & staggerTimeStep);
4291 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
4292 o verification:
4293 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
4294 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
4295 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
4296 - update output of exp. global_ocean.cs32x15.viscA4 after changing
4297 grid-file angles (used here for coriolis-3d);
4298 - remove (or gzip) few files not needed to run fizhi-cs experiments.
4299 o pkg/exf (vector interpolation):
4300 - rotate vector component toward local grid-axis orientation using grid-angles
4301 (stored in GRID.h) instead of locally computed rotation angle; keep old code
4302 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
4303 o pkg/seaice:
4304 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
4305 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
4306 o pkg/PKG_OPTIONS.h files:
4307 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
4308 outside of the #ifdef ALLOW_THISPKG / #endif block.
4309 - update verification/*/code/PKG_OPTIONS.h files.
4310 o add a verification experiment (offline_exf_seaice/input.seaice) that test
4311 the B-grid LSOR solver
4312 o pkg/seaice: sort out emissivity and long wave radiation step 2:
4313 - add emissivity for snow and ice as new run-time parameters
4314 (unfortunately) that default to the corresponding exf values; this
4315 changes results in most verification experiments so that for backward
4316 compatibility these parameter have to be set explicitly to inconsistent
4317 values (ugly);
4318 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
4319 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
4320 until we agree how to handle this bug properly
4321 o pkg/exf (interpolation):
4322 - add a set of run-time param ({inputfield}_interpMethod), one for
4323 each interpolated input field, to select the interpolation method
4324 with a value of zero switching off the interpolation;
4325 - print interpolation parameters to standard output;
4326 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
4327 (to use instead runoff_interpMethod=0 in data.exf).
4328 - simplify default setting of interpolation parameters (for all fields,
4329 set position to match model grid cell-center position, leading to trivial
4330 interpolation in case of regular Lat-Lon grid) and fix for the case of
4331 non-uniform delY.
4332 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
4333 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
4334 this factor is absolutely required, because the lw exitance (= out-going
4335 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
4336 where the reflectivity rho = 1-emissivity for conservation reasons. Once
4337 this is established, we can remove the CPP-Flag (if we want to).
4338 o pkg/seaice:
4339 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
4340 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
4341 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
4342 what the name implies (and not emissivity*BoltzmannConstant), this means
4343 the old default value of 5.5e-8 now means
4344 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
4345 S/R exf_readparms
4346 - FV-discretization of the B-grid LSOR solver, turn on with
4347 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
4348 of the calling routine dynsolver, so that B and C-grid code look a
4349 little more alike.
4350 - fix index bugs in ostres.F (B-grid code)
4351 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
4352 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
4353 default for SEAICE_emissivity, if useEXF; requires setting a wrong
4354 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
4355 backward compatiblity
4356 o model/src: use sigmaR in calc_ivdc
4358 checkpoint63g (2011/12/16)
4359 o pkg/seaice/seaice_growth.F:
4360 fix heat conservation of the coupled ocean-seaice system.
4361 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
4362 solid vs liquid water treatment is resolved via QNET.
4363 o pkg/seaice/seaice_growth.F:
4364 add missing term for sublimation in saltFlux, which was breaking conservation.
4365 o pkg/seaice/seaice_model.F:
4366 Remove this patholigical case treatment in evolution branch,
4367 where it is un-necessary and breaks conservation.
4368 Update global_ocean.cs32x15/results accordingly for
4369 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
4370 o model/src:
4371 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
4372 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
4373 o pkg/obcs:
4374 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
4375 tendency for temperature and salinity that is then applied to update
4376 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
4377 horizontal advection and diffusion contributions on the boundary (in
4378 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
4379 removing the mask in S/R timestep_tracer. The advantage of this approach is
4380 that the updated tracer values include contributions from the surface
4381 forcing and vertical diffusion.
4382 This modification changes exp4.stevens because of vertical diffusion.
4383 o model/src:
4384 change non-curvilinear grid setting to also work with exch2 + blank tiles:
4385 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
4386 face dimensions.
4387 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
4388 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
4390 change test-experiment global_ocean.90x40x15:
4391 - split the domain in many more tiles (9x4 tiles of 10x10 each);
4392 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
4393 - update results of both test (std & dwnslp).
4394 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
4395 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
4396 o model/src:
4397 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
4398 and fix initialisation when using sigma-coords.
4399 o model/src:
4400 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
4401 to their current value at the beginning of forward_step.F": add a new run-time
4402 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
4403 - set doResetHFactors=T in the following test exp:
4404 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
4405 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
4406 and tutorial_global_oce_in_p (nonLinFS in p)
4407 o pkg/ecco
4408 - added IES cost term
4409 o verification/advect_xz
4410 - scale down the depth by 1/100 (from 200 km to just 2.km)
4411 - add secondary test using divergent flow, r-star and implicit vertical advection.
4412 - add note (check_conserve_TS.txt) and matlab script to check global
4413 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
4414 o pkg/rbcs:
4415 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
4416 o pkg/obcs (Stevens BCs):
4417 - fix various problems in the phase speed computations of the Stevens
4418 boundary conditions:
4419 - sign error for western and southern boundaries,
4420 - time tendencies were underestimated by factor of dTracerLev and some just
4421 zero (for multidim advection schemes) -> now estimate time tendencies
4422 from difference between previous (n) time level and the one before (n-1);
4423 this requires storing a field per tracer per boundary, also in the pickup
4424 files.
4425 - replace deltaTmom in cflMer/Zon computation with dTracerLev
4426 - set default phase velocity to cflMer/Zon
4427 - update verification experiment exp4.stevens
4428 o pkg/generic_advdiff (implicit_r):
4429 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
4430 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
4431 - fix implicit vertical diffusion or advection with NonLin FreeSurf
4432 (was using current recip_hFacC instead of future recip_hFacC): set future
4433 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
4434 solver S/R ;
4435 - fill diagnostics of vertical advective fluxes (computed from tendency)
4436 when using implicit vert. advection;
4437 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
4438 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
4439 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
4440 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
4441 o pkg/diagnostics:
4442 - add diags for T & S tendency which goes through Adams-Bashforth.
4444 checkpoint63f (2011/11/30)
4445 o pkg/obcs/obcs_calc_stevens.F:
4446 - join some loops to reduce number of if-statements
4447 - fix a bug in code for northern and southern boundaries.
4448 o pkg/seaice/seaice_init_varia.F
4449 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
4450 caused zero ice-velocities for the B-grid code
4451 o pkg/seaice/seaice_init_fixed.F
4452 - fix a bug in the initialisation of the second metric terms
4453 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
4454 - this affects all seaice configurations with useCurviLinearGrid = .true.
4455 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
4456 = .true. (default)
4457 - the only verification experiment affected is global_ocean.cs32x15:
4458 icedyn, seaice, and seaice_dynmix (AD)
4459 o pkg/thsice/thsice_diagnostics_state.F
4460 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
4461 not contain garbage that can lead to surprises in diagstats_calc.F
4462 o model/src:
4463 - move bi,bj loops inside INTEGR_CONTINUITY ;
4464 - call INTEGR_CONTINUITY directly from forward_step.F
4465 (previously called from momentum_correction_step.F)
4466 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
4467 forward_step.F and pkg/ecco/the_main_loop.F
4468 o model/src/do_oceanic_phys.F:
4469 - reset addMass to zero only if useICEFRONT ;
4470 - separated k-loop for rhoInSitu calculation ;
4471 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
4472 and at constant T,S (= WdRHOdP);
4473 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
4474 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
4475 transport of locally-referenced potential density);
4476 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
4477 o gluemnc:
4478 - replace ncrcat with ncks when adding variables to *.glob.nc
4479 - change the way variables without record dimensions are handled so that
4480 files that have variables with and without record variables can be glued:
4481 add a record dimension with a new unique name to be able to differentiate
4482 between variable with and without a-prior record dimensions. Remove
4483 this record dimension before adding the variable to the *.glob.nc file.
4484 This procedure automatically works also for grid.*.nc files that do not
4485 have any record dimension.
4486 o verification/cpl_aim+ocn:
4487 - generate new reference output on baudelaire (gfortran, mpich2) (previously
4488 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
4489 o pkg/obcs/obcs_calc_stevens.F:
4490 - add code for northern and southern boundaries.
4491 - reorder some loops to save some operations and so that drFBar can be scalar
4492 o model/src:
4493 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine