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Revision 1.2192 - (show annotations) (download)
Fri Oct 23 12:31:57 2015 UTC (8 years, 4 months ago) by jmc
Branch: MAIN
CVS Tags: checkpoint65p
Changes since 1.2191: +5 -4 lines
new tag "checkpoint65p"

1 $Header: /u/gcmpack/MITgcm/doc/tag-index,v 1.2191 2015/10/22 15:51:59 mlosch Exp $
2 $Name: $
3
4 Notes on tags used in MITgcmUV
5 ==============================
6
7 checkpoint65p (2015/10/23)
8 o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
9 there is no adjoint test for EVP, we don't know what it does to the adjoint
10 solution, but at least there are no more recomputation warnings left
11 o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
12 a chance of giving the same results as a fully converged VP (JFNK) solver
13 o tools/adjoint_options/adjoint_diva:
14 - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
15 o pkg/streamice:
16 - spotted bug in streamice_driving_stress using dyG where should have been dxG
17 o pkg/exf:
18 - remove STOP statement that prevented to use wind or (wind-)stress
19 interpolation for constant-in-time forcing fields (wind/stress period = 0).
20 o pkg/seaice:
21 - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
22 5 additionals 2D fields and 6 new store directives
23 - change logic in seaice_readparms.F: EVP code can now be turned on in
24 various ways, setting SEAICE_deltaTev is no longer required,
25 alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
26 or SEAICEaEVPcoeff
27 o pkg/shelfice/shelfice_thermodynamics.F
28 - redefining uLoc/vLoc to u/v, instead of 2u/v
29 o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
30 - this is an intermediate state of a truely converging EVP that has
31 the potential of outperforming implicit VP methods, I do not recommend
32 using it yet.
33 - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
34 and all parameters are hardwired
35 - for convergence it still requires very smooth regularisations, that means,
36 if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
37 different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
38 specific averaging appears to be required, still subject to tuning
39 - still needs cleaning and I need to turn parameter into runtime parameters
40 - add code to compute and print residuals of iteration, compile with
41 defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
42 o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
43 that entered with r1.54 on Sep04, 2015, -> update results
44
45 checkpoint65o (2015/09/14)
46 o pkg/mom_vecinv & mom_common:
47 - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
48 called from there.
49 - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
50 allows to use Vector-Invariant form in deep atmos and anelastic formulation
51 o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
52 and Koenig-Beatty+Holland (2012)
53 - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
54 - global 2D field tensileStrength, computed in seaice_calc_ice_strength
55 - requires an extra input argument for S/R seaice_calc_viscosities
56 - tensileStrength's depth dependence is different from Itkin et al. (2015)
57 (to be changed and played with, for now exponential)
58 o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
59 - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
60 by AREA according to Connelly et al. (2004), JPO.
61 - For EVP and the LSR solver, the implicit part of the drag term is
62 the only non-zero term in the denominator when there is no ice (which
63 prevented running the model with zero ice-ocean drag). If
64 SEAICEscaleSurfStress = .TRUE., this results in a division by zero
65 (or zero main diagonals BU/BV) which need to be caught. A practical
66 consequence is that for open water, the momentum equation reduce
67 to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
68 they happen to be zero, often leading to a non-zero solution over
69 open water.
70 o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
71 efficient EVP method.
72 - introduce area-weighted averages for e12 (analogously to
73 seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
74 remain, but also changing the order of terms in the previous average
75 changed the results as much) -> update experiment
76 - add SEAICE_DELTA_SMOOTHREG code
77 - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
78 TEM-code
79 - adjust loop bounds so that only required fields are computed
80 - add new averaging code for zetaZ/deltaZ (again similar to
81 seaice_calc_viscosities.F), inactive by default for now (will change
82 results again), but will replace old code eventually
83 o eesupp/src:
84 - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
85 to always cumulate tile local-sum in the same order
86 (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
87 Still uses MPI_Allreduce (like standard code) but on array of tiles
88 and should be faster than GLOBAL_SUM_SEND_RECV code.
89 - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
90 (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
91 - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
92 aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
93 fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
94 natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
95 tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
96
97 checkpoint65n (2015/07/29)
98 o pkg/thsice:
99 - add a warning when used with pkg/aim but without updating SST
100 (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
101 o pkg/offline:
102 - change where Offline-Fields are loaded, from load_fields_driver.F to
103 directly within FORWARD_STEP, just after updating iter number and time;
104 - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
105 S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
106 These changes allow:
107 a) to recover exactly on-line results using deltaToffline=deltaTClock,
108 tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
109 both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
110 time-step, both with GM & KPP files and with recomputing these fields;
111 b) no needs to switch on staggerTimeStep anymore;
112 c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
113 - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
114 o pkg/offline:
115 - change (rarely used) offset-iteration parameter to an offset time (in s):
116 can easily recover previous offset-iter effect by setting offset-time
117 (offlineTimeOffset) to offset-iter x deltaToffline;
118 - do not turn-off Temp & Salinity surface relaxation when using KPP (used
119 in KPP as part of surface buoyancy forcing) in offline run.
120 - fix ptracers KPP non-local term in the case where KPP is re-computed.
121 o OpenAD
122 - Adding preliminary ggl90 test to OpenAD verification.
123 Config. with ggl90 currently diverges after 64 time steps
124 so will need more work to become more stable
125 - Adding preliminary kpp test to OpenAD verification.
126 required small tweakes in kpp_routines.F
127 - Merge and update from Krishna Narayanan's contrib area:
128 * Add one variable for preliminary OpenAD DIVA
129 * Add replacement time-stepping for OpenAD DIVA
130 * genmake2 flag -diva (but only for OpenAD; preliminary)
131 * required modifs for OAD_support
132 successful preliminary test for tutorial_global_oce_biogeo/
133 o pkg/seaice:
134 - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
135 - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
136 delta with a smooth function in s/r seaice_calc_viscosity
137 (no effect on EVP)
138 - rename local suffix "sqr" into "sq" for more consistent variable names
139 o pkg/seaice:
140 add new parameter SEAICE_deltaMin that is used ***only***
141 for regularizing Delta (and nothing else, like the parameter
142 which is also used for all sorts of things SEAICE_EPS).
143 Defaults to SEAICE_EPS for backward compatibility only.
144 o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
145 the wrong key by inialising it before use -> fixes a recomputation
146 problem but does not fix the gradient
147 o pkg/layers:
148 - move resetting of flux arrays to outside the iLa loop
149 (this caused layers_diapycnal to not work with more than one layer coord.)
150 - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
151 o pkg/layers:
152 - remove from common block 3D layers fields (used to diagnose transport
153 in tracer coords) and declare them as local arrays in layers_calc.F
154 o pkg/seaice:
155 - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
156 in lab_sea forward experiment (changes results -> updated)
157 - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
158 o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
159 computations; for SEAICE_VECTORIZE_LSR
160 - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
161 sweep to the outside,
162 - remove store directives and add "CADJ loop sequential" directives
163 in analogy to model/src/solve_tridiagonal.F
164 - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
165 boundaries to yield more readable code. This has also the charming side
166 effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
167 SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
168 seaice_lsr_tridiagu/v now requires either of these flags, vectorization
169 still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
170 an additional option)
171 The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
172 but the adjoint gradients (which are affected by this change) still explode.
173 o coupler (atm & ocn _compon_interf):
174 - avoid using Exch2 IO mapping if not suitable.
175
176 checkpoint65m (2015/06/15)
177 o pkg/layers:
178 - clean-up old parameters setting (from Sep 2012):
179 + remove old parameters setting from common block (declared locally);
180 + stop if any old parameter is mixed with new parameters;
181 + check for valid or consistent parameter setting (e.g., layers_name)
182 - check that layers_bounds for Pot.Density are in the right range;
183 this is supposed to catch un-updated setting after recently shifting
184 potential density field "prho" by -1000 (now in "sigma" scale).
185 o pkg/layers:
186 - Added missing call to layers_fill for keeping track of tottend in
187 pkg/diagnostics/diagnostics_fill_state.F
188 o pkg/layers:
189 - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
190 of diapycnal fluxes
191 o pkg/layers:
192 - reverted changes to interpolation to previous treatment; there
193 was never actually a problem
194 o pkg/layers:
195 - fix interpolation of layers tracers in the presence of partial cells
196 - add lots of new functionality to compute water mass transformation
197 (enabled by CPP flag LAYERS_THERMODYNAMICS)
198 - add new calls from main code (diags_oceanic_surf_flux.F,
199 thermodynamics.F, impldiff.F) and gad to save the necessary fields
200 for layers_thermodynamics calculations
201 o pkg/ptracers:
202 - add capability of stepping a passive tracer forward without advection
203 by setting PTRACERS_advScheme to 0.
204 o pkg/diagnostics:
205 - add few (threads) _BARRIER around any update of "diag_pkgStatus".
206 o pkg/layers:
207 - shift potential density field "prho" by -1000 for density layer averaging so
208 that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
209 Note that density bin boundaries (layers_bounds in data.layers) have
210 to be set accordingly (i.e., shifted, in sigma scale).
211 o pkg/layers:
212 - fix snap-shot output of layer thickness @ V.pt and output of pot.density
213 - fix calculation of layer non-weighted velocity and layer probability
214 - add diagnostics for pot.density used for layer averaging
215 o pkg/seaice:
216 - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
217 positiveness, modify a few comments and improve variable names,
218 - the changed computation of deltaC affects most seaice-related
219 experiments at the truncation level.
220 seaice_itd.thermo is affected by far the most, with
221 only 7 digits of agreement remaining; update experiments.
222
223 checkpoint65l (2015/05/04)
224 o pkg/shelfice:
225 - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
226 factor drKp1 to zero where it is negative (ie. do not use
227 SHELFICEBoundaryLayer if hFacC>1)
228 - the same for factor drLoc in shelfice_forcing.F
229 o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
230 with modules in ptracers, when using testreport option "-small_f"
231 o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
232 - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
233 o verification/testreport
234 - add new option -small_f
235 with this option testreport first makes the target small_f (*.f files)
236 before running make (all). This is useful for explicit inlining when
237 all sources need to be full available.
238 o pkg/exf/exf_interp.F:
239 remove previous changes related to reverse (decreasing) input grids latitude
240
241 checkpoint65k (2015/04/01)
242 o pkg/ecco:
243 fix missing cosphi initialization; use eccoiter in place of optimcycle;
244 if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
245 instead of active read/write
246 o pkg/ctrl:
247 if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
248 instead of active read/write.
249 o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
250 return if .NOT.useAUTODIFF
251 o pkg/seaice: add CPP brackets (cost function related).
252 o model/src:
253 add useAUTODIFF run time switch.
254 o pkg/exf/exf_interp.F:
255 add code to allow input grids with latitude starting in the north (i.e. when
256 j=1 corresponds to northern edge of field); modify global_with_exf to test
257 this feature.
258 o verification/testreport:
259 - replace "grep -A3" with POSIX conformal sed command, because there are
260 implementations of grep that cannot do contextual searches
261 - replace "cat -n" by "nl" (two occurrences), because not all implementations
262 of "cat" have the option "-n"
263 o model/src:
264 add new file gsw_teos10.F that contains 3 functions, more or less a copy
265 of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
266 convert from conservative to potential temperature. For now they are not
267 called anywhere.
268 o pkg/ggl90: make "useIDEMIX" useful
269 - re-organize code in s/r ggl90_calc a little to move computations that
270 are different for idemix into separate loops (changes verification
271 experiment idemix at truncation level, 12 digits remain -> updated)
272 - requires 2 new 2D fields KappaM, verticalShear
273 - make hFacI and recip_hFacI local 3D variables that are passed to
274 s/r ggl90_idemix
275 - fix and improve some comments
276
277 checkpoint65j (2015/02/25)
278 o pkg/openad
279 - synchronize seawater.F with version in model/src: replace routine
280 body of sw_temp by calling sw_ptmp and fix/add a few comments.
281 o pkg/mnc:
282 - change default value of pickup_read/write_mnc params to FALSE
283 (since few features are missing in reading MNC pickup files).
284 o model/src:
285 - change default (background) vertical diffusivity for salt to be the
286 temperature (background) vertical diffusivity.
287 - change background vertical diffusivity in vertical mixing pkgs ggl90,
288 kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
289 This makes ptracers default diffusivity (that uses salt diffKr) more
290 consistent with vertical mixing schemes.
291 o verification/testreport:
292 - fix typo in "-pcls" option ;
293 - put temp files in /tmp (instead of in local dir)
294 - add option "-ncad" to use genmake2 new option "-nocat4ad"
295 - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
296 o pkg/ggl90 (idemix code):
297 - apply few fixes ; add some missing "_d 0" ; update output of exp.
298 global_ocean.90x40x15.idemix
299 o OpenAD
300 - enable active file I/O and begin removal of work-around code
301 for OpenAD for handling control variables (memory vs. active files)
302 - new CPP options file OPENAD_OPTIONS.h
303 - revert to genarr2d gradient check for hs94.1x64x5
304 - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
305 - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
306 o tools/genmake2:
307 - add option for an alternative Makefile (from Martin) where multiple
308 source files are sent to TAF (instead of all in one file).
309 o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
310 - code provided by Carsten Eden as an extension of ggl90
311 - so far the code is turned on within ggl90 by setting a CPP-flag at
312 compile time; a runtime flag implementation is not yet complete
313 - tested in new verification experiment global_ocean.90x40x15.idemix
314 o verification:
315 - reduce length of the AD test run by half for experiments
316 global_ocean.cs32x15 (std + thsice) and isomip
317 - enable active file I/O for OpenAD, adjust verifications accordingly
318 - halfpipe_streamice: change gradient check from genarr2d to gentim2d
319 o verification/testreport:
320 - fix two non-POSIX sed statements so that there are no error messages
321 on Mac OS X
322 - replace hostname -s with hostname | sed 's/\..*$//'
323 o model/src/seawater.F:
324 - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
325 (following the matlab code), which would have avoided the bug caught
326 by Matt (see below) in the first place
327 o pkg/shelfice:
328 - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
329 and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
330 - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
331 ice-shelf case (i.e., within surface level).
332 - add config summary in shelfice_check.F
333 - remove global variable recip_SHELFICElatentHeat and replace by a local
334 variable recip_latentHeat
335 - introduce diagnostics for friction velocity uStar (in case of
336 SHELFICEuseGammaFrict)
337 - change verification experiment isomip.htd:
338 + start from pickup (as input_ad at nIter0=8640)
339 + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
340 + test SHELFICEuseGammaFrict = .TRUE.
341 + test SHELFICEadvDiffHeatFlux = .TRUE.
342 o model/src:
343 - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
344 in-situ Temp) and in routine SW_TEMP (in pkg/openad);
345 update output of experiments global_with_exf.yearly and isomip (all 6).
346 o pkg/shelfice:
347 - change setting of kTopC to also be zero where there is no ice-shelf.
348 - zero out surface forcing arrays (for now, for T & S + EmPmR) where
349 ice-shelf is.
350 - first attempt to get RealFreshWaterFlux effects: for now, only without
351 SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
352 o pkg/seaice: add the option to prescribe a fixed thickness PDF
353 for thermodynamic calculations
354 - because of divisions of the type 7/7 not exactly equal to 1, this change
355 affects results of some verification experiments by up to 4 digits:
356 global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
357 seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
358 adjoint: lab_sea, lab_sea.noseaicedyn
359 -> updated
360
361 checkpoint65i (2015/01/23)
362 o model/src:
363 - change units of frictionHeating field from W to W/m^2
364 - fix bug in frictional heating from stratospheric drag in
365 S/R ATM_PHYS_TENDENCY_APPLY_V
366 - with synchronous time-stepping: move resetting to zero of frictionHeating
367 field from load_fields_driver.F to thermodynamics.F ;
368 - add diagnostics for frictional heating.
369 o model/src & gmredi K3D:
370 - add frictionHeating field to pickup-files (for synchronous time-stepping)
371 - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
372 - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
373 and name in pickup file).
374 - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
375 o model/src:
376 - move (from ini_forcing.F) initialisation of all arrays in header file
377 FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
378 (since Nov 2012) with option selectAddFluid=1.
379 o pkg/shelfice:
380 - change units (+ document) of newly added field "shelfIceMassDynTendency"
381 - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
382 o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
383 o pkg/seaice: two new runtime parameters:
384 - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
385 long overdue
386 - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
387 parameterization of tensil stress for fast ice (does not do anything yet)
388 o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
389 for LSR: move checking overlaps out of JFNK-if-block
390 o pkg/atm_phys:
391 - move copy of grid and dynamical fields out of atm_phys_driver.F into
392 new S/R ATM_PHYS_DYN2PHYS.
393 - fix level height for Linear Free-Surf case (to be consistent with
394 fixed-in-time pressure levels).
395 o pkg/mom_common (bottomdrag):
396 - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
397 to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
398 update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
399 o pkg/shelfice (u/v_drag):
400 - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
401 - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
402 (now similar to shelfice_u_drag.F)
403 - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
404 from mom_vecinv.F (similar to mom_fluxform calls).
405 o pkg/mom_common (bottomdrag):
406 - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
407 - add options for alternative discretisation of velocity norm in quadratic
408 bottom drag: averaging of grid-cell-center KE to U.point and V.point
409 (selectBotDragQuadr=0, original code) can produce noisy patterns; this
410 improves when averaging only the other component (e.g. vVel for U bottom
411 drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
412 - add options (bottomVisc_pCell) to account for partial-cell in bottom
413 friction (no-slip BC) thus getting the true distance from the bottom;
414 off by default since this also reduces model stability (explicit bottom
415 friction). Changes produce different machine truncation with linear-drag
416 + no-slip BC: update output of experiments exp4.stevens (10 digits) and
417 front_relax (bvp & mxl, 10 & 11 digits).
418 o model/src & mom pkgs:
419 - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
420 since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
421 - for now and until vertical mixing scheme are updated to fill up level Nr+1,
422 just copy level Nr value to level Nr+1.
423 o doc:
424 - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
425 o pkg/streamice:
426 - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
427 SHELFICE.h: move array shelficemass to init_varia, initialise
428 from array shelficemassinit, which is set in init_fixed and
429 has option to be set from file; introduce array
430 shelficeMassDynTend array, set thru file in init_fixed
431 - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
432 shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
433 pkg/streamice
434 - shelfice_thermodynamics.F: call shelfice_step_icemass if
435 SHELFICEMassStepping = .true.
436 - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
437
438 checkpoint65h (2014/12/17)
439 o verification/global_ocean.90x40x15, global_ocean_ebm:
440 - update to generic controls.
441 o pkg/ctrl:
442 - ctrl_map_ini_genarr.F: test for igen>0
443 - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
444 - move gentim2d part of ctrl_map_ini_genarr.F to
445 new separate routine : ctrl_map_ini_gentim2d.F
446 - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
447 add time variable weights and cyclic controls (time mean,
448 seasonal cycle, etc) capabilities to gentim2d
449 o pkg/ecco:
450 - move reading of error, conversion to weights from
451 ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
452 o global_oce_llc90, cs32:
453 - activte sbo.
454 - CTRL_SIZE.h : add maxCtrlProc.
455 - activate the new genctrl capabilities.
456 - update following reorganization of global_oce_input_fields.tar.gz
457 o pkg/ctrl/ctrl_ad_diff.list:
458 - add missing ctrl_init_rec.f
459 o tools/OAD_support/keepOriginal:
460 - add ctrl_init_rec.F
461 o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
462 - avoid recomputations of xx_gentim2d_dummy.
463 o momentum diagnostics:
464 - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
465 mom_vecinv.F to timestep.F (to include Smag-3D contribution).
466 o pkg/seaice/seaice_lsr.F:
467 - fix computation of BU/BV, make sure they are non-zero, only necessary
468 for cubed sphere exchanges and SEAICE_OLx/y>0.
469 This makes calling s/r fill_cs_corner_rl obsolete (removed).
470 o verification/global_ocean.cs32x15/input.seaice
471 - add test for strong implicit coupling and restricted addtive Schwarz
472 methods for LSR
473 - update results/output.seaice.txt
474 o verification/tutorial_global_oce_biogeo:
475 - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
476 and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
477 update output_adm,_oadm,_tlm.txt
478 o pkg/dic:
479 - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
480 - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
481 for tracer 1 & 2 is set (to avoid double counting of dilution effect).
482 o verification/tutorial_global_oce_biogeo:
483 - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
484 dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
485 update output_adm,_oadm,_tlm.txt
486 o eesupp/src:
487 - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
488 and call it in seaice_lsr when using nonzero SEAICE_OLx/y
489 o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
490 LSR (following Hutchings et al. 2004)
491 - introduce zetaZ as a global variable (requires adjustments in
492 seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
493 in seaice_calc_viscosities.F
494 - new flag SEAICEuseStrImpCpl (default off)
495 - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
496 momentum equations
497 - JFNK-solver (preconditioner) adjusted to allow using this method
498 (where it does not have any positive effect)
499 o pkg/seaice
500 - add overlap for restrictive additive Schwartz method also to LSR, but
501 turn it off by default (because it only seems to work for non-cubed
502 sphere/llc topologies)
503 o pkg/autodiff
504 - add extra exchanges in addummy_in_steppging also for mnc output
505 o pkg/seaice:
506 - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
507 to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
508 o pkg/obcs:
509 - add option to specify domain-connected piece Id along OB though files
510 (for now, only used to diagnose PhiVel; default =1 -> global correction)
511 - modify obcs_diag_balance.F to process each connected-part separately;
512 exclude OB where Id = 0 but keep the full divergence there (-> constant
513 Psi along this portion of OB and all inflow derived from grad(Phi))
514 - add example of OB-conect files in verification/so_box_biogeo/input.
515 o pkg/diagnostics:
516 - improve treatment of Open-Boundaries in Velocity-Potential calculation:
517 a) use non zero matrix element across OB and solve for Phi 1 grid point
518 outside OB (i.e, where tracer OBCS are applied).
519 b) global imbalance of inFlow/outFlow across OB: instead of modifying
520 velocity across OB, spread it uniformly along the OB in the RHS.
521
522 checkpoint65g (2014/11/19)
523 o pkg/diagnostcis:
524 - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
525 o pkg/my82,pp81,kl10:
526 - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
527 field diffKr as background diffusivity to set minimum diffusivity value.
528 o pkg/seaice:
529 - add new parameter SEAICEuseEVPrev (for revisited EVP by
530 Bouillon et al 2013)
531 - add SEAICE_evpAlpha/Beta to namelist
532 - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
533 involve trivial re-ordering of divisions/multiplications that should not
534 have any effects, but ... they do change the results of lab_sea.hb87 so
535 that only 2 digits of agreement remain, in line with the general
536 instability/fragility of the evp-code. For now, I do not care and just
537 update the verification experiment
538 o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
539 - remove xx_genarr2d_numsmooth etc
540 - use xx_genarr2d_preproc etc instead
541 - carry out smooth_correl2D at initialization stage rather than during
542 time stepping.
543 - get smoothOpNb from xx_gentim2d_preproc
544 o global_oce_cs32 :
545 - add test of generic ecco capabilities.
546 o pkg/exf/exf_getsurfacefluxes.F :
547 - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
548 o pkg/ctrl,ecco :
549 - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
550 is defined.
551 o pkg/seaice: add diagnostics for Delta (deformation parameter)
552 o model/src:
553 - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
554 diffusivity (background) is specified but ignored.
555 o verification:
556 - in testreport, convert hostname to lower case for default output dir name
557 o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
558 o pkg/dic: add modifications from Hajoon:
559 - add iron sedimentation flux function of the flux of PO4 out of bottom layer
560 - light attenuation: add self-shading effect by climatological Chlorophyll
561 (read from file).
562 o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
563 compiles when SEAICE_ALLOW_DYNAMICS is undefined
564 o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
565 AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
566 ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
567 approach where CPP_OPTIONS.h includes an omnipotent
568 ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
569 o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
570 ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
571 o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
572 to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
573 (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
574 o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
575 add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
576 - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
577 - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
578 - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
579 o pkg/ctrl,ecco,exf :
580 - remove variables associated with NON-generic costs,
581 unless ECCO_CTRL_DEPRECATED is defined.
582 - remove NON-generic NON-obcs controls,
583 unless ECCO_CTRL_DEPRECATED is defined.
584 o pkg/ctrl : added ctrl_local_params.h
585 o pkg/ecco : added ecco_local_params.h
586 o verification : added ECCO_CTRL_DEPRECATED to most as and oad
587 experiments, which will progressively be removed once the
588 experiments are revised to use only generic controls/costs.
589
590 checkpoint65f (2014/10/13)
591 o pkg/ctrl, ecco, seaice : minor changes in headers
592 o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
593 cost function and control capabilities added since checkpoint65c.
594 o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
595 o pkg/ecco: increase modularity and improve logic
596 - ecco_toolbox.F (new) : basic operations that are often used,
597 including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
598 ecco_addcost, ecco_add, ecco_div, ecco_readbar.
599 - cost_gencal.F (new) : determine filnames and records.
600 - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
601 - cost_generic.F : use spzeroloc rather than hard-coded -9999,
602 and exploit the above functions leading to more compact code.
603 - cost_genread.F : rm un-necessary arguments, re-arrange args order.
604 - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
605 using_ers, using_gfo, using_mdt is now only defined within gencost)
606 o pkg/ecco: extend generic cost capabilities
607 - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
608 capabilities via gencost_preproc (+ _c,_i,_r related params),
609 gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
610 gencost_outputlevel arguments to cost_generic
611 - pkg/ecco/cost_genread.F (new) : interface between cost_generic
612 and active_read, making room for gencost_preproc to take effect.
613 Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
614 - pkg/ecco/cost_generic.F :
615 compute and store misfit maks*(model-data) in localdif that is
616 then used in cost and for output, output misfit if outlev.GT.0
617 - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
618 rather gencost_barfile for deciding whether to write barfile
619 - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
620 - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
621 ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
622 - pkg/ecco/ecco_summary.F : report gencost variables
623 - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
624 o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
625 o pkg/ecco: internal re-organization
626 - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
627 (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
628 mv relevant variables definition from ecco_cost.h to ecco.h,
629 make sure gencost routines only include ecco.h)
630 - throughout : add missing CCP switches, rm unused variables,
631 and rm un-necessary CPP switches
632 - throughout gencost routines : replace modelstartdate with
633 gencost_startdate when needed
634 - cost_bp_read.F : use arguments, instead of common blocs
635 so that it can be used also by (new) cost_gencost_bpv4.F
636 - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
637 - ecco_phys.F : compute etanFull
638 - ecco_readparms.F : rename using_topex as using_tpj, add
639 bpv4-grace to gencost list, initialize added parameters
640 - ecco_summary.F : include SIZE.h needed for augmented ecco.h
641
642 checkpoint65e (2014/09/28)
643 o pkg/obcs:
644 - replaced the just-added CPP options with run-time variables
645 (see pkg/obcs/OBCS_PARAMS.h for details)
646 o pkg/obcs:
647 - add additional CPP options for sponge boundary layers
648 (see pkg/obcs/OBCS_OPTIONS.h for details)
649 o pkg/atm_phys:
650 - implement simple (obliquity only, assuming circular planet orbit)
651 seasonal cycle for incoming insolation ; used when run-time parameter
652 "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
653 o pkg/exf, pkg/ecco, pkg/ctrl:
654 - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
655 - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
656 - implement gentim2d for xx_tauu, xx_tauv
657 o pkg/ctrl, pkg/ecco :
658 - fix and complement the generic controls implementation
659 o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
660 pkg/shelfice/shelfice_thermodynamics.F,
661 verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
662 verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
663 - add weight in CTRL_GET_GEN calls
664 o pkg/ctrl :
665 - ctrl_get_gen.F : add weight as input parameter, and apply
666 it directly rather than using smooth_correl2Dw (to be retired).
667 - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
668 o pkg/ctrl :
669 - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
670 ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
671 - re-activate ctrl_summary (call in ctrl_init.F)
672 o pkg/ctrl/ctrl_cost_gen.F :
673 - fix CCP brackets, remove un-necessary myiter, mytime
674 o pkg/ecco, pkg/ctrl :
675 - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
676 - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
677 - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
678 - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
679
680 checkpoint65d (2014/09/15)
681 o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
682 - add xx_genarr2d_bounds,xx_genarr3d_bounds,
683 xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
684 o pkg/ctrl/ctrl_map_ini_genarr.F :
685 - remove compilation failure
686 - replace hard coded example
687 - use ctrl_map_ini_gen2D, 3D
688 o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
689 - on/off switch based upon xx_genarr2d_weight,3d
690 o src/packages_init_variables.F :
691 - regroup pkg/estimation calls
692 - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
693 (moved to ctrl_init_variables)
694 o cost/cost_init_varia.F :
695 - remove ecco_cost_init_varia
696 (moved to ecco_init_varia)
697 o ctrl/ctrl_init_variables.F :
698 - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
699 - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
700 o ctrl/ctrl_map_ini.F :
701 - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
702 (moved to ctrl_init_variables)
703 o ctrl/ctrl_map_ini_ecco.F :
704 - remove ECCO_PHYS (mv to ecco_init_varia)
705 - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
706 o ecco/ecco_ad_diff.list :
707 - add ecco_init_varia.f
708 o ecco/ecco_init_varia.F
709 - new routine
710 o pkg/streamice:
711 - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
712 to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
713 - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
714 o pkg/generic_advdiff:
715 - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
716 o pkg/exf:
717 - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
718 xxg_precip capability
719 - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
720 o pkg/ctrl:
721 - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
722 o model/src/load_fields_driver.F :
723 - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
724 so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
725 o OpenAD verification experiments:
726 - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
727 in src files (to enable to skip the ECCO_CPPOPTIONS.h);
728 for now, only in pkgs used in OpenAD verification experiments.
729 - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
730 specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
731 instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
732 This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
733 o OpenAD verification tests:
734 - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
735 - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
736 tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
737 - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
738 and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
739 o model/src & generic_advdiff:
740 - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
741 forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
742 dynamics requires valid tracer forcing only over tile interior but, for
743 some diagnostics, may need to extend it over 1 point in tile halo region.
744 - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
745 tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
746 setting in temp/salt/ptracer_integrate.F
747 o pkg/dic:
748 - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
749 gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
750 in gchem_forcing_sep.F
751 o pkg/autodiff & obcs:
752 - add storage of current OB values for U & V (was already done for T & S).
753
754 checkpoint65c (2014/08/30)
755 o pkg/dic:
756 - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
757 and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
758 AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
759 o verification:
760 - new experiment testing OBCS and DIC pkgs, using params & output from
761 tutorial_global_oce_biogeo but limited to a sub-domain around Drake
762 passage: take OBCS from the last year of a 2 yrs simulation and initial
763 conditions from t=1.yr while keeping the same forcing.
764 o model/src:
765 - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
766 (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
767 o pkg/diagnostics (Stats-Diags):
768 - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
769 a) refine region where stats are computed, excluding where arrhFac=0 ;
770 b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
771 c) extend regional stats over the region edges (for U or V pt location).
772 o pkg/gchem:
773 - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
774 pkg/dic is currently changing/updating ptracers values beyond the OB).
775 o verification (hs94):
776 - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
777 bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
778 hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
779 apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
780 o pkg/ptracers:
781 - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
782 switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
783 - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
784 with AB-2 code (so that it get tested).
785 o model/src:
786 - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
787 with AB-2 code (previously only available with AB-3 code).
788 Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
789 to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
790 there, by calling CYCLE_AB_TRACER).
791 o pkg/generic_advdiff:
792 - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
793 GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
794 + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
795 S/R temp/salt/ptracers_integrate.F
796 o model/src & pkg/ptracers:
797 - remove common block variables gT,gS (in DYNVARS.h), except when
798 USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
799 - remove common block variable gPtr.
800 o model/src & pkgs:
801 - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
802 ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
803 IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
804 GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
805 + change accordingly all calling S/R.
806 - use local temperature/salinity/ptracer tendency array (without bi,bj)
807 in S/R temp/salt/ptracers_integrate.F
808 o pkg/seaice:
809 - move computation of stress contributions to rhsU/V in s/r seaice_lsr
810 to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
811 - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
812 in seaice_lsr
813 - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
814 in s/r seaice_lsr_calc_coeffs
815 o pkg/mdsio:
816 - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
817 (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
818 too long (e.g., > MAX_LEN_FNAM/2 )
819
820 checkpoint65b (2014/08/12)
821 o pkg/matrix:
822 - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
823 o model/src:
824 - fix initialisation of geothermalFile; compile geothermal-flux code in
825 natl_box verification experiment.
826 o model/src & pkg/down_slope:
827 - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
828 - in dwnslp_apply.F, update tracer tendency instead of the future tracer
829 field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
830 results at machine truncation level: update output of experiments
831 global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
832 o pkg/diagnostics (Stats-Diags):
833 - do not cumulate the full volume when DIAGNOSTICS_FILL is
834 called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
835 This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
836 times (but Min,Max and StD are still wrong).
837 o model/src:
838 - add geothermal flux forcing: read in ini_forcing.F as time-constant
839 field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
840 o model/src:
841 - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
842 _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
843 arrays are already updated while adjustments (filters, conv.adjustment) are
844 still applied later, in S/R TRACERS_CORRECTION_STEP.
845 o model/src:
846 - store in common bloc array "rhoInSitu" the virtual potential temperature
847 anomaly that is used to compute geopotential: this make the atmos code
848 more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
849 o pkg/seaice/seaice_lsr.F
850 - rename integer variable ilcall to ipass (that's what it is called
851 in the residual diagnostics
852 - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
853 default) for improved non-linear convergence of the first few steps
854 - adjust a few comments and add new ones to explain some of the store
855 directives
856 o pkg/generic_advdiff (& ptracers):
857 - re-work the code to check for valid advection scheme and for minimum
858 size of overlap (now stored in local common bloc in gad_advscheme.F)
859 o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
860 - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
861 - add an auxilliary variable "bet" and fix store directives and keys in
862 seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
863 less exact gradients in my tests); but there are still
864 recomputation warning (although gradients are sort of OK), when
865 SEAICE_LSR_VECTORIZE is not defined, so this flag and
866 SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
867 - update verification experiments lab_sea.
868 - change some comments in S/R seaice_calc_viscosities
869 o model/src:
870 - if staggerTimeStep=T, always apply exchange to velocity field in
871 do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
872 (independent of using multi-dim advection or not); no effect on FWD run
873 but affects AD results (at machine truncation level): update output of
874 experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
875 and isomip (oad: 12.d).
876 o pkg/generic_advdiff:
877 - stop if doAB_onGtGs is set to FALSE but ignored
878 - refine warning related to stability of tracer time-stepping
879 regarding internal wave dynamics.
880 - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
881 on staggerTimeStep & implicitIntGravWave (will now get a warning
882 if potentially unstable).
883 o pkg/kl10:
884 - add new pkg "kl10" for mixing due to internal wave breaking, from
885 http://www.sciencedirect.com/science/article/pii/S1463500310000144
886 (contribution from Jody Klymak), tested in verification experiment
887 verification/internal_wave/input.kl10/
888 o isomip experiment:
889 - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
890 (input.htd) and update the output.
891 o cd_code experiments:
892 - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
893 #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
894 global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
895 update the corresponding output.
896 o pkg/seaice:
897 - reduce the number of include files and store directives in
898 S/R seaice_lsr_tridiagu/v
899 - change the order of loops in one case in S/R seaice_lsr_tridiagv
900 (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
901 get rid off one store directive (a TAF bug?)
902 - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
903 S/R seaice_lsr_tridiagv to change the loop range for consistency
904 - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
905 - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
906 S/R seaice_lsr_tridiagu/v (requires update of
907 offline_exf_seaice/input.dyn_jfnk)
908
909 checkpoint65a (2014/07/27)
910 o model/src:
911 - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
912 surrounding hFacC=1 @ edge of a step with different kSurfC on either side
913 (topo in p-coords, ice-shelf in z-coords); update output of experiments
914 tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
915 o model/src:
916 - collect momentum forcing tendency into local 2-D array (passed as argument
917 to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
918 parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
919 affects results at machine truncation level (e.g., if using OBCS_SPONGE).
920 - collect T & S forcing tendency into local 2-D array (passed as argument to
921 apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
922 affects results at machine truncation level (e.g., ocean: if using
923 SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
924 correction due to vertical advection).
925 - update output of experiments: fizhi-cs-32x32x40 (13 digits),
926 global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
927 seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
928 obcs_ctrl (ad & fwd grd @ 12 & 7).
929 o pkg/ptracers & diagnostics:
930 - use ptracers (short) name (instead of long one) to make ptracers diagnostics
931 title (to avoid some unexpected truncation); sort out ptracers diags units.
932 - collect ptracer forcing tendency into local 2-D array (passed as argument
933 to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
934
935 checkpoint65 (2014/07/18)
936 o pkg/fizhi:
937 - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
938 affects results at machine truncation level. Update output of experiments
939 fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
940 o pkg/seaice: more clean up
941 - rename TAF common block tapes to be more consistent and remove
942 unnecessary duplicates
943 - add store directives to remove more recomputations, but use smaller
944 tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
945 The idea behind this flag is to reduce the memory footprint when the
946 adjoint of the LSR is not required. As of now, defining the flag
947 SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
948 a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
949 For experiment offline_exf_seaice, this means on a linux box with gfortran
950 nearly a factor of 10 (but keep in mind there is mostly seaice code in
951 this experiment):
952 > size mitgcmuv_ad
953 text data bss dec hex
954 5100659 1216 220458952 225560827 d71c8fb
955 5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
956 but only a moderate increase of 36% for global_ocean.cs32x15:
957 text data bss dec hex
958 6695027 1648 1014578664 1021275339 3cdf6ccb
959 6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
960 - note: there are still recomputations in global_ocean.cs32x15 and
961 offline_exf_seaice and the gradient agreement changes (gets a
962 little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
963 - in general, the AD gradients still are wrong
964 o OpenAD
965 - clean up code_oad/ directories somewhat by moving files
966 dontCompile, dontTransform, keepOriginal to OAD_support/
967 o model/src:
968 - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
969 (not currently tested): add dissipation terms before NLFS rescaling of
970 tendencies (previously done after).
971 o pkg/diagnostics:
972 - write stats-diags in ascii file with more digits (same as in monitor).
973 o pkg/down_slope:
974 - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
975 NLFS (not tested), use new recip_hFac value in order to conserve tracer.
976 o model/src:
977 - new file "apply_forcing.F" containing all the code previously in
978 external_forcing.F, but with new argument list: pass, as new argument,
979 the current level tendency array to update (instead of a direct update
980 of the common bloc array). Change the corresponding calls.
981 - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
982 EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
983 o pkg/seaice/seaice_lsr, a little bit of clean up
984 - rearrange some code blocks, so that now all calculations for
985 setting up the right-hand-sides done within one single block
986 (I find that easier to read and understand)
987 - rearrange freedrift-code to reduce the number of ifdefs
988 - adjust some indentations and comments
989
990 checkpoint64z (2014/07/10)
991 o model/src and several pkgs:
992 - change argument list of all S/R called from external_forcing.F and
993 called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
994 to pass, as argument, the current level tendency array to update
995 (instead of a direct update of the common bloc array).
996 - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
997 - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
998 o pkg/seaice/seaice_lsr.F
999 - always initialize local arrays in seaice_lsr_tridiagu/v
1000 - add more local tapes to seaice_lsr_tridiagu/v
1001 - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1002 keep it in bi/bj loop; this seems to be essential
1003 - gradients are still wrong but only by 4-7 orders of magnitude
1004 instead of 15 orders of magnitude, lab_sea improves a little
1005 o pkg/seaice
1006 - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1007 generates unnecessary code in seaice_lsr_ad
1008 - add more store directives in seaice_lsr to avoid unnecessary code
1009 in seaice_lsr_ad
1010 - exclude some residual computations in seaice_lsr when
1011 ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1012 in seaice_lsr_ad
1013 - add more storing, a new tape (model/src/the_main_loop.F) and
1014 another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1015 and klockey should be checked by a specialist)
1016 - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1017 and update lab_sea after previous changes in pkg/seaice below
1018 o pkg/autodiff:
1019 - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1020 viscFacInAd : run time parameters allowing for adjoint switches
1021 note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1022 o pkg/ecco:
1023 - introduce cost_gencost_boxmean.F that computes a box mean
1024 temperature (for use in adjoint sensitivity studies).
1025 o model/src/set_defaults.F : initialize viscFacAdj to 1.
1026 o pkg/mom_common/mom_calc_visc.F:
1027 - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1028 o pkg/seaice/seaice_summary.F:
1029 - statement for SEAICEadjMODE now in autodiff_readparms.F
1030 o pkg/seaice:
1031 - remove some store directives and add new ones in an effort to get
1032 finally rid off the recomputation warnings. This is successful
1033 when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1034 defined (i.e. no extensive recomputation warnings left), but there
1035 are still too many recomputations on the solver iteration level
1036 - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1037 - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1038 SEAICE_SIZE.h
1039 - add a store directive in S/R seaice_calc_viscosities
1040 o pkg/seaice (ITD code):
1041 - fix definition of Hlimit for multi-threaded case
1042 - use double precision arithmetic to compute Hlimit: this affects results;
1043 update output of experiment seaice_itd.
1044 o replace content of verification/seaice_itd
1045 - instead of a 1D column use the configuration of offline_exf_seaice
1046 to test the ice thickness distribution code with ridging
1047 - this is a first shot at this experiment
1048 - change of some defaults of ridging parameters SEAICEhStar (from
1049 100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1050 and lot of new comments.
1051
1052 checkpoint64y (2014/06/20)
1053 o pkg/seaice/seaice_reg_ridge.F:
1054 - modify the regularization of very small volumes of ice; only check
1055 total volume HEFF, and do not apply correction to individual ice
1056 classes because that leads to funny patterns in the heat and fw-fluxes
1057 into the ocean. Adjust seaice_itd/results/output.txt
1058 - replace nITD by SEAICE_multDim in loop-ranges
1059 o pkg/exf:
1060 - add code to process the case field period = -12. with UV interpolation.
1061 - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1062 into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1063 o verification/global_with_exf:
1064 - switch all fields period to -12. (was previously untested) in input/data.exf
1065 (but keep secondary test ".yearly" unchanged); update the reference output.
1066 o pkg/cal:
1067 - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1068 o pkg/exf:
1069 - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1070 to replace logical switch "exf_verbose"
1071 - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1072 o pkg/sbo:
1073 - update from Katherine Quinn: evaluate mass directly from density and SSH
1074 (budget using Finite Volume method) instead of from bottom pressure.
1075 - allow testreport to collect few selected SBO output ; tested in exp.
1076 global_ocean.90x40x15 (after updating the results, to include SBO output).
1077 - fix some multi-threading issues (in output part).
1078 o model/src & most packages:
1079 - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1080 - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1081 PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1082 "data.{pkg}" exist ; and leave the S/R (return) just after.
1083 - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1084 + call LAND_READPARMS from packages_readparms.F
1085 o pkg/seaice:
1086 - remove code that resets useThSice in S/R seaice_readparms and
1087 replace it by a warning in S/R seaice_check
1088 - remove parameter MULTDIM, replace with nITD and runtime
1089 parameter SEAICE_multDim (still hard-wired to nITD if
1090 SEAICE_ITD is defined)
1091
1092 checkpoint64x (2014/05/24)
1093 o verification/lab_sea:
1094 - update adjoint and TLM output following changes to pkg/salt_plume
1095 - un-do the update after putting back local recip_Cp in few places.
1096 o pkg/salt_plume: modifications by An Nguyen:
1097 - add capability to do brine rejection (salt-plume) as function of
1098 volume+tracers (instead of only salinity tracer).
1099 - conserve volume by exchanging volume from each kLev to above to
1100 accommodate in-coming brine volume
1101 - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1102 - switch KPP surf buoyancy due to brine forcing to 3-d
1103 (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1104 - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1105 - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1106 in East/West Arctic.
1107 o pkg/sbo:
1108 - incorporate modifications from Katherine Quinn to enable the use of sbo
1109 pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1110 output for future testreport verification (unfinished).
1111 o pkg/atm_phys:
1112 - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1113 skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1114 output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1115 o pkg/seaice
1116 seaice_calc_ice_strength.F: modify expression to avoid divisions
1117 (affects truncation)
1118 seaice_do_ridging.F: clean up the insectarium
1119 - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1120 - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1121 - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1122 - add some debugging information and error messages (warnings)
1123 o model/src: modifications relatd to atmosphere p*:
1124 - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1125 - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1126 of vertical profile tRef in geopotential background and anomaly.
1127 - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1128 and pkg/atm_phys.
1129 - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1130 fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1131 o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1132 o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1133 not used right now, but can be used in BGC packages to fix conservation.
1134 o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1135 other packages too.
1136 o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1137 SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1138 o model/src:
1139 - since we have several heat capacity (even in model/src), define "recip_Cp"
1140 as local variable (no longer in common block) to avoid any confusion.
1141 - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1142 o pkg/exf:
1143 - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1144 air density as function of air Temp, Humidity and atm pressure.
1145
1146 checkpoint64w (2014/05/02)
1147 o verification:
1148 - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1149 seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1150 code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1151 seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1152 (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1153 o model/src: for atmosphere in p* coords:
1154 - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1155 - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1156 but not yet activated.
1157 o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1158 - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1159 - this changes the results (but not for any verification experiment, because
1160 none tests this), but avoids having an extra field in the restart files
1161 o pkg/seaice: remove global variable TICE (not needed)
1162 - replace by TICES or local variable where necessary (cost_seaice_test,
1163 seaice_diagnostics_state)
1164 - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1165 - use specific read/write routines for reading and writing individual leves
1166 of a multilevel field
1167 o pkg/ctrl & model/inc:
1168 - move additional anomaly fields of control vars (related to options:
1169 ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1170 from DYNVARS.h into new header file: CTRL_FIELDS.h
1171 o pkg/seaice: some small modifications to the ridging code
1172 - make fw2ObyRidge a global variable and add the freshwater flux to
1173 seaice_growth
1174 - pass actual thickness from seaice_prepare_ridging, so that it is
1175 computed only in one place and compute it in the same way as in
1176 seaice_growth
1177 - initialise more fields in seaice_do_ridging that where cause floating
1178 point exceptions over land
1179 o pkg/seaice: preparations for ridging code and first real ridging code
1180 - move most of "PART 1" of S/R seaice_growth into a new and separate
1181 S/R seaice_reg_ridge that will both regularize the state variable after
1182 advection call the actual ridging routine;
1183 - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1184 d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1185 - remove ridging code from seaice_advdiff
1186 - clean up remaining part 1 of seaice_growth in an attempt to make it
1187 more readable (this is probably subjective)
1188 - call seaice_itd_redist once in the initialisation phase to have the initial
1189 conditions in the correct category
1190 - finally: add new ridging routine for ITD code
1191
1192 checkpoint64v (2014/04/11)
1193 o pkg/ecco:
1194 - add runtime parameters mdt[start,end]date[1,2]
1195 - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
1196 o pkg/seaice:
1197 - make deltaC a global variable, so that it can be used in ridging code
1198 - first step towards ridging: introduce new routines that compute
1199 ice strength based on ridging parameters
1200 - add diagnostic for HSNOWITD
1201 - add opnWtrFrac as a global variable (required for ridging scheme)
1202 o pkg/salt_plume + pkg/seaice/seaice_growth.F
1203 - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
1204 AREA exceeds a threshold (code contributed by I.Fenty in 2011)
1205 o verification/hs94.1x64x5:
1206 - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
1207 - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
1208 o autodiff:
1209 - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
1210 and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
1211 For now, only in pkgs used in verification/hs94.1x64x5.
1212 - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
1213 which are specific to TAF/TAMC).
1214 - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
1215 since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
1216 is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
1217 - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
1218 building mitgcmuv_ad (make adAll).
1219 o pkg/ecco:
1220 - cost_gencost_seaicev4.F:
1221 reformulate proxy cost as function of sst and local param SEAICE_freeze
1222 change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
1223 - add stop statement if old names siv4-[sst,vol] are used
1224 - add snapshots + cost reports for atmospheric longwave
1225 - remove factor 0.1 in front of wtau[u,v]
1226 - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
1227 ALLOW_TMI_SST_COST_CONTRIBUTION
1228 o pkg/atm_phys:
1229 - add some diagnostics for Short-wave and for convection S/R.
1230 o pkg/seaice/seaice_growth:
1231 - fix a bug in the lateral melt parameterization for SEAICE_ITD
1232 in seaice_growth; tempFrz needs to be computed inside the i/j-loop
1233 - rearrange loop order for better vector code in the same code block
1234 - rewrite the floeDiameter formula to have fewer divisions
1235 - (miraculously) none of this changes the results of seaice_itd
1236 o pkg/smooth:
1237 - move param smooth2Ddiffnbt to pkg/ecco
1238 o pkg/salt_plume:
1239 - salt_plume_frac.F:
1240 clean up local param names
1241 reformulate (1-frac) to frac; original 1-frac was based on swfrac code
1242 o pkg/rw:
1243 - add RS version of S/R READ_MFLDS_LEV.
1244 o pkg/streamice:
1245 - fix the restart test by writing/reading pickup_streamice files.
1246 o pkg/seaice:
1247 - refine checks for jfnk-related parameters
1248 - comment out if statement with SEAICEuseIMEX parameter as long as there
1249 is no IMEX code to avoid confusion and surprises
1250
1251 checkpoint64u (2014/03/07)
1252 o verification/MLAdjust:
1253 - rename secondary test suffix:
1254 1.leith -> A4FlxF + switch to flux-form & add side-drag
1255 0.leithD -> AhFlxF + switch to flux-form
1256 0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag
1257 0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag
1258 o pkg/mom_vecinv:
1259 - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
1260 to be before mom_calc_visc.F)
1261 - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
1262 - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
1263 this is simpler for the adjoint and for diagnostics.
1264 o model/src + pkg/momentum:
1265 - add input files for 2-D additional Western and Southern cell-edge wall
1266 (e.g., to add "thin-wall" where it is =1).
1267 - fix sideDrag option for thin-walls with Non-Lin Free-Surf
1268 using 2nd hFacZ that is computed from initial (fix domain) hFac
1269 - known limitations of thin wall implementation: not yet coded for sigma
1270 coords; not working with CD-scheme neither.
1271 o pkg/seaice:
1272 - rename recently introduced parameters from (wrong name) AB to
1273 BDF (backward difference time discretisation)
1274 - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
1275 o tools/adjoint_options:
1276 - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
1277
1278 checkpoint64t (2014/02/01)
1279 o pkg/ecco
1280 - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
1281 runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
1282 - replace hard-coded record number and period which only work for monthly
1283 with read-in runtime param that works for other periods (month,day,year)
1284 o pkg/thsice
1285 - corrected store directive fixes thsice adjoint gradient checks
1286 o genmake2 & testreport:
1287 - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
1288 in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
1289 Update testreport accordingly. No need to set "export OPENAD=true"
1290 in adjoint_options/adjoint_oad anymore (will be removed later).
1291 o pkg/shelfice:
1292 - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
1293 only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
1294 so that surface forcing applies to k=kSurf if using pkg/shelfice.
1295 o pkg/ctrl, pkg/grdchk, pkg/ecco:
1296 - Changes to make GENARR more modular (i.e. invisible if not used)
1297 o model/src/temp_integrate.F and salt_integrate.F
1298 - re-include store directives that were removed on Dec 27th.
1299 o model/src/external_forcing_surf.F
1300 - add storage directives for EmPmR and PmEpR to avoid recomputation of
1301 seaice_model in the adjoint that is problematic when seaice_model is
1302 turned off in the adjoint. The resolved issue dated back to July when
1303 EXTERNAL_FORCING_SURF call was moved.
1304 Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
1305 o pkg/exf/exf_check.F
1306 - fix a small bug again (originally found by Wentao Liu, now found again)
1307 - streamline error output
1308 o pkg/streamice and aim_v23:
1309 - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
1310 Apple's /usr/bin/cpp knows what to do:
1311 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
1312 Target: x86_64-apple-darwin13.0.0
1313
1314 checkpoint64s (2014/01/05)
1315 o tools/adjoint_options:
1316 - switch to fastopt.net TAF server (instead of default fastopt.de) for
1317 AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
1318 o model/src:
1319 - remove some unnecessary TAF storage directives in forward_step.F and
1320 in dynamics.F (note: not always removed by TAF, e.g., double storage
1321 of kappaRU,kappaRV in former version of dynamics.F).
1322 o model/src & pkg/ptracers:
1323 - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
1324 salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
1325 and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
1326 - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
1327 - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
1328 - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
1329 o useSingleCpuInput separates single-CPU input from single-CPU output;
1330 for now only implemented for in exf_interp_read.F
1331 o verification/advect_xy:
1332 - fix missing EXCH call in local version of ini_salt.F and update output.
1333 o momentum diagnostics:
1334 - fix which deltaT is used in Total-Tendency diagnostics.
1335 - fix typo in diagnostics for momentum tendency from AB.
1336 o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
1337 SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
1338
1339 checkpoint64r (2013/12/08)
1340 o verification/*/results:
1341 - Update reference output of experiments that were passing with just 13 digits
1342 (make it easier to detect future changes in results)
1343 o model/src & pkg/ptracers:
1344 - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
1345 inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
1346 to inside ptracers_integrate.F ; remove ptracers_advection.F
1347 o coupling interface pkgs:
1348 [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
1349 - change the config check to test the agreement of Ocean Depth
1350 with ATM land/sea mask (instead of ATM orography);
1351 - send to coupler the number of coupler time-steps to do for this run:
1352 this allows to check for consistency and don't need anymore to be
1353 specified in parameter file "data";
1354 in coupler:
1355 - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
1356 - improve report to log-file of config setting (pass log-file unit to few S/R)
1357 o pkg/compon_communic:
1358 - add coupling send/receive for non-tiled integer vector;
1359 - add S/R to check and stop if any proc has an error (similar to
1360 eesupp/src/stop_if_error.F but single thread and across Comm_World).
1361 o pkg/exch2:
1362 - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
1363 through list of all tiles my proc owns.
1364 o model/src:
1365 - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
1366 from rTrans) to simplify dependencies (no need to store rTrans anymore in
1367 calling S/R); this affects AD results at machine truncation level:
1368 update AD-output (TAF) of experiments: 1D_ocean_ice_column,
1369 bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
1370 o tools/build_options:
1371 - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
1372 o coupling interface pkgs:
1373 [compon_communic, atm_compon_interf & ocn_compon_interf]
1374 - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
1375 to each S/R that needs it; remove un-used variables.
1376 - change component tile registration (cpl_register.F in both compon_interf
1377 and mitcomponent_tile_register.F) to pass the full list of tiles
1378 information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
1379 - with pkg/exch2: adopt the same convention used for I/O to define mapping
1380 towards coupler global array (unless W2_useE2ioLayOut=F):
1381 a) can now use different tiling between atm & ocn comp.
1382 b) no needs to modify the run-Off map when changing tiling (was needed
1383 even if using the same tiling between atm & ocn).
1384 c) will allow to run with blank-tiles in 1 component (e.g., for ocean
1385 full land tiles); not yet tested.
1386 - check for valid mapping from comp. tile to coupler global array
1387 - improve report of tile registration results to log file.
1388 o pkg/exch2:
1389 - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
1390 tile-registration (CPL_REGISTER);
1391 - activate (un-comment) definition and setting of "W2_tileIndex" list to
1392 store the local bi,bj indices of each tile;
1393 - also print bi,bj in local report to log file;
1394 - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
1395 Jun 2009 modif of pkg/exch2).
1396 o testing on baudelaire:
1397 - run 2 tests at a time: no significant slow down (since enough cpu) and
1398 get the full set of test done earlier
1399 - switch the ifort test to "-devel" ; run the OpenAD test everyday.
1400 o model/src/thermodynamics.F and routines called from it:
1401 - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
1402 gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
1403 velocity (outp) by adding bolus velocity.
1404 - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
1405 mass transport from velocity + lateral grid cell area
1406 - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
1407 - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
1408 in thermodynamics.F
1409 - remove k from thermodynamics.F and move it to temp_integrate.F
1410 salt_integrate.F and ptracers_integrate.F (now done inside the tracer
1411 loop).
1412 - compute locally (in thermodynamics.F) 3-D velocity field that is used to
1413 advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
1414 PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
1415 GAD_IMPLICIT_R and PTRACERS_IMPLICIT
1416 - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
1417 global_ocean.90x40x15, tutorial_global_oce_biogeo and
1418 tutorial_tracer_adjsens (+ TLM output).
1419 o tools/OAD_support and (verification/*/) code_oad:
1420 - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
1421 module conversion ; remove unneeded CPP_EEOPTIONS.h.
1422 - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
1423 version (closer to model/inc/CPP_OPTIONS.h).
1424 o model/src:
1425 - remove parameter "useOldFreezing" from PARAMS.h and push it to the
1426 retired list of parameters (routine FREEZE has been replace by surface
1427 freezing (10.yrs ago) and by pkg/frazil (interior freezing).
1428 o pkg/gmredi:
1429 - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
1430 velocity (same scheme but affects machine truncation) for GM_AdvForm.
1431 - update output of FWD experiments: front_relax.bvp,
1432 global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
1433
1434 checkpoint64q (2013/11/17)
1435 o verification:
1436 - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
1437 tutorial_global_oce_biogeo and global_ocean.90x40x15.
1438 - generate new output (growth & melt) for seaice_itd experiment after
1439 updating the input pickup_seaice files (previously wrong).
1440 o pkg/cost:
1441 - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
1442 (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
1443 o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
1444 cannot be applied to var in common block).
1445 o allows to get results independent of tile-per-proc setting (if using
1446 slower GLOBAL_SUM_SEND_RECV option).
1447 - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
1448 thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
1449 forward gradients: update output).
1450 - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
1451 S/R and, for most exp., also comment out GLOBAL_SUM_R8.
1452 o pkg/mom_common:
1453 - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
1454 code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
1455 viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
1456 ensure that all field value that are used are set.
1457 o tutorial_deep_convection (smag3d):
1458 - add missing scaling in mom_calc_smag_3d.F;
1459 - set smag3D_coeff in input.smag3d such that results do not change.
1460 o pkg/dic:
1461 - change dic_cost.F to compute cost on each tile first and then apply
1462 GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
1463 tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
1464 - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
1465 o eesupp/src & pkg/mdsio:
1466 - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
1467 (from pkg/mdsio) since they are no longer used for tape IO.
1468 - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
1469 (+ keep a copy in pkg/atm_ocn_coupler).
1470 o verification/isomip:
1471 - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
1472 o tools/build_options:
1473 - optfile linux_amd64_ifort11, fast (no ieee) case:
1474 to get a working restart for all experiments, add "-fp-model source"
1475 to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
1476
1477 checkpoint64p (2013/10/20)
1478 o pkg/autodiff:
1479 - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
1480 criteria, return to simple (default) tape IO format.
1481 o pkg/mdsio (+ eesupp/src):
1482 - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
1483 previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
1484 - fix globalFile and singleCpuIO options using simpler global mapping.
1485 - new pairs of scatter/gather vector S/R (one for each type, generated from
1486 template) corresponding to simpler global mapping.
1487 - adread_write.F: switch to new S/R (but leave old calls commented) and write
1488 to globalFile when parameter globalFiles is set to True.
1489 - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
1490 o pkg/autodiff:
1491 - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
1492 with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
1493 missing, just add a STOP if array type do not match.
1494 o pkg/exf:
1495 - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
1496 rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
1497 and rename array obsSIce to exf_iceFraction.
1498 o tutorial_deep_convection:
1499 - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
1500 for now all in this exp. code dir.
1501 - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
1502 testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
1503 o eesupp/src:
1504 - added SINGLE_DISK_IO option because reading of parameter files on
1505 very large number of processors did not work with existing set-up
1506
1507 checkpoint64o (2013/09/25)
1508 o pkg/atm_phys & atm_compon_interf:
1509 - allows for coupling of gray-atmosphere (atm_phys) with ocean.
1510 o tools/build_options:
1511 - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
1512 & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
1513 remove CPP setting (was identical to genmake2 default).
1514 o pkg/gmredi & model/src: Some updating and work done on the residual model.
1515 - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
1516 - fixed up the calculation of the eddy stress and how it is added to the
1517 external forcing via taueddy_external_forcing.F
1518 - at the moment, it is very experimental and only works with the variable eddy
1519 diffusivity calculated in gmredi_k3d.F
1520 o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
1521 lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
1522 o testreport (& tools/do_tst_2+2):
1523 - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
1524 o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
1525 - remove CPP='cpp -traditional -P' (this is genmake2 default)
1526 - add switch (for big setups) to use 'medium' memory-model (but leave it
1527 commented out for now). Note: needed with FC 19 to compile big setups.
1528 o pkg/atm_compon_interf:
1529 - regroup per field origin (model & pkgs) the coupling storage routines
1530 (which accumalate in time each coupling field)
1531 - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
1532 update accordingly + simplify aim_do_physics.F
1533
1534 checkpoint64n (2013/08/26)
1535 o pkg/bbl:
1536 - update formulation to reduce dispersion of tracer properties in bbl
1537 - replaced horizontal and vertical transport parameters with velocities
1538 - changes results for verification/global_with_exf.yearly
1539 o verification/halfpipe_streamice:
1540 - change to matrix construction; update both Fwd & AD output.
1541 o verification/tutorial_tracer_adjsens:
1542 - OpenAD test: switch to vector-invariant momentum since fluxform with
1543 rStar causes problems with OpenAD; update output.
1544 o tools:
1545 - genmake2: define a common prefix for all temp-file names ; move them
1546 to local /tmp disk (but would be easy to move them back);
1547 - xmakedepend: apply the same switch for temp-files.
1548 o pkg/offline:
1549 - changes for use with rStar (NLFS): assume that we continue to provide
1550 UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
1551 output files) and apply r* scaling at each time-step (function of the time
1552 varying Eta field); use normal pickup files (needed for restart with NLFS).
1553 o adjoint with OpenAD:
1554 - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
1555 package openad. This package has to be compiled for all runs with OpenAD
1556 instead of specifying code_oad_all as a modification directory.
1557 - link the fortran templates from tools/OAD_support to the build directory
1558 for preprocessing to avoid conflicts between different setups compiled
1559 simultaneously and simplify cleanup.
1560 o pkg/exf:
1561 - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
1562 main model or other pkgs are exchanged in EXF_MAPFIELDS).
1563 o model/src:
1564 - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
1565 (similar to do_fields_blocking_exchanges.F).
1566 o tools/genmake2:
1567 - remove TAF output src code just before calling staf (when not doing a fresh
1568 built, will stop if things go wrong with staf).
1569 - fix target "adobj" (left from TAF version-2 transition)
1570 o pkg/diagnostics:
1571 - add a parameter to track the status of pkg/diagnostics activation;
1572 this replace/extend the use of logical param "settingDiags" (to check
1573 when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
1574 New S/R to print error message and stop when pkgStatus is not right.
1575 - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
1576
1577 checkpoint64m (2013/08/13)
1578 o model/inc:
1579 - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
1580 8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
1581 o pkg/kpp & aim_v23:
1582 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
1583 o pkg/seaice:
1584 - restore (last time on 2011/12/24) ability to compile pkg/seaice with
1585 undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
1586 - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
1587 o eesupp/src:
1588 - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
1589 in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
1590 o switch to TAF version-2:
1591 - add flow directives to "freeze" naming convention for ad-routines that
1592 are used in I/O routines of adjoint state and associated common blocks
1593 that are used in adcommon.h (backward compatible with version-1)
1594 - update all ad-optfiles (in tools/adjoint_options + few local to some
1595 verification exp) to switch to latest TAF version (currently 2.5.5);
1596 merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
1597 out except for diva).
1598 - the major change with TAF version-2 is that both the differentiated
1599 routines and the forward routines (new) are returned as part of the TAF
1600 output source code. Update genmake2 accordingly.
1601 - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
1602 with version-2 when compared to TLM or FWD gradient); other experiments
1603 output show minor changes (machine truncation level); update the few AD &
1604 TLM output with 12 matching digits only (some prior to version-2 switch).
1605
1606 checkpoint64l (2013/08/05)
1607 o model/src:
1608 - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
1609 - main_do_loop.F: no longer includes additional (AUTODIFF) header files
1610 when using TAF but only if using OpenAD.
1611 o pkg/mom_common+fluxform+vecinv:
1612 - always set horiz. viscosity arrays to background value before calling
1613 MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
1614 only when using variable horiz. viscosity (useVariableVisc=T);
1615 - simplify mom_vecinv.F (only 1 block for momViscosity).
1616 o pkg/mom_common: variable horiz. viscosity in NH code
1617 - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
1618 from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
1619 - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
1620 useBiharmonicVisc & useVariableVisc.
1621 - fix old bug (already in 1rst implementation of variable horizontal viscosity
1622 in calc_gw.F, version 1.27, 2006/06/20):
1623 horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
1624 even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
1625 - change background horiz viscosity in vertical momentum (gW) to always be
1626 viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
1627 any type of variable viscosity, e.g., viscAh/4Grid)
1628 - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
1629 viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing
1630 horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
1631 default viscAh,viscA4 is zero).
1632 o model/src:
1633 - extend length of drC & recip_drC from Nr to Nr+1.
1634 o Divided Adjoint (DIVA) with MPI:
1635 - genmake2: do not create local ./mpi_headers dir when no file to copy into.
1636 - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
1637 and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
1638
1639 checkpoint64k (2013/07/23)
1640 o tools/OAD_support:
1641 - avoid the need for file "oadtempflile" in insertTemplateDir.bash
1642 and remove it from genmake2.
1643 o tools/build_options:
1644 - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
1645 MPI_HEADER_FILES list (let genmake2 find the missing headers)
1646 o verification/halfpipe_streamice:
1647 - change to driving stress formulation; update both Fwd & AD output.
1648 o tools/genmake2 and Divided Adjoint with MPI:
1649 - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
1650 - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
1651 - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
1652 Makefile, which is set by genmake2, and check which mpi-headers are needed.
1653 Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
1654 - update target "CLEAN" (to also remove ./mpi_headers/ dir).
1655 o testreport:
1656 - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
1657 perform additional runs (number of additional runs is "add_DIVA_runs" taken
1658 from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
1659 o verification/lab_sea (AD test):
1660 - change to test Divided Adjoint Run in this set-up (both standard AD test
1661 and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
1662 o pkg atm_ & ocn_compon_interf:
1663 - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
1664 staggerTimeStep implementation) and disable (retired) corresponding
1665 parameter.
1666 o pkg/offline:
1667 - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
1668 - add S/R OFFLINE_CHECK to print offline parameter summary
1669 and stop if loading a file that is not used;
1670 - enable to calculate GMRedi tensor, KPP mixing and convective index
1671 when the corresponding file(s) is/are not specified (but pkg is used).
1672 - comment out resetting of monitorFreq (to endTime) since it still useful
1673 for monitoring CFL numbers and checking offline fields.
1674 o OpenAD:
1675 - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
1676 smaller standard output) and generate new (smaller) output (on baudelaire
1677 using gfortran with -ieee) for exp. tutorial_tracer_adjsens
1678 o model/src:
1679 - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
1680 (where external_forcing_adjust was called) and change list of arguments;
1681 - merge external_forcing_adjust.F into external_forcing_surf.F
1682 - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
1683 which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
1684 previously in file "balance_relax.F", now removed); remove corresponding
1685 arrays in FFIELDS.h.
1686 - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
1687 a hack for getting back surfaceForcingS (loaded from file) when using
1688 ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
1689 - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
1690 (was getting only 11 digits for AD-grad, due to different truncation
1691 error in AD code).
1692
1693 checkpoint64j (2013/07/04)
1694 o pkg/offline:
1695 - to enable the use of other features with pkg offline (e.g., obcs),
1696 also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
1697 - comment out "allowFreezing" (now active) in 2 offline testing exp.
1698 o pkg/exf ALLOW_RUNOFTEMP
1699 - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
1700 - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
1701 - changes verification/global_ocean.cs32x15/results/output.seaice.txt
1702 o pkg/atm_phys:
1703 - allows to add some damping on uVel,vVel (strength only function of k).
1704 o verification, ad-tests:
1705 - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
1706 global_ocean_ebm and offline_exf_seaice.thsice.
1707 o verification/halfpipe_streamice:
1708 - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
1709 flux input boundary conditions to be ignored; a fix for this bug changed
1710 verification results for forward test.
1711 - add adjoint test.
1712 o pkg/ptracers:
1713 - allow to restart without SOM pickup (resetting SOM to zero).
1714 o pkg/gmredi:
1715 - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
1716 - It uses mixing length theory and suppression by steering level effects to
1717 calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
1718 to JPO, for more details).
1719 - It also uses the diffusivity to calculate an eddy induced streamfunction
1720 based on a PV closure (rather than a buoyancy closure as in GM).
1721 - New files added to pkg/gmredi:
1722 gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
1723 induced overturning streamfunction (called from gmredi_calc_tensor)
1724 gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
1725 for use in gmredi_k3d
1726 gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
1727 the eddy diffusivity
1728
1729 checkpoint64i (2013/06/18)
1730 o pkg/cheapaml:
1731 - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
1732 that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
1733 with pkg/cheapaml.
1734 o utils/python: add subpackage for cubed sphere function, first example is
1735 simple cs.pcol to plot 2D fields on a map
1736 o pkg/streamice:
1737 - This is a new package in MITgcm, which solves dynamic equations for ice
1738 sheets and ice streams
1739 - At the moment it is independent of atmosphere/ocean dynamics, or any
1740 other physical packages in MITgcm, even ShelfIce (although it is anticipat-
1741 ed that this will change)
1742 - There is a new verification exercise that tests it, halfpipe_streamice,
1743 evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
1744 rectangular embayment
1745 - halfpipe_streamice is forward-only for now, will have TAF test soon
1746 - for questions, email dgoldber@mit.edu
1747 o pkg/thsice:
1748 - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
1749 of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
1750 - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
1751 call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
1752 - allow precip from pkg/cheapaml to make snow over seaice.
1753 o pkg/cfc:
1754 - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
1755 - remove atmos CFC 2-D arrays from common bloc (now local variables)
1756 - change some hard-coded constant to run time parameter for reading and
1757 and interpolating atmospheric CFC ; keep same default as previously.
1758 - more flexible reading of Atmos CFC (number of records no longer hard-coded)
1759 - put arguments in standard order: myTime, myIter, myThid
1760 - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
1761 atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
1762 - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
1763 - new routine to print summary of CFC params and check for consistency.
1764 o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
1765 similar to thsice_advdiff.
1766 Note that for the B-grid case the routine parameters uc/vc are overwritten.
1767 o pkg/cfc:
1768 - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
1769 update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
1770 - fix interpolation of atmphspheric CFC between Sorthern and Northern
1771 hemisphere value.
1772 o pkg/seaice:
1773 - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
1774 o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
1775 so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
1776 - requires an additional time level that is stored in the pickup
1777 - you can start with AB2 from a pickup without this time level with
1778 pickupStrictlyMatch = .false.
1779
1780 checkpoint64h (2013/05/26)
1781 o pkg/cheapaml:
1782 - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
1783 affect machine truncation (but exp cheapAML_box still pass with 13 digits).
1784 - consistent treatment of uWind,vWind location: assume everywhere in
1785 pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
1786 (Note: was already the case for Tair,Qair advection);
1787 add option (INCONSISTENT_WIND_LOCATION) to recover old results.
1788 - compute diabatic forcing only in the interior (excluding overlap regions)
1789 - fill in array "Qsw" (for short-wave heating);
1790 - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
1791 before any update (consistent with MITgcm state var diagnostics);
1792 - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
1793 non periodic ; + adjusted for uWind,vWind (C-grid).
1794 o pkg/seaice:
1795 - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
1796 add explicitly pkg/exf in experiments that currently use pkg/seaice.
1797 - allows to compile pkg/seaice without pkg/exf.
1798 o tools/OAD_support:
1799 - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
1800 of array "ourStepOf" in function rvNextAction (revolve.F90).
1801 o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
1802 - change pkg name (to be used with other atmospheric physics pkg)
1803 but by-pass CVS when making the new pkg so that we keep the CVS history.
1804 o pkg/offline:
1805 - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
1806 (previously called from pkg/dic_surfforcing_init.F)
1807 o model/src:
1808 - re-order sequence of calls within packages_init_variables.F, using
1809 standard order, except for:
1810 DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
1811 CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
1812 o new pkg: atm_phys
1813 - add entry point and source code (previously in contrib
1814 verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
1815 (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
1816 - re-order sequence of calls within packages_readparms.F,
1817 packages_init_fixed.F and packages_write_pickup.F
1818 (but skip packages_init_variables.F because of TAF issues).
1819 - update contrib/*/atm_gray/ experiment.
1820 o pkg/seaice (ITD code):
1821 - simplify and fix the writing of pickup-files for ITD case
1822 o pkg/seaice (ITD code):
1823 - introduce floe size dependent lateral melt for ITD case;
1824 - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
1825 - update seaice_itd experiment main output.
1826 o pkg/thsice:
1827 - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
1828 declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
1829 changed accordingly pkg/atm2d.
1830
1831 checkpoint64g (2013/05/01)
1832 o pkg/exf ALLOW_RUNOFTEMP
1833 - if defined, river and glacier runoff temperature can be read-in from
1834 runoftempfile; runoftempfile needs to have same format as runofffile
1835 o pkg/thsice (& pkg/bulk_force):
1836 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
1837 for energy content of Precip + RunOff & Evap (like with pkg/exf).
1838 - change computation domain to always be the interior (without overlap).
1839 - fix bug (wrong overlap) when using EXF and stressReduction > 0.
1840 o verification/tutorial_global_oce_biogeo:
1841 - add preliminary OpenAD setup (still has problems)
1842 o pkg/seaice:
1843 - turn some parameters for choosing the convergence criterion of
1844 the inexact Newton method (JFNK) into runtime parameters for convenience
1845 - clean up seaice_calc_viscosities.F: remove/retire two options for
1846 SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
1847 the results of lab_sea/input because a division has been replaced by
1848 a multiplication with the reciprocal (sumNorm)
1849 - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
1850 convergence of solver (changes results, of course), and to test some
1851 new features
1852 o model/src:
1853 - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
1854 - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
1855 - move forcing adjustment (balancing surface forcing) in specific S/R
1856 where might also be applied exchanges (if needed) to forcing arrays.
1857 o pkg/shelfice:
1858 - allow to specify the Ice-Shelf mass per unit area (instead of
1859 shelficeLoadAnomaly) and do the conversion from one to the other
1860 - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
1861 to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
1862 (b) will be loaded in time (before calling INI_PRESSURE) in case it is
1863 needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
1864 - update isomip experiment forward output (get machine truncation error
1865 from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
1866 o verification/offline_exf_seaice:
1867 revise data.seaice in input.thermo and input_ad and update results accordingly
1868 HO = 0.2, SEAICE_areaLossFormula = 2,
1869 SEAICE_growMeltByConv = .TRUE.,
1870 SEAICE_doOpenWaterMelt = .TRUE.,
1871 Improve consistency with input.thsice and fix the spurious 500m ice corners
1872 o verification/global_ocean.cs32x15:
1873 - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
1874 in icedyn (thsice+seaice-dyn) test and update output.
1875 o verification/offline_exf_seaice:
1876 - adjust list of tested variables (with testreport) and update
1877 standard test output with better slection of monitored fields.
1878 o pkg/cd_code:
1879 - swtich off Adams-Bashforth on the 1rst iteration. Update output of
1880 experiment lab_sea.hb87
1881 o tools/genmake2:
1882 - change default makedepend from the system default to tools/xmakedepend:
1883 When no makedepend is specified, select tools/xmakedepend it the test pass,
1884 otherwise select the system default (if exist and pass the test) or
1885 try to build cyrus-makedepend ; stop if none of the 3 works.
1886 o pkg/exf & pkg/thsice:
1887 - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
1888 for energy content of Precip + RunOff & Evap. Assumes:
1889 1) Rain has same temp as Air.
1890 2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
1891 3) Run-Off comes at the temp of surface water (with same Cp)
1892 4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
1893 put directly into Latent Heat flux & should use water-vapor heat capacity.
1894 5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
1895 with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
1896 o pkg/seaice: simplify the use of CPP flags in JFNK-related files
1897 (compile when SEAICE_ALLOW_JFNK is defined)
1898 o pkg/thsice:
1899 - fix oceanic flux diagnostics & timeave (left from new sequence of calls
1900 implementation): move THSICE_AVE call after the advection (called directly
1901 from thsice_do_advect.F).
1902 o verification/global_ocean.90x40x15 and OpenAD:
1903 New experiment for OpenAD is identical to the one in input_ad except that
1904 multiDimAdvection=.FALSE.,
1905 There is still an issue with this.
1906 o pkg/thsice:
1907 - account for ice velocity (ocean relative velocity) in turbulent heat flux
1908 at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
1909 and offline_exf_seaice (main test).
1910
1911 checkpoint64f (2013/03/31)
1912 o verification/OpenAD:
1913 - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
1914 o verification/isomip, pkg/shelfice and OpenAD:
1915 - add OpenAD setup to this exp and make shelfice package work with OpenAD
1916 o verification/tutorial_global_oce_biogeo:
1917 - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
1918 o verification/offline_exf_seaice:
1919 - replace adjoint experiment (now similar to fwd input.thermo/ setup).
1920 o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
1921 - add OpenAD setup to this exp and make ptracers package work with OpenAD
1922 o pkg/seaice/seaice_evp.F:
1923 mask the asymmetric contribution of the ice-ocean stress (when
1924 the turningAngle is non-zero) over open water to avoid stripes
1925 in the EVP-solutions after many EVP-substeps. This does not change
1926 the verification experiment (because turningAngle=0 in that experiment),
1927 but will affect other EVP solutions with turningAngle.ne.0
1928 o verification, AD & TLM output:
1929 - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
1930 additions and multiplications which affect results at machine truncation
1931 level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
1932 lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
1933 (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
1934 digits of matching.
1935 o pkg/seaice:
1936 modify lsr-algorithm so that it vectorizes AND converges by using a
1937 "zebra" method: split vector loop into two with step size 2; this
1938 solves a general convergence problem for the JFNK solver on a vector
1939 computer. It has the potential to even improve convergence for
1940 non-vector machines, but it does change the results so it is turned
1941 off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
1942 SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
1943
1944 checkpoint64e (2013/03/05)
1945 o pkg/ecco and several verification experiments:
1946 Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
1947 from ecco package, and revert to unified routine in model/src/
1948 Adjust verification experiments accordingly, especially gloal_oce_llc90
1949 Should conclude long-standing work by Gael to reconsile the_main_loop with
1950 ECCO and will enable OpenAD's revolve loop in ECCO setup.
1951 o pkg/generic_advdiff:
1952 - implement compressible flow method for multi-dim advection (similar to
1953 gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
1954 TAF generates many recomputations) to use it; no yet coded with implicit
1955 vertical advection.
1956 - change experiment advect_cs (new output) and advect_xy (same output)
1957 to test compressible flow multi-dim advection.
1958 o pkg/generic_advdiff:
1959 - fix SOM advection for unusual cases (linear Free-Surf in r*, other
1960 cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
1961 o pkg/seaice:
1962 - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
1963 bug affects two verification experiments (lab_sea and lab_sea.hb87),
1964 recover old (wrong) results by setting noSlipFac = 2. in
1965 seaice_calc_strainrates.F;
1966 - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
1967 - add runtime parameter SEAICE_JFNKepsilon for that finite difference
1968 gradient in the Jacobian times vector operation (s/r seaice_jacvec)
1969 - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
1970 o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
1971 - new subroutines seaice_lsr_tridiagu/v
1972 - introduce loop bounds i/jmin/max to be able to use a restricted
1973 additive Schwarz method, but not used for now.
1974 - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
1975 - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
1976 o OpenAD support
1977 Reorganize S/R call for overall time-stepping loop to facilitate
1978 OpenAD revolve loop replacement
1979 (new S/R main_do_loop.F)
1980 o model/src:
1981 - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
1982 - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
1983 ADAMS_BASHFORTH2.
1984 o pkg/cheapaml:
1985 - add new parameter (default=F, same as before) to disable full domain
1986 (including land) periodicity in X & Y dir.
1987 - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
1988 prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
1989 into single S/R CHEAPAML_TIMESTEP.
1990
1991 checkpoint64d (2013/02/17)
1992 o pkg/monitor (angular momentum):
1993 - do not add Eta contribution to the total AM if using rigid-lid;
1994 - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
1995 - horizontal discretisation: compute Zonal wind contribution separately for
1996 each component (instead of from cell centered averaged) and use the 4
1997 grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
1998 - Check that AM is conserved with linear dynamics (momAdvection=F and linear
1999 FreeSurf) if using vectorInvariant momentum.
2000 o model/src (horizontal grid):
2001 - move initialisation of all horizontal grid arrays to null value
2002 from specific horizontal grid S/R to main S/R INI_GRID;
2003 - add 2 new arrays to project model C-grid velocity on to zonal direction
2004 (similar to AngleCosC & -AngleSinC but at U and V point location) and
2005 compute them in S/R CALC_GRID_ANGLES.
2006 o pkg/seaice: replace a hard coded parameter by a runtime parameter
2007 SEAICE_JFNK_tolIter
2008 o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
2009 preconditioner for JFNK (run LSR into the overlaps as far as possible,
2010 i.e OLx/y-2, but overwrite the solution in the overlaps)
2011 - extend loop range in seaice_calc_viscosity
2012 - add new parameters SEAICE_OLx/y (default = OLx/y-2)
2013 - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
2014 - slightly modify loops in tridiagonal solver lsr-preconditioner
2015 - by default remove the extra exchange in seaice_preconditioner with a
2016 replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
2017 - modify offline_exf_seaice so that old results without RAS are reproduced
2018 for output.dyn_jfnk.txt
2019 in seaice_fgmres.F (unrelated to RAS)
2020 - add a cpp-flag option for a re-ordered mapping (potentially more
2021 efficient), but because this changes the results, turn it off by
2022 default
2023 - replace the save statement by local common blocks
2024 o utils/matlab:
2025 - fix tile-offset in rdmnc.m when output was produced using EXCH2.
2026 - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
2027 instead of local script "load_cs.m".
2028 o pkg/seaice:
2029 - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
2030 to the scalarProductMetric and the unrolling. By chance this does not
2031 change the verification experiment, because of the particular domain
2032 decomposition
2033 o pkg/diagnostics:
2034 - change default missing_value from UNSET_RL to -999.
2035 o pkg/layers: improve vectorization of layers_fluxcalc.F
2036 - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
2037 time spent in this routine by more than a factor of 3 on an NEC-SX8
2038 - step 2: replace search algorithm by a bisection algorithm found in
2039 Press et al. Numerical Recipes in Fortran. This algorithm can be
2040 vectorized and finds the correct bin in approx. log2(Nlayers) steps.
2041 For now, use this algorithm only for TARGET_NEC_SX defined.
2042 - moved the search algorithm into a separate subroutine, that is kept
2043 within the same file for automatic inlining.
2044 - modified catching potential errors
2045 o pkg/ecco:
2046 - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
2047 o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
2048 - modifications for ALLOW_GENTIM2D_CONTROL
2049 -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
2050 -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
2051 -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
2052 -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
2053 o model/src:
2054 - account for moist thermodynamics in (dry) potential temperature equation;
2055 update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
2056 and cpl_aim+ocn.
2057 - also switch to standard compiler (gfortran, was using ifort previously)
2058 for fizhi-cs experiments reference output.
2059 o pkg/ctrl:
2060 - 1st step toward generic time-varying control variable (2D) via CPP option
2061 ALLOW_GENTIM2D_CONTROL
2062 - note new namelist ctrl_nml_genarr in data.ctrl
2063 o verification/global_ocean.cs32x15:
2064 - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
2065 thsice calling sequence and update "output.icedyn.txt" output file.
2066 o pkg/ptracers:
2067 - from Ryan A.: code to allow to restart a tracer at regular time interval
2068 specifying a reset frequency and a reset-phase (for each tracers).
2069 o pkg/thsice:
2070 - implement new sequence of calls for thsice+seaice:
2071 previously: ice-Dyn,ice-Advect,ice-Thermo(thsice)
2072 new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
2073 - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
2074 in CPP_OPTIONS.h) to recover old sequence;
2075 - update diagnostics for Intermediate State thsice diagnostics: now filled
2076 just before advection (instead of just after advection in old sequence);
2077 - update output of experiment offline_exf_seaice (standard test);
2078 - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
2079 by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
2080 o pkg/aim_v23:
2081 - use tiled array for aim_CO2 and surface wind speed for export to coupler;
2082 - use standard pkg/mdsio routines to read & write CO2 pickup file;
2083 - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
2084 - Implement new sequence of calls for seaice advection (with thsice and
2085 seaice diffusion): do ice advection after ice-Thermodynamic (previously
2086 was done before); change aim_do_physics.F (split the bi,bj loops block);
2087 - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
2088 o pkg/thsice:
2089 - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
2090 where just seaice diffusion is used without seaice-dynamics.
2091
2092 checkpoint64c (2013/01/18)
2093 o pkg/seaice:
2094 - add a parameter JFNKres_tFac that can replace JFNKres_t
2095 (= JFNKres_tFac*JFNKresidual before JFNK solver)
2096 - add a line search option to the JFNK solver
2097 - move update of u/vIce and computation of initial residual into a separate
2098 routine (same file); makes the code a little easier to read (?)
2099 - the line search requires computation of the residual and for some reason
2100 I cannot do the update of u/vIce at the beginning of the Newton loop
2101 without changing the results, so we move computation of the new residual
2102 also to the end of the Newton loop, even without the line search
2103 o pkg/mdsio:
2104 - write missing value (corresponding to undefined array value) to meta files;
2105 skip this if missing value is one (UNSET_RL would be a better value for the
2106 case of undefined missing value but it's current the default missing-value);
2107 Also update mdsio_read_meta.F (reading timeInterval & missing-value).
2108 o pkg/exf & thsice:
2109 - for diagnostics purpose, fill-up and update Qsw array (+ fill the
2110 diagnostics) even when SHORTWAVE_HEATING is #undef;
2111 o verification/cfc_example:
2112 - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
2113 illustrate how to use it).
2114 o verification/offline_exf_seaice:
2115 in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
2116 files to only one time-record.
2117 in input.thermo: narrow the 2 bands of low initial ice-concentration near
2118 N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
2119 snapshot output; same mcPheePiston value as in thsice with
2120 surf-current=0.2m/s.
2121 in input.thsice: similar set-up as in input.thermo (channel with same seaice
2122 initial conditions).
2123 o verification/cfc_example:
2124 - update file "data" with more standard choice (default rotationPeriod,
2125 exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
2126 set deltaTFreeSurf to deltaTtracer) and update the output.
2127 o pkg/layers:
2128 - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
2129 - ensure that "layers_bolus" is switched to False when useGMRedi=False.
2130 o verification/offline_exf_seaice:
2131 - set all {field}period to zero for constant-in-time forcing (not tested
2132 anywhere else).
2133 o verification/offline_exf_seaice:
2134 - dyn_lsr : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
2135 - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
2136 o model/src:
2137 - implement Finite-Volume method for (hydrostatic) presure gradient
2138 from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
2139 o pkg/seaice: implement EVP* by Lemieux et al. (2012).
2140 - In order to be compatible with the default EVP code, this requires changing
2141 the EVP code around a little; and because any small change immediately
2142 breaks the lab_sea.hb87 verification experiment, the reference output is
2143 updated two times (each time the remaining aggrement was only 2 digits):
2144 - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
2145 - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
2146 The adjoint test lab_sea.evp also needed to be updated.
2147 - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
2148 SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
2149 a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
2150 explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
2151 INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
2152 kept obscure, because I need to test it a little more.
2153 o pkg/cheapaml:
2154 - fix few incorrect type (_RL/_RS) in subroutine calls.
2155 o pkg/seaice:
2156 - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
2157 to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
2158 o model/src:
2159 - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
2160 change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
2161 experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
2162 o pkg/cheapaml:
2163 - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
2164 update output of experiment cheapAML_box.
2165 - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
2166 and set them only in one place (cheapaml_readparms.F).
2167 - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
2168 - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
2169 and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
2170 o model/src/the_main_loop.F:
2171 - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
2172 o pkg/seaice:
2173 - remove legacy branch code.
2174 - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
2175 o verification/*/code*/SEAICE_OPTIONS.h:
2176 - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
2177 SEAICE_CAP_HEFF).
2178 o pkg/cheapaml:
2179 - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
2180 to load new forcing fields.
2181 - add missing "_d 0" where it's needed; + some editing (improve indentation).
2182 - remove switch to "-r8" compiler option (no longer needed) in verification
2183 cheapAML_box, keep same output (small trucation error differences).
2184 o verification/offline_exf_seaice:
2185 - add thermodynamics only test.
2186 o verification/cheapAML_box:
2187 - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
2188 keep same output (same 14 digits for cg2d).
2189 - switch on "-r8" compiler option (some numerical values are missing
2190 the "_d 0") and update output (only 6 digits for cg2d were preserved).
2191
2192 checkpoint64b (2012/12/24)
2193 o pkg/cheapaml:
2194 - remove un-used variables (Qnet,EmPmR) from pickup files.
2195 - store tendency of advected variables into cheapaml pickup file
2196 and fix the AB-2 restart.
2197 o verification/offline_exf_seaice and lab_sea adjoint:
2198 - switch to new code (#undef SEAICE_GROWTH_LEGACY).
2199 - switch to 4 time steps in offline, consistent with lab_sea.
2200 - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
2201 - update results after change of experiment seaice.
2202 o pkg/seaice:
2203 - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
2204 parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
2205 still defined since SEAICE_multDim needs to be set to MULTDIM value (from
2206 SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
2207 o model/src:
2208 - add run-time parameter to select CG2D solver minimum-residual solution
2209 (in case of a poor convergence).
2210 o pkg/seaice/seaice_lsr.F
2211 - move calculation of matrix coefficients into new
2212 S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
2213 file; the main purpose of this change is to be able to reuse the code
2214 in S/R SEAICE_PRECONDITIONER
2215 - modify the computation of the residual so that the mass of sea-ice
2216 is not used twice; this simplifies the calculations, but since
2217 the residual is never used except when LSR_mixIniGuess.ge.4---and this is
2218 not tested in testreport---this does not affect the testreport results.
2219 o verification/seaice_obcs:
2220 - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
2221 verification/lab_sea/input.salt_plume; changes results/output.txt*
2222 o model/src:
2223 - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
2224 o pkg/seaice:
2225 - improve description of parameters in seaice_fgmres.F and start
2226 cleaning up the code
2227 - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
2228 second argument
2229 - add a metric based on grid cell area to SEAICE_SCALPROD; update
2230 results of offline_exf_seaice.dyn_jfnk
2231 - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
2232 o pkg/aim_v23:
2233 - fix an other bug in dissipation heating (grid-cell area was missing).
2234 o model/src + pkg/seaice:
2235 - add global (multi-tile) linear solver for pair of tri-diagonal system
2236 along X and Y lines, respectively for U and V component.
2237 Note: 1) MPI and cube-exchange not yet coded.
2238 2) probably not accurate for poorly conditioned / large size problem.
2239 - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
2240 default: not compiled and not used.
2241 o pkg/seaice:
2242 - first attempt at a multi-threaded fgmres solver for the JFNK solver:
2243 introduce bi/bj loops and use global_sum_tile_rl instead of
2244 mpi_allreduce in seaice_fgmres.F
2245 - improve diagnostics output for fgmres solver (seaice_fgmres.F)
2246 - replace a few unnecessary goto statements by if-blocks (seaice_fgmres.F)
2247 - add a verification experiment for JFNK in offline_exf_seaice
2248 o verification:
2249 - change (for now, only fwd test) offline_exf_seaice experiment:
2250 use a re-entrant channel with idealized coastline (trapezoidal shape)
2251 at southern boundary to explore seaice dynamics and thermodynamics
2252 with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
2253 secondary test (input.thsice) use thermodynamics only with SST relaxation.
2254 - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
2255 o pkg/exf:
2256 - disable "sstExtrapol" when Nr=1
2257 o verification:
2258 - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
2259 to test pkg/cheapaml.
2260 o pkg/aim_v23 & pkg/shap_filt:
2261 - fix dissipation heating (erroneous gravity multiplication factor).
2262 o pkg/seaice:
2263 - remove unused field pressPre from jfnk solver
2264 - rename two subroutines in seaice_preconditioner.F
2265 o eesupp/src:
2266 - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
2267 o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
2268 - remove wrong parts of the rhs and the lhs (were in there
2269 because I did not understand the concept of this preconditioner)
2270 - add an exchange between u- and v-sweep. This increases communication
2271 by a factor of two but improves the convergence of jfnk. Ideally,
2272 one would like the u- and v-sweep to be independent. So far within
2273 undocumented ifdefs
2274 - reorganize the extra computations for printing the residuals
2275 o tools/genmake2:
2276 - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
2277 since it's not necessary (and was preventing to use MNC in some cases).
2278
2279 checkpoint64a (2012/11/16)
2280 o pkg/autodiff:
2281 - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
2282 autodiff_readparms.F no longer depends on calling order (within
2283 packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
2284 rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
2285 and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
2286 o pkg/obcs:
2287 - adding tidal velocity forcing capability to obcs
2288 for usage example, see verification/seaice_obcs/input.tides
2289 o pkg/seaice:
2290 - turn the LSR-relaxation parameters WFAU/V into runtime parameters
2291 SEAICE_LSRrelaxU/V
2292 - introduce runtime parameter SEAICEetaZmethod (=0 by default)
2293 o pkg/aim_v23:
2294 - implement heating from friction (bottom friction and stratospheric drag).
2295 o pkg/shap_filt:
2296 - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
2297 dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
2298 o model/src:
2299 - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
2300 time-constant addMass field from file (addMassFile);
2301 - support for heating due to friction (and Kinetic Energy dissipation):
2302 add option, run-time switch and 3-D field array + support code ; each pkg
2303 or S/R can add heating contribution (if there is a sink of KE); the sum is
2304 accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
2305 o pkg/seaice:
2306 - complete merge of ITD code into seaice_growth.F
2307 from MITgcm_contrib/torge/itd/code/
2308 no verification so far, but Torge Martin tested
2309 "1-D test case and Beaufort set up;
2310 deliver okay results after 1 model year."
2311 - complete merge of SEAICE_SIZE.h into all relevant routines
2312 - move computation of eta at Z-points into calc_viscosities
2313 + introduce global field etaZ
2314 + add different methods for computing etaZ, for now the old
2315 method (simple averages of eta to Z-points) is hardwired
2316 + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
2317 seaice_preconditioner
2318 - simplify computations for SEAICE_ZETA_SMOOTHREG
2319 - seaice_preconditioner:
2320 + replace one remaining press by pressLoc (mistake)
2321 + adjust printing of residuals
2322 - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
2323 + add (SEAICE.h) and rename some counters (initiliased in
2324 seaice_init_fixed.F)
2325 + add _BEGIN/END_MASTER (myThid) around print statements
2326 + print total number of iterations and failures over SEAICE_monFreq
2327 interval to STDOUT
2328 - move control over output-messages by fgmres to seaice_jfnk to save
2329 some operations
2330 - move resetting initial guess for fgmres outside of seaice_fgmres_driver
2331 in order to make restarts with sol .ne. zero (fgmres with restarts)
2332 (seaice_jfnk.F, seaice_fgmres.F)
2333 - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
2334 a serious convergence problem when open boundaries are involved
2335 o pkg/ggl90: fix computation of control volumes for the case of
2336 ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
2337 up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
2338 o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
2339 o pkg/autodiff
2340 - Add inAdMode switch for SEAICEuseDYNAMICS:
2341 SEAICEuseDYNAMICSinAdMode
2342 (extend logic in ADAUTODIFF_INADMODE_SET)
2343 o pkg/seaice
2344 - Step 1 of merging ice-thickness distribution (ITD) code from
2345 MITgcm_contrib/torge/itd/ (author: Torge Martin)
2346 The code implements concept laid out in Thorndike et al. (1975);
2347 code is enabled via CPP flag SEAICE_ITD
2348 nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
2349 code is not complete yet!!
2350 - SEAICE_SIZE.h now included in almost all seaice routines
2351 o verification (using seaice):
2352 - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
2353 global_ocean.cs32x15.seaice ; update results.
2354 - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
2355 - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
2356 offline_exf_seaice (previously compiling B-grid).
2357 o pkg/exf:
2358 - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
2359 to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
2360 forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
2361 o pkg/layers (adjust changes from Sept 19):
2362 - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
2363 this allows to remove "layers_maxNum" dimension from all layers arrays.
2364 o pkg/layers (adjust changes from Sept 19):
2365 - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
2366 - snap-shot extended to all type of layers (not just the 1rst type);
2367 - remove layers variables when corresponding CPP option is undef.
2368 o pkg/layers:
2369 - rename pkg/layers variable and add new output (layer exist & un-weighted
2370 velocity in layer)
2371 o pkg/seaice:
2372 - simplify (?) ocean-drag coefficent computations by using
2373 the same routine in all three solvers (saves some code lines)
2374 - remove global fields DRAGA and DRAGS from C-grid code and
2375 declare them locally in lsr.F (the only place where they are
2376 still used)
2377 - update AD output of lab_sea.evp (very sensitive anyway).
2378 o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
2379 (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
2380 and SEAICEuseJFNK=.true. A few things to note:
2381 - involves a FGMRES, that is parallel but very inefficient,
2382 because of many scalar products (global sums) in the Gram-Schmidt
2383 orthogonalization method. Needs to be replaced. Original code
2384 from J.-F. Lemieux
2385 - preconditioner for FGMRES is a stripped down version of LSOR
2386 - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
2387 preconditioner. For the preconditioner, the default is set to 10.
2388 - Jacobian times vector is computed with finite differences
2389 - marginally related to JFNK-solver: add a smooth regularization for
2390 zeta with tanh that will improve convergence (Lemieux and Tremblay,
2391 2009) for any implicit solver (not implemented for EVP because EVP
2392 does not need this regularization in the first place). Define
2393 SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
2394 o eesupp/src:
2395 - check in genmake2 that intrinsic S/R flush is available.
2396 - add S/R to flush IO unit (if intrinsic S/R flush is available)
2397 - flush standard & error msg unit before MPI termination
2398 - if debugMode, flush IO unit after printing msg
2399 o pkg/ctrl:
2400 - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
2401 to ctrl_set_unpack_xyz.
2402
2403 checkpoint64 (2012/10/09)
2404 o pkg/shelfice
2405 - in mom_fluxform.F, mom_vecinv.F:
2406 CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
2407 Bug fix KappaRU -> KappaRV
2408 does not change verification/isomip but may change other setups
2409 (presumably constant KappaRU=KappaRV)
2410 - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
2411 o pkg/obcs:
2412 - fixed some indexing bugs in obcs_seaice_sponge.F
2413 - added obcs relaxation subroutines for HSALT and HSNOW
2414 - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
2415 o pkg/seaice:
2416 - add "multicategory" parameterization for snow in analogy to ice,
2417 default is off for now.
2418 o pkg/obcs:
2419 - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
2420 see verification/seaice_obcs/input.seaiceSponge for example application.
2421 - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
2422 index setting by master-thread. This fix multi-threads Pb in previous modifs.
2423 o pkg/layers :
2424 - add diagnostics to pkg/layers
2425 - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
2426 (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
2427 o pkg/generic_advdiff/gad_implicit_r.F :
2428 - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
2429 o pkg/seaice/seaice_growth.F:
2430 - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
2431 o pkg/obcs:
2432 - change default setting of OBCS_UVICE_OLD from defined to undef;
2433 - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
2434 in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
2435 - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
2436 - change OB null index value (OB_indexNone) to -99 ; this fix the problem
2437 with Southern & Western OB at a tile edge (at least in a simple set-up).
2438 o pkg/obcs:
2439 - change settings of OB index in case OB coincides with tile edge (shared by
2440 2 tiles), so that common OB location is registered by both tiles (instead of
2441 only 1). However, for Southern and Western OB, index value = 0 is not
2442 recognized as valid OB index (=default null value) and needs to be fixed.
2443 - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
2444 - new parameter "OB_indexNone" for null index value (for now, still zero)
2445 to replace hard-coded null index value of zero.
2446 o pkg/exch2:
2447 - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
2448 always check buffer-size (but outside the loop); move checking for valid
2449 index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
2450 print each tile and point connection only if |W2_printMsg|>= 2 and 3.
2451 o pkg/ctrl (pack & unpack):
2452 - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
2453 (locally defined) for different variables (+ remove the variable-specific
2454 file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
2455 (to be extended to other local file names in ctrl.h).
2456 o pkg/flt:
2457 - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
2458 o pkg/mdsio:
2459 - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
2460 o tools/genmake2:
2461 - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
2462 (added by Alistair in version 1.51 for building without make depend);
2463 - remove Header files list (H_SRC_FILES) from the dependence of targets
2464 ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
2465 place in version 1.23): this save going through staf when unrelated header
2466 file has been modified.
2467 Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
2468 "make depend" step, still need to do "make links" before "make adtaf".
2469 o eesupp/src (+ few pkg src files) & genmake2:
2470 - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
2471 - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
2472 - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
2473 upper/lower case ; account for space between "#" and undef/define)
2474 o pkg/flt (with exch2):
2475 - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
2476 - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
2477
2478 checkpoint63s (2012/09/05)
2479 o pkg/ecco:
2480 - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
2481 - add more relevant #ifdef ALLOW_SMOOTH ones.
2482 - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
2483 o pkg/ctrl:
2484 - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
2485 ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
2486 - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
2487 doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
2488 ctrlSmoothCorrel3D (new).
2489 The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
2490 - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
2491 - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
2492 controls when useAtmWind, and vice versa.
2493 - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
2494 - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
2495 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
2496 - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
2497 #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
2498 - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
2499 replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
2500 o pkg/smooth:
2501 - remove un-necessary includes.
2502 - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
2503 Those CPP options were never defined, and not necessary.
2504 o model/src:
2505 - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
2506 - standard treatment of useSMOOTH.
2507 o pkg/autodiff:
2508 - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
2509 useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
2510 o pkg/exch2:
2511 - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
2512 + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
2513 - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
2514 and tiles to process mapping.
2515 - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
2516 moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
2517 rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
2518 from w2_eeboot.F to w2_readparms.F.
2519 o eesupp/src:
2520 - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
2521 ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
2522 also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
2523 - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
2524 is defined (remove condition on usingMPI) to match cases where MPI_INIT
2525 has been called.
2526 - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
2527 - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
2528 (so that on 1 proc, get same myPid independently of usingMPI)
2529 - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
2530 useCubedSphereExchange with EXCH-1 (safer).
2531 - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
2532 o pkg/ggl90:
2533 - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
2534 used in ALLOW_GGL90_SMOOTH code.
2535 o pkg/flt:
2536 - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
2537 floats at the Southern end of the domain).
2538 o eesupp/inc:
2539 - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
2540 but not used (and not to be used) anywhere, just for documentation.
2541 o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
2542 - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
2543 a) can damage previously written records in any other multi-record files.
2544 b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
2545 o tools/genmake2:
2546 - define variable MAKE within Makefile and use it in place of 'make';
2547 - update AD_CONFIG.h (if needed) before building any of the executable
2548 (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
2549 and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
2550 - always print usual warning comment 'this file is automatically generated'
2551 from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
2552 o pkg/cheapaml:
2553 - updated to correspond to the code used in accepted paper (Nico Wienders).
2554 o pkg/exf:
2555 added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
2556 ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
2557 and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
2558 o pkg/exf, autodiff, ctrl, ecco and seaice:
2559 remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
2560 o pkg/ctrl, ecco:
2561 allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
2562 Depending on useAtmWind, one is inactive, and the other is active (see
2563 exf_getffields.F/exf_getsurfacefluxes.F).
2564 o tools/genmake2:
2565 - improve error msg when failing in 2nd test of check_for_broken_Ff
2566 - fix option '-makefile' short-name (-mf according to genmake2 -help)
2567 - source local config file "genmake_local" just after processing the genmake2
2568 command arguments (previously done before processing arg).
2569 o pkg/grdchk:
2570 - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
2571 to this routine from cost_final has been dropped in g_cost_final)
2572 - improve printed information (more explicit msg, no longer using "print *,"
2573 fix fcpertminus printed value).
2574 o model/src:
2575 - move call to COST_INIT_VARIA out of packages_init_variables.F directly
2576 into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
2577 this prevents getting cost-funct reset in adinitialise_varia recomputations.
2578 o pkg/dic:
2579 - move initialisation of "freefe" array from from dic_biotic_forcing.F to
2580 fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
2581 o pkg/grdchk:
2582 - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
2583 - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
2584 o pkg/autodiff/ctrl/grdchk :
2585 - attempt to sort out what works and what does not,
2586 with regard to I/O, and to warn/stop accordingly.
2587 o pkg/grdchk:
2588 - attempt to fix grdchk in the case of useSingleCpuIO.
2589 - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
2590 statements were moved from grdchk_main.F and into
2591 grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
2592 - a global sum is applied to record numbers icvrec/layer
2593 out of grdchk_loc so that they be passed to I/O routines.
2594 o pkg/smooth:
2595 - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
2596 smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
2597 o verification/testreport:
2598 - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
2599 - can also use compressed (gzip) reference output file;
2600 - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
2601 to be easier to collect by testreport.
2602 - update existing TLM output (half out-of-date by more than 3 yrs).
2603 - report NETCDF & LAPACK settings (from genmake2) in output dir.
2604 - report run-time in each individual summary (previously only for AD test);
2605 for TLM test, add also TAF version.
2606 - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
2607
2608 checkpoint63r (2012/08/15)
2609 o tools/genmake2:
2610 - fix Makefile for target ftlall (+ update files to clean after make ftlall)
2611 o pkg/ecco/ecco_cost_final.F :
2612 - fix fc print statements (to stdout and costfunction0000) so
2613 that the printed value is always after the global sum.
2614 o pkg/seaice/seaice_dynsolver.F :
2615 - fix ice strength assymptote at SEAICE_area_max<1
2616 (no change for the standard case of SEAICE_area_max=1)
2617 o some cleaning:
2618 - pkg source files: ensure that all *.F files from each pkg included the
2619 corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
2620 only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
2621 code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
2622 includes;
2623 - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
2624 - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
2625 is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
2626 ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
2627 - update option-file CPP_OPTIONS.h of all AD experiments:
2628 * no longer include PACKAGES_CONFIG.h ;
2629 * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
2630 * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
2631 including ECCO_CPPOPTIONS.h).
2632 o pkg/cost, pkg/ctrl, pkg/ecco option-file:
2633 - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
2634 separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
2635 not necessary accurate).
2636 - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
2637 pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
2638 deliberately break compilation (a remainder that it needs to be customized)
2639 - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
2640 - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
2641 - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
2642 o tools/genamke2:
2643 - check for lapack.
2644 o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
2645 - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
2646 jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
2647 from both packages.
2648 - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
2649 - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
2650 - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
2651 of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
2652 o pkg/cost : add comments to explain special and/or untested setups.
2653 o pkg/exf:
2654 - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
2655 (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
2656 o verification/*/code_ad:
2657 mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
2658 - reccord when this file is included (define ECCO_CPPOPTIONS_H)
2659 - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
2660 allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
2661 o pkg/seaice :
2662 - added possibility to change ice strength/PRESS0 relationship to
2663 HEFF, according to the following run time parameters
2664 SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
2665 SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
2666 SEAICEpresH0 :: HEFF threshold for ice strength (m)
2667 o pkg/ggl90 :
2668 - added run time flag mxlSurfFlag to include the code that ensure
2669 mixing between first and second level (previously included as a comment)
2670 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
2671 - add test of newly added dumpAdByRec=T option where
2672 we write all records to one file per variable.
2673 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
2674 - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
2675 to check that this code is ok with taf and compiles in adjoint.
2676 o pkg/autodiff :
2677 - added run time param dumpAdByRec : ad dump format switch.
2678 If true then write all records to one file per variable.
2679 Else write one file per record (remains the default).
2680 - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
2681 o pkg/seaice:
2682 - Added SEAICEuseTILT run time switch : if set to
2683 false then omit the tilt term in seaice dynamics.
2684 - Fix free drift calculation.
2685 o pkg/shelfice:
2686 When initializing SHELFICEDragQuadratic, set default to be
2687 consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
2688 but retain option to set it independently
2689 (inconsistenty spotted by Veronique Dansereau)
2690 o eesupp/inc:
2691 - in EEPARAMS.h, add real-type constant for some frequently used simple number
2692 (0,1,2,1/2), with name explicitly referring to RS/RL type.
2693 o model/src:
2694 - move balancing of relaxation terms to new S/R balance_relax.F.
2695 o pkg/autodiff:
2696 re-write active I/O high-level (control) S/R:
2697 - rename S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
2698 - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
2699 - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ and
2700 MDS_READ/WRITE_FIELD); change loops to multi-threads.
2701 - update and merge active_file_control_slice.flow into active_file_control.flow
2702 - update the calls in lower level S/R (active_file.F, active_file_g.F and
2703 active_file_ad.F) keeping the argument list and function unchanged.
2704 - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
2705 =.TRUE.") and remove high-level (control) _loc version (not called anymore).
2706 - new low-level active I/O routines, one for each type (RL/RS), for active var
2707 of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
2708 fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
2709 right type.
2710 o autodiff and RS=real*4:
2711 - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
2712 ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
2713 - change argument type of 3-D mask argument to _RS to match type in the call
2714 (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
2715 o pkg/thsice:
2716 - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
2717 - option to correct ocean fresh-water flux for imbalance of Atmos+Land
2718 fresh-water flux: uniform correction or proportional to local precip.
2719 o pkg/ctrl:
2720 - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
2721 - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
2722 ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
2723 - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
2724
2725 checkpoint63q (2012/07/30)
2726 o pkg/autodiff:
2727 note about monitor and snap-shot of ad-variables:
2728 a) need to apply ADEXCH before monitor or output of ad-vars to include
2729 overlap contributions (was done for adjDump but missing for monitor).
2730 b) since ADEXCH implies adding overlap values to interior array, machine
2731 truncation error is expected when adding an ADEXCH call in the middle of
2732 the time-stepping (although mathematically identical).
2733 modifs:
2734 - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
2735 declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
2736 - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how to
2737 apply ADEXCH before monitor or snap-shot of ad-variables:
2738 =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
2739 - implement new method (copy+adexch) for snap-shot and monitor of main model
2740 ad-vars (initially not used by default -> output unchanged).
2741 - change default (set to 2) to use new method and update few output_adm.txt
2742 with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
2743 and both tutorial_tracer_adjsens tests).
2744 - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
2745 and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
2746 o pkg/ctrl:
2747 enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
2748 generic control variables via
2749 #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
2750 Only required customization should be S/R ctrl_map_ini_genarr.F
2751 (routine in repository contains example)
2752 o pkg/exf:
2753 - fix and refine checking of surface-relaxation setting when using EXF
2754 o verification (adjoint exp):
2755 - reduce length of simulation by half for experiment global_ocean.cs32x15
2756 (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
2757 o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
2758 - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
2759 of KE that can occur with aggressive optimization
2760 + put quadratic bottom drag calculation in separated loops (only done if
2761 using bottomDragQuadratic)
2762 o model/src: CG2D_NSA
2763 - clean-up: stop if cg2dNormaliseRHS=T and AUTODIFF
2764 and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
2765 - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
2766 change cg2d residual target to be expressed in Wunits (=> do not normalise
2767 RHS ; this fix global_max Pb with TAF); update output.
2768 o verification/tutorial_tracer_adjsens:
2769 improve parameter consistency (and get rid of warnings):
2770 - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
2771 - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
2772 - use staggerTimeStep (for stability) in som81; use default rotation period.
2773 o pkg/exch2:
2774 - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
2775 reset to 0 = 1 long line in X)
2776 o pkg/mdsio:
2777 - fix reading of dimensions from meta file for large-size domain
2778 o model/src:
2779 - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
2780 - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
2781 Cubed-Sphere Exch with CS-corners inside the domain;
2782 make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
2783 globalArea and to set hasWetCSCorners.
2784 - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
2785 metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
2786 - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
2787 useCDscheme and useCubedSphereExchange).
2788 o pkg/seaice/seaice_growth.F :
2789 - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
2790 for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
2791 when the previous code was not correct.
2792 - in all cases diagnoze the boundary condition mismatch to SIaaflux
2793 - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
2794 that term to QNET (essentially to set the melt/freeze water to 0degC).
2795 when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
2796 o verification/global_ocean.cs32x15/input.seaice :
2797 - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
2798 - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
2799 - update results (output.seaice.txt) accordingly.
2800 o verification/lab_sea/input/data.seaice :
2801 - remove SEAICEheatConsFix, which is now be tested
2802 in global_ocean.cs32x15. The presently coded fix
2803 is only consistent with real fresh water + nlfs.
2804 - update results (output.txt) accordingly.
2805 o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
2806 o AD_CONFIG.h file:
2807 - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
2808 - remove #include "AD_CONFIG.h" from all included OPTIONS files and
2809 add it explicitly in each fortran src file where it is needed.
2810 motivation: header file AD_CONFIG.h is generated/modified after "make depend"
2811 thus introducing potentially wrong dependency; therefore, better to include
2812 it only where it's really needed, and after any other included OPTIONS file
2813 (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
2814 or ALLOW_TANGENTLINEAR_RUN).
2815
2816 checkpoint63p (2012/07/06)
2817 o pkg/autodiff:
2818 - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
2819 - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
2820 which are now read from new parameter file "data.autodiff" (inAdExact
2821 previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
2822 - add file "data.autodiff" in all verification/*/input_ad/ directories.
2823 - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
2824 mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
2825 o verification/tutorial_tracer_adjsens/
2826 - add extra sub-verification which uses "SOM" advection scheme
2827 (2nd Order-Moment Advection Scheme, Prather Limiter) with
2828 #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
2829 and in data:
2830 multiDimAdvection=.TRUE.,
2831 tempAdvScheme=81,
2832 saltAdvScheme=81,
2833 o model/src:
2834 - introduce ALLOW_BALANCE_RELAX which allow the removal
2835 of the global mean of relaxation terms by setting
2836 balanceThetaClimRelax and balanceSaltClimRelax
2837 - disable balanceEmPmR and balanceQnet in the case when useSeaice.
2838 This case is now treated appropriately in seaice_growth.F
2839 o pkg/seaice:
2840 - do balanceEmPmR and balanceQnet based on the net fluxes
2841 (SItflux) that enter the ocean+ice system rather than QNET
2842 and EMPMR. Works best in real fresh water.
2843 - SIatmFW, SIatmQnet, and SItflux computations had to be moved
2844 out of the diagnotics bloc, and stored in global arrays.
2845
2846 checkpoint63o (2012/06/29)
2847 o vertical mixing schemes:
2848 - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
2849 - replace computation of density (in Function STATE1, opps_calc.F) by a call
2850 to S/R FIND_RHO_SCALAR
2851 - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
2852 and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
2853 affects output (vermix.ggl90) at truncation level.
2854 o testreport:
2855 - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
2856 (nSx,nSy) for the number of threads (from eedata.mth)
2857 o model/src:
2858 - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
2859 related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
2860 o verification/tutorial_tracer_adjsens/
2861 - compile with ALLOW_CG2D_NSA
2862 - run with nonlinFreeSurf=3
2863 - update reference output_adm.txt
2864 o tools/genmake2:
2865 - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
2866 refine usePROFILES switching off (only when NetCDF is not available).
2867 o verification (atmospheric set-up):
2868 - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
2869 o pkg/profiles : refine profiles and files handling.
2870 o model/src and pkg/ecco : introduce run-time switch usePROFILES.
2871 o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
2872 - changes to use model/src/the_main_loop.F rather than the ecco version
2873 in ecco type adjoint runs.
2874 o model/src:
2875 - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
2876 - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
2877 - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
2878 o model/src:
2879 - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
2880 update output of test experiment bottom_ctrl_5x5.
2881 o pkg/generic_advdiff:
2882 - implement vertical bi-harmonic diffusion (for now, only for T & S and
2883 only explicitly).
2884 o verification/bottom_ctrl_5x5/
2885 update reference output (results changed quite some time ago,
2886 not sure when; but new reference results look ok in terms of grdchk)
2887 o verification/1D_ocean_ice_column/
2888 For verification purposes, the exact adjoint rather than an approx.
2889 should be used (e.g., to comare against F.D. or TLM).
2890 removed autodiff_inadmode*_ad.F routines in code_ad/
2891 Update results/ accordingly.
2892 o pkg/cal:
2893 - change cal_getdate.F so that output date is function of input time only
2894 (less ambiguous, not mixed up with input iteration number).
2895 - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
2896 o pkg/diagnostics:
2897 - implement calendarDumps also for stats-diags
2898 - implement calendarDumps also for snap-shot output (negative freq)
2899 - for now, ignores calendarDumps if non-zero phase-lag.
2900
2901 checkpoint63n (2012/06/04)
2902 o model/src:
2903 - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
2904 between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
2905 - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
2906 similar to calc_r_star.F); update results of experiment internal_wave and
2907 tutorial_global_oce_in_p (affected @ truncation level).
2908 o pkg/shelfice:
2909 - add parameterisation of advective-diffusive flux into the ice shelf
2910 according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
2911 - simply eps3/3a computation
2912 o eesupp:
2913 - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
2914 between tiles, just fill-in edges assuming locally periodic subdomain) and
2915 add corresponding exchange subroutines (EXCH0);
2916 - new CG-solver version (_EX0) for disconnected-tiles special case.
2917 o model/src (CG-solvers):
2918 - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
2919 (similar final residual output and max-Iter number as with standard version);
2920 - allows to store and use lowest-residual solution (standard & _SR versions);
2921 - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
2922 - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
2923 o eesup/src:
2924 - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
2925 ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
2926 o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
2927
2928 checkpoint63m (2012/04/27)
2929 o pkg/shelfice:
2930 - account for partical cells in surface level below ice-shelf for hydrostatic
2931 pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
2932 o ad test experiments:
2933 - update and rename to "ad_optfile.local" local AD-optfile specific to a
2934 particular adjoint verification experiment (in verification/*/code_ad/)
2935 o pkg/seaice & pkg/exf:
2936 - Part two of ECCO-CLIVAR code merges.
2937 Completes merge of seaice area relax. code.
2938 Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
2939 to be set in EXF_OPTIONS.h since this pkg controls its I/O
2940 (and avoids second CPP option in SEAICE_OPTIONS.h)
2941 - change default value of costIceStart & costIceEnd to a valid date.
2942 - add snowPrecip to HSNOW in seaice_growth
2943 o pkg/ptracers:
2944 - move ptracers summary and setup check into separated S/R ; add a check for
2945 valid PTRACERS_Iter0 value (error+stop or just warning).
2946 o pkg/cal (+ pkg/ecco):
2947 - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
2948 as input; and for AD, unless both are not differentiable (e.g., k index)).
2949 o model/src:
2950 - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
2951 is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
2952 temporary set to usingZCoords value (to be changed to F when using shelfice).
2953 - hydrostatic pressure: implement partial cell near the surface also for
2954 Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
2955 usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
2956 o pkg/ctrl/ctrl_init.F:
2957 - add a formal parameter to s/r ctrl_init_rec to print
2958 xx_$(ctrl_valiable)_file for easier debugging
2959 - move call of cal_* routines into the if-block where they are really
2960 needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
2961 to specify a startdate
2962 o pkg/seaice:
2963 - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
2964 global_ocean.cs32x15/code versions).
2965 - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
2966 verification experiment global_ocean.cs32x15.seaice and update results.
2967 o pkg/exf:
2968 - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
2969 (according to useExfYearlyFields).
2970 o pkg/cal:
2971 - move calendar setting & summary (previously in cal_readparams.F) into new
2972 S/R CAL_INIT_FIXED to be called later in the initialisation process, once
2973 length of the simulation is set (after SET_PARMS call); This is an attempt
2974 to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
2975 - For safety: keep a record of pkg/cal parameter settings status
2976 to allow to STOP if one pkg/cal S/R is called too early.
2977 - add a stop in all basic pkg/cal subroutines if called before setting is done.
2978 - modify cal_getdate.F: stop when nothing was returned;
2979 if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
2980 this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
2981
2982 checkpoint63l (2012/04/04)
2983 o pkg/bbl:
2984 - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
2985 update global_with_exf output.yearly.txt file.
2986 o pkg/cal:
2987 - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
2988 - remove 2 unsused and very short (1 line only) functions ;
2989 - remove unsused subroutines from AD-Diff list.
2990 o model/src:
2991 - start to implement clean wait to stop in initialization S/R (config_check.F,
2992 packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
2993 o folowing PRINT_MESSAGE changes:
2994 - remove reminder multiple print to the same file (STDOUT) when multi-threads.
2995 o pkg/bbl:
2996 - modification so it can work with z*
2997 - replace deltaT with dTtracerLev(k) for asynchronous time stepping
2998 - global_with_exf/input.yearly verification; changes output.yearly.txt
2999 o eesupp/src:
3000 - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
3001 writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
3002 - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
3003 # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
3004 - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
3005 - when using MPI, always set usingMPI=T ; set default accordingly and stop
3006 if not consistent.
3007 - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
3008 argument is zero (in case called within single-thread section).
3009 o pkg/fizhi:
3010 clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
3011 in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
3012 o pkg/exch2:
3013 - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
3014 activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
3015 - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
3016 but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
3017 with bad ones coming from a not-yet-updated halo.
3018 This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
3019 o pkg/frazil:
3020 move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
3021 http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
3022 o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
3023 o verification/lab_sea
3024 * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
3025 * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
3026 * nTimeSteps 3 -> 4
3027 * changed reference output accordingly
3028 o pkg/ctrl:
3029 * fix ctrl_get_gen for xx_sst, xx_sss
3030 o pkg/fizhi:
3031 - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
3032 update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
3033 - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
3034 fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
3035 clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
3036 o pkg/gmredi:
3037 - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
3038 o pkg/fizhi:
3039 - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
3040 (old)aces open64 tuv test.
3041 o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
3042 o pkg/mom_vecinv:
3043 - fix 1 loop range in mom_vecinv.F to be like all the other loops which
3044 set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
3045 with non-lin free-surf).
3046 o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
3047 in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
3048 some compilers (gfortran 4.6.0 on MacOS)
3049 o momentum:
3050 - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
3051 & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
3052 fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
3053
3054 checkpoint63k (2012/03/17)
3055 o model/src:
3056 - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
3057 flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
3058 - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
3059 (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
3060 o model/src: solve_*diagonal.F
3061 - replace division with multiplication by inverse (similar to original version)
3062 update output of AD exp. global_ocean.90x40x15.
3063 - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
3064 to enable the use of the vectorized & differentiable solve_tridiagonal.F
3065 - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
3066 vertical advection (to get solve_tridiagonal tested in AD mode).
3067 o pkg/seaice: ECCO-CLIVAR merge:
3068 1. seaice AREA relaxation
3069 * CPP option: SEAICE_ALLOW_AREA_RELAXATION
3070 * runtime flag: SEAICE_tauAreaObsRelax
3071 2. modified global mean cost imbalance code: CPP option
3072 ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
3073 o another iteration on solve_*diagonal.F
3074 Make choices independent of AUTODIFF
3075 Default will be the adjoinable vectorized version.
3076 Alternative choices are:
3077 * non-adjoinable original version with low memory footprint:
3078 #define SOLVE_DIAGONAL_LOWMEMORY
3079 * still adjoinable but does not vectorize (k as inner-most loop):
3080 #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
3081 o testreport
3082 - add option to use a home made wrapper around "make"
3083 - remove MITGCM_IEEE env. variable (no longer active)
3084 o pkg/shelfice
3085 - improve computation of friction velocity for velocity dependent
3086 exchange coefficients: include velocities into SHELFICEBoundaryLayer
3087 block to average velocities vertically
3088 - add TAF store directives for SHI_ALLOW_GAMMAFRICT
3089 o Modify diagonal solvers, now three versions (upon request):
3090 #ifndef SOLVE_DIAGONAL_AUTODIFF
3091 1. default version (dating back a while ago)
3092 #else /* def SOLVE_DIAGONAL_AUTODIFF */
3093 # ifdef SOLVE_DIAGONAL_KINNER
3094 2. adjoinable version with k-innermost loop (G. Forget)
3095 # else
3096 3. adjoinable vectorized version of 2.
3097 # endif
3098 #endif /* SOLVE_DIAGONAL_AUTODIFF */
3099 All flags are currently set within routines, but could/should be moved to CPP-options.
3100 Array bounds for 1. are as before, for 2.,3. cover the entire domain
3101 (could be changed for 1. too).
3102 o verification/lab_sea (fwd):
3103 - update the 4 fwd lab_sea test experiment: no longer SEAICE_GROWTH_LEGACY,
3104 use 7 categories (except hb87), new solve4temp params (except salt_plume),
3105 constant salinity (=4) or variable salinity (salt_plume) done through
3106 SItracer.
3107 o pkg/seaice:
3108 - rename parameters: SIsalFrac to SEAICE_saltFrac & SIsal0 to SEAICE_salt0;
3109 - remove old parameters ( SEAICE_freeze, SEAICEturbFluxFormula, SEAICE_gamma_t,
3110 SEAICE_gamma_t_frz, SEAICE_availHeatTaper & SEAICE_availHeatFracFrz)
3111 from SEAICE_PARMS.h ; still need to fix seaice_cost_sst.F (broken when
3112 SEAICE_freeze got retired) but already better than previously with
3113 SEAICE_freeze=123456.7 deg.C;
3114 - move setting of facOpenGrow/Melt from SEAICE_INIT_FIXED to SEAICE_READPARMS
3115 (safer multi-threaded setting); always set SEAICEuseEVP;
3116 - setting of ocean-ice turb. flux coeff: moved from SEAICE_CHECK to
3117 SEAICE_READPARMS & SEAICE_INIT_FIXED (this fixes wrong summary report);
3118 stop if multiple specifications for the same coeff; make sure default
3119 SEAICE_mcPheePiston is compatible with drF(1) & deltaT.
3120 o pkg/obcs:
3121 - allow to switch to upwind 1rst order advection scheme for the advective
3122 flux computation at the open-boundary; disabled for adjoint built.
3123 o pkg/ptracers:
3124 - rename PTRACERS_RESTART.h -> PTRACERS_START.h
3125 - rename ptracers_fields_blocking_exchanges.F -> ptracers_fields_blocking_exch.F
3126 - add parameter to decide when to start a tracer; use internal flag to
3127 know which tracer to step-forward; switch this internal flag at the top
3128 of forward_step.F (new S/R PTRACERS_SWITCH_ONOFF); for now, not enabled
3129 for adjoint built.
3130 o pkg/seaice:
3131 - add SEAICE_SIZE.h anywhere in the code where SEAICE.h is included ;
3132 - move MULTDIM declaration and setting from SEAICE.h to SEAICE_SIZE.h ;
3133 - keep experiment offline_exf_seaice truly single category (set MULTDIM=1).
3134 o pkg/ecco:
3135 - fix writing of output file DiagnosCost_ClimSalt/Theta
3136 and DiagnosCost_DriftSalt/Theta (if multi-tiles per proc).
3137 o pkg/seaice:
3138 - add missing initialisation of COR_ICE array in dynsolver.F
3139 - merging SEAICE_MULTICATEGORY define and undef cases. Now the same code is
3140 compiled either way, and is tested in all exps (multidim was only tested
3141 in lab_sea ad before).
3142 - cosmetic change to prepare for future addition of ITD. no change to results.
3143 no defaults change.
3144 - added run time param SEAICE_multDim (7 for SEAICE_MULTICATEGORY, 1 otherwise).
3145 - by lack of adequate verification experiments, I further used custom versions
3146 of global_ocean.cs32x15 to test multicat or not, with pickup or not. All
3147 should be correct.
3148 - avoid recomputations in ad.
3149 o array initialisation in adjoint mode:
3150 1) pkg/mom_common/mom_calc_ke.F:
3151 add full array initialisation of KE inside mom_calc_ke.F (ALLOW_AUTODIFF_TAMC):
3152 The S/R which calls MOM_CALC_KE initialises KE but in some recomputation
3153 part this initialisation is gone, resulting in Floating Point Exception
3154 (caught by open64 compiler with debug option).
3155 2) model/src/convective_weights.F
3156 set output convectCount over the full array range (instead of doing
3157 an update): this fix a similar issue when called within recomputation (adjoint)
3158 which could by-pass the initialisation (normally done in the caller S/R).
3159 o pkg/seaice:
3160 - final version of turbulent flux params, as agreed at MIT ice meet:
3161 SEAICE_mcPheePiston (default is ~ 0.000875)
3162 SEAICE_mcPheeTaper (default is 0.)
3163 SEAICE_frazilFrac (defualt is 1.)
3164 SEAICE_mcPheeStepFunc (default is false)
3165 - changes results at trunction error level
3166 - ifdef SEAICE_EXTERNAL_FLUXES, disallow SEAICE_waterAlbedo
3167 o added pkg/frazil:
3168 - see frazil_description.tex for details
3169 - verification experiment is global_with_exf/input.yearly; changes output.yearly.txt
3170 o pkg/shelfice/shelfice_thermodynamics.F
3171 - fix exponents for velocity dependent exchange coefficients: change
3172 from 2/3(=0) to 0.66666666666666667
3173 - move computation of velocity dependent exchange coefficients into
3174 separate loop, so that it applies to both thermodynamics
3175 - move some divisions by constants out of loops
3176
3177 checkpoint63j (2012/02/16)
3178 o pkg/seaice:
3179 - overhaul of seaice_summary.F after feb 2012 clean-up of seaice_growth.F etc.
3180 - SItracer: added run time params, and allow coupling to ocn salinity.
3181 o pkg/seaice: remove (almost) all divisions by constants within loops
3182 in seaice_growth.F and seaice_solve4temp.F, this changes (only) the cg2d
3183 results of global_ocean.cs32x15.seaice from 16 to 11 digits (but only
3184 those, caused by 1/QI -> recip_QI) -> update output.seaice.txt,
3185 output_adm.seaice_dynmix.txt and also lab_sea: output_adm.evp.txt
3186 o pkg/seaice :
3187 - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula
3188 = 1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
3189 - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
3190 - add permanent SItflux diag that corresponds to TFLUX but includes
3191 ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
3192 - allow activation/testing of a fix for suspected missing term in
3193 ocn-ice heat budget (to be confirmed). To test this, you want to
3194 undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
3195 SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
3196 - no change in results, fwd or ad.
3197 o global_ocean.cs32x15/results: 3 changes following from the pkg/seaice commit below:
3198 - switch to variable freezing point.
3199 Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
3200 - bug fix : the sublimation term that was missing is now activated.
3201 Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
3202 - bug fix : flooding sign term for SIsal0.NE.0.
3203 Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
3204 o pkg/seaice:
3205 - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
3206 is now the default, and the old default constant freezing point is recovered
3207 with SEAICE_tempFrz0 = -1.96,
3208 SEAICE_dTempFrz_dS = 0.,
3209 - retire SEAICE_freeze (= the old way of specifycing the constant freezing point)
3210 - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
3211 - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
3212 activated. To reproduce old results with this bug define SEAICE_DISABLE_SUBLIM.
3213 - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
3214 was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
3215 - bug fix (thanks to O. Jahn) : area loss for melting got messed up in
3216 seaice_growth r149 for legacy branch (no results change).
3217 - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code
3218 from I. Fenty).
3219 - results did not change except for global_ocean.cs32x15, mostly due to the
3220 switch to variable freezing point (see above item for detail).
3221 o pkg/thsice:
3222 - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
3223 seawater freezing in thsice_calc_thickn (not used).
3224 o pkg/seaice: turbulent flux term specification via run time params.
3225 - replace CPP switches with run time switches to facilitate testing
3226 - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX,
3227 GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
3228 - added runtime parameter : SEAICEturbFluxFormula
3229 - move Mcphee constants to SEAICE_PARAMS.h
3230 - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
3231 SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply);
3232 remove seaice_summary call (moved to seaice_init_fixed)
3233 - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
3234 SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
3235 - seaice_summary.F : add missing report of read turbulent flux term set up
3236 and SITRACER.
3237 - seaice_check.F : check range; inform and stop if retired CPPs are used
3238 (incl. SEAICE_AGE).
3239 - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
3240 CPP switch, same computation as before for the different options.
3241 - change results at the truncation level.
3242 o pkg/seaice:
3243 - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
3244 useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
3245 SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
3246 - update verification/*/input*/data.seaice:
3247 to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
3248 code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
3249 and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
3250 set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
3251 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
3252 - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
3253 algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
3254 difference in results only due to machine truncation.
3255 - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
3256 MaykutPolySatVap; keep MIN_LWDOWN.
3257 - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
3258 - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
3259 + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
3260 o pkg/salt_plume:
3261 - isolate saltPlumeFlux array exch into a specific S/R called from
3262 do_oceanic_phys.F
3263 - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
3264 o verification:
3265 - move untested set-up to MITgcm_contrib/verification_other.
3266 o pkg/seaice:
3267 - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
3268 o pkg/seaice:
3269 - seaice_solve4temp.F (keeping results unchanged):
3270 * add 2 future run-time params to select which saturation vapor pressure
3271 formula is used and how post-iteration fluxes are set.
3272 Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
3273 * New piece of code (not used) to update surf. atmos. heat flux F_ia using
3274 the linearized expression to stay consistent with tsurf finding.
3275 - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
3276 can be < 0.
3277 o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
3278 - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
3279 conductive heat flux F_c , and add it explicitly when updating tsurf as
3280 solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
3281 so that now F_ia has a consistent meaning through the entire routine.
3282 This causes differences at truncation level: update output of fwd exp.
3283 global_ocean.cs32x15.seaice.
3284 o pkg/seaice:
3285 - lots of editing/cleaning in seaice_solve4temp.F + better documentation
3286 of arrays, sign/direction of fluxes; no effect on results.
3287 - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
3288 in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
3289 note: this should have been done before changing celsius2K default.
3290 - to keep results unchanged, add back old value of celsius2K in verification
3291 exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
3292 - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
3293 SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
3294 value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
3295 freezing temp is consistent with value in seaice_growth.F ; this causes
3296 differences at machine truncation level: update lab_sea AD output (3/4).
3297 o pkg/seaice:
3298 - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
3299 and climsst/sss even when using seaice (to prevent calculation that might
3300 use SST on land); does not affect any verification exp.
3301 - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
3302 of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
3303 o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
3304 over land (non-legacy code)
3305 o vectorize salt_plume package:
3306 - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
3307 - this code computes plumebk everywhere (also over land), thus requires
3308 code to avoid divisions by zero and catch the case of kLev=Nr.
3309 - efficiency of salt_plume_frac is still sub-optimal
3310 o tools (genmake2):
3311 - fix makefile NAME specification (option: -makefile NAME) by adding
3312 "-f $MAKEFILE" in few places where it was missing including makedepend
3313 command (contribution from Paul).
3314
3315 checkpoint63i (2012/01/24)
3316 o model/src:
3317 - add factorized versions of some EOS code to find_rho.F,
3318 define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
3319 o model/src:
3320 - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
3321 - change default celsius2K from 273.16 to 273.15
3322 - to keep results unchanged, add back old value of celsius2K in verification
3323 exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
3324 global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
3325 o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
3326 to make TAF generate vectorizable code
3327 o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
3328 Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
3329 have flags that do this more efficiently.
3330 o pkg/diagnostics/diagstats_calc.F
3331 - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
3332 o pkg/obcs (with exch2):
3333 - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
3334 and remove code (in obcs_readparms.F) which was based on EXCH of indices
3335 (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
3336 o pkg/exf and seaice exp:
3337 - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
3338 so that switching off area & heff advection flags does not affect results.
3339 - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
3340 - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
3341 EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
3342 results of verification experiments: 1D_ocean_ice_column(fwd),
3343 global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
3344 and offline_exf_seaice (all 4).
3345 o pkg/seaice:
3346 - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
3347 remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
3348 - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
3349 but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
3350 not multi-dim advection;
3351 - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
3352 SHORTWAVE_HEATING #undef.
3353 o optim: make Makefile more robust (?)
3354 o pkg/obcs:
3355 * fix treatment of obcs_read_pickup for TAF
3356 o pkg/shelfice:
3357 * add missing initialisation of num_shifwflx
3358 * new adjoint verification exp. for isomip
3359 * change Prandtl and Schmidt numbers from generic formulations
3360 (in terms of model diffus. and visc.) to separate runtime
3361 parameters, with Holland and Jenkins (1999) default values.
3362 o pkg/exf (interpolation):
3363 - extended input field (2 rows) near the N & S poles:
3364 * fill in with the symetric value (when even Nb of data in longitude)
3365 * add average value at the poles only for scalar quantities ; for vector
3366 component interpolation, skip the averaging and keep duplicated values,
3367 unless the 2 components have same location (uvInterp=T) in which case
3368 interpolate the 2 components together using S/R EXF_INTERP_UV.
3369 - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
3370 together: this allows to account properly for local orientation when
3371 averaging at N & S pole.
3372 - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
3373 exf-interpolation near N & S poles. Undef by default.
3374 - add debug check/print on 1rst iter if debugLevel >=2.
3375 o pkg/exf:
3376 - change masking flags definition (no longer "parameter"), put them in
3377 common block and set them in S/R EXF_INIT_FIXED.
3378 - change recognized masking flag from s,u,v to c,w,s since the mask
3379 to use (maskC,W,S) depends on position on model grid and has little to
3380 do with scalar/vector difference; fix masking if using P-coordinates.
3381 - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
3382 and update results of exp. global_with_exf (x2).
3383 - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
3384 o pkg/obcs
3385 - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
3386 o pkg/exf (interpolation):
3387 - assume periodicity in X only if input field cover full longitude range.
3388 - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
3389 and should vectorise).
3390 - fix input lat of the 2 added row (in case we provide N.pole data).
3391
3392 checkpoint63h (2011/12/30)
3393 o pkg/seaice:
3394 - change declaration of UVM from _RL to _RS in order to get B-grid
3395 uIce,vIce monitor when _RS = real*4
3396 o pkg/offline:
3397 - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
3398 - compute vertical velocity if not read from file (switch on exactConserv
3399 & staggerTimeStep);
3400 - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
3401 o verification:
3402 - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
3403 with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
3404 fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
3405 - update output of exp. global_ocean.cs32x15.viscA4 after changing
3406 grid-file angles (used here for coriolis-3d);
3407 - remove (or gzip) few files not needed to run fizhi-cs experiments.
3408 o pkg/exf (vector interpolation):
3409 - rotate vector component toward local grid-axis orientation using grid-angles
3410 (stored in GRID.h) instead of locally computed rotation angle; keep old code
3411 available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
3412 o pkg/seaice:
3413 - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
3414 undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
3415 o pkg/PKG_OPTIONS.h files:
3416 - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
3417 outside of the #ifdef ALLOW_THISPKG / #endif block.
3418 - update verification/*/code/PKG_OPTIONS.h files.
3419 o add a verification experiment (offline_exf_seaice/input.seaice) that test
3420 the B-grid LSOR solver
3421 o pkg/seaice: sort out emissivity and long wave radiation step 2:
3422 - add emissivity for snow and ice as new run-time parameters
3423 (unfortunately) that default to the corresponding exf values; this
3424 changes results in most verification experiments so that for backward
3425 compatibility these parameter have to be set explicitly to inconsistent
3426 values (ugly);
3427 - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
3428 emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
3429 until we agree how to handle this bug properly
3430 o pkg/exf (interpolation):
3431 - add a set of run-time param ({inputfield}_interpMethod), one for
3432 each interpolated input field, to select the interpolation method
3433 with a value of zero switching off the interpolation;
3434 - print interpolation parameters to standard output;
3435 - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
3436 (to use instead runoff_interpMethod=0 in data.exf).
3437 - simplify default setting of interpolation parameters (for all fields,
3438 set position to match model grid cell-center position, leading to trivial
3439 interpolation in case of regular Lat-Lon grid) and fix for the case of
3440 non-uniform delY.
3441 o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
3442 within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
3443 this factor is absolutely required, because the lw exitance (= out-going
3444 long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
3445 where the reflectivity rho = 1-emissivity for conservation reasons. Once
3446 this is established, we can remove the CPP-Flag (if we want to).
3447 o pkg/seaice:
3448 - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
3449 ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
3450 - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
3451 what the name implies (and not emissivity*BoltzmannConstant), this means
3452 the old default value of 5.5e-8 now means
3453 5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
3454 S/R exf_readparms
3455 - FV-discretization of the B-grid LSOR solver, turn on with
3456 SEAICE_LSRBNEW. This new solver also involves a slight re-organization
3457 of the calling routine dynsolver, so that B and C-grid code look a
3458 little more alike.
3459 - fix index bugs in ostres.F (B-grid code)
3460 o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
3461 o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
3462 default for SEAICE_emissivity, if useEXF; requires setting a wrong
3463 parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
3464 backward compatiblity
3465 o model/src: use sigmaR in calc_ivdc
3466
3467 checkpoint63g (2011/12/16)
3468 o pkg/seaice/seaice_growth.F:
3469 fix heat conservation of the coupled ocean-seaice system.
3470 when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
3471 solid vs liquid water treatment is resolved via QNET.
3472 o pkg/seaice/seaice_growth.F:
3473 add missing term for sublimation in saltFlux, which was breaking conservation.
3474 o pkg/seaice/seaice_model.F:
3475 Remove this patholigical case treatment in evolution branch,
3476 where it is un-necessary and breaks conservation.
3477 Update global_ocean.cs32x15/results accordingly for
3478 output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
3479 o model/src:
3480 useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
3481 external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
3482 o pkg/obcs:
3483 modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
3484 tendency for temperature and salinity that is then applied to update
3485 theta and salt in S/R obcs_apply_ts; this requires proper masking of all
3486 horizontal advection and diffusion contributions on the boundary (in
3487 S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
3488 removing the mask in S/R timestep_tracer. The advantage of this approach is
3489 that the updated tracer values include contributions from the surface
3490 forcing and vertical diffusion.
3491 This modification changes exp4.stevens because of vertical diffusion.
3492 o model/src:
3493 change non-curvilinear grid setting to also work with exch2 + blank tiles:
3494 - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
3495 face dimensions.
3496 - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
3497 as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
3498 and INI_SPHERICAL_POLAR_GRID.
3499 change test-experiment global_ocean.90x40x15:
3500 - split the domain in many more tiles (9x4 tiles of 10x10 each);
3501 - switch to exch2 and remove 1 blank-tile (but only for MPI test).
3502 - update results of both test (std & dwnslp).
3503 o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
3504 tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
3505 o model/src:
3506 - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
3507 and fix initialisation when using sigma-coords.
3508 o model/src:
3509 - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
3510 to their current value at the beginning of forward_step.F": add a new run-time
3511 switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
3512 - set doResetHFactors=T in the following test exp:
3513 global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
3514 global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
3515 and tutorial_global_oce_in_p (nonLinFS in p)
3516 o pkg/ecco
3517 - added IES cost term
3518 o verification/advect_xz
3519 - scale down the depth by 1/100 (from 200 km to just 2.km)
3520 - add secondary test using divergent flow, r-star and implicit vertical advection.
3521 - add note (check_conserve_TS.txt) and matlab script to check global
3522 conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
3523 o pkg/rbcs:
3524 - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
3525 o pkg/obcs (Stevens BCs):
3526 - fix various problems in the phase speed computations of the Stevens
3527 boundary conditions:
3528 - sign error for western and southern boundaries,
3529 - time tendencies were underestimated by factor of dTracerLev and some just
3530 zero (for multidim advection schemes) -> now estimate time tendencies
3531 from difference between previous (n) time level and the one before (n-1);
3532 this requires storing a field per tracer per boundary, also in the pickup
3533 files.
3534 - replace deltaTmom in cflMer/Zon computation with dTracerLev
3535 - set default phase velocity to cflMer/Zon
3536 - update verification experiment exp4.stevens
3537 o pkg/generic_advdiff (implicit_r):
3538 - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
3539 (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
3540 - fix implicit vertical diffusion or advection with NonLin FreeSurf
3541 (was using current recip_hFacC instead of future recip_hFacC): set future
3542 recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
3543 solver S/R ;
3544 - fill diagnostics of vertical advective fluxes (computed from tendency)
3545 when using implicit vert. advection;
3546 - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
3547 global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
3548 tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
3549 and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
3550 o pkg/diagnostics:
3551 - add diags for T & S tendency which goes through Adams-Bashforth.
3552
3553 checkpoint63f (2011/11/30)
3554 o pkg/obcs/obcs_calc_stevens.F:
3555 - join some loops to reduce number of if-statements
3556 - fix a bug in code for northern and southern boundaries.
3557 o pkg/seaice/seaice_init_varia.F
3558 - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
3559 caused zero ice-velocities for the B-grid code
3560 o pkg/seaice/seaice_init_fixed.F
3561 - fix a bug in the initialisation of the second metric terms
3562 k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
3563 - this affects all seaice configurations with useCurviLinearGrid = .true.
3564 and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
3565 = .true. (default)
3566 - the only verification experiment affected is global_ocean.cs32x15:
3567 icedyn, seaice, and seaice_dynmix (AD)
3568 o pkg/thsice/thsice_diagnostics_state.F
3569 - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
3570 not contain garbage that can lead to surprises in diagstats_calc.F
3571 o model/src:
3572 - move bi,bj loops inside INTEGR_CONTINUITY ;
3573 - call INTEGR_CONTINUITY directly from forward_step.F
3574 (previously called from momentum_correction_step.F)
3575 - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
3576 forward_step.F and pkg/ecco/the_main_loop.F
3577 o model/src/do_oceanic_phys.F:
3578 - reset addMass to zero only if useICEFRONT ;
3579 - separated k-loop for rhoInSitu calculation ;
3580 - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
3581 and at constant T,S (= WdRHOdP);
3582 NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
3583 of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
3584 transport of locally-referenced potential density);
3585 to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
3586 o gluemnc:
3587 - replace ncrcat with ncks when adding variables to *.glob.nc
3588 - change the way variables without record dimensions are handled so that
3589 files that have variables with and without record variables can be glued:
3590 add a record dimension with a new unique name to be able to differentiate
3591 between variable with and without a-prior record dimensions. Remove
3592 this record dimension before adding the variable to the *.glob.nc file.
3593 This procedure automatically works also for grid.*.nc files that do not
3594 have any record dimension.
3595 o verification/cpl_aim+ocn:
3596 - generate new reference output on baudelaire (gfortran, mpich2) (previously
3597 from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
3598 o pkg/obcs/obcs_calc_stevens.F:
3599 - add code for northern and southern boundaries.
3600 - reorder some loops to save some operations and so that drFBar can be scalar
3601 o model/src:
3602 - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
3603 truncation) and add diagnostics for Adams-Bashforth tendency increment.
3604 - update test-exp. AD output:
3605 1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
3606 and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
3607 front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
3608 global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
3609 matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
3610 tutorial_global_oce_in_p, tutorial_global_oce_latlon and
3611 tutorial_plume_on_slope.
3612 o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
3613 that vectorises. This code uses 3 extra 2D fields, F90 array assignments
3614 and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
3615 does not even come with an F77 compiler anymore, this should not be
3616 a limitation
3617
3618 checkpoint63e (2011/11/06)
3619 o pkg/seaice adjoint of LSR:
3620 - substantially rework STORE dirs.
3621 - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
3622 this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
3623 and only perform SOLV_MAX_FIXED adjoint iters.
3624 If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
3625 always goes to same record, meaning that the last forward field will be
3626 the one used in the adjoint - an approximation.
3627 - now produces non-zero LSR-related gradients, and acceptable gradients for
3628 An's zonal (x-z) test case (to be checked in)
3629 - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
3630 (but these are screwed up by the thermodynamics in the first place);
3631 reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
3632 output_adm.txt also reflects changes to seaice_lsr
3633 - global_ocean.cs32x15:
3634 * the "default" input_ad.seaice has been re-defined to always exclude dynamics
3635 (output_adm.seaice.txt was updated)
3636 * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
3637 (output_adm.seaice_dynmix.txt)
3638 o test-exp. exp4+stevens:
3639 - switch off pTracers and nonHydrostatic (restart problems with NH); update output
3640 o pkg/seaice (lsr solver):
3641 - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
3642 update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
3643 - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
3644 - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
3645 into initial guess for linearised solver; use weight ~ (1/err)^2,4.
3646 - compute (with new S/R) and print initial (+ free-driff sol. if available)
3647 and final residual of linearised system.
3648 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
3649 (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
3650 o pkg/obcs: Stevens BCs (still only for east and west)
3651 - fix Stevens BCs by using intermediate velocities of previous
3652 time step as "baroclinic" contribution rather velocity of one grid cell
3653 inside the boundaries; more consistent but makes the entire treatment
3654 more complicated, requires new pickup files and two new S/Rs:
3655 obcs_copy_uv_n and obcs_save_uv_n
3656 keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
3657 (undefined by default)
3658 - silently move computation of some grid factors into separate loops to
3659 save some recomputations
3660 - add a hack for non-linear free surface
3661 - add a verification experiment to exp4 that tests this code
3662 o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
3663
3664 checkpoint63d (2011/10/25)
3665 o pkg/obcs + seaice-dynamics:
3666 - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
3667 solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
3668 values (consistent with an implicit method).
3669 - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
3670 return to older implementation (same results as before); note that none of
3671 the "experimental" OBCS_SEAICE options are implemented in the new version.
3672 - switch test exp. seaice_obcs to use new version (update output).
3673 o pkg/seaice:
3674 - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
3675 - add parenthesis in Water-Ice drag calculations (evp & lsr);
3676 - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
3677 and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
3678 - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
3679 and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
3680 o pkg/layers:
3681 - Include potential density as new coordinate (Thanks to David Munday)
3682 o pkg/dic:
3683 - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
3684 carbonate computation/output to CALC_PCO2_APPROX
3685 o pkg/generic_advdiff
3686 - make TAF generate code that vectorizes:
3687 gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
3688 o model/src:
3689 - improve vectorization also for adjoint code of
3690 solve_tridiagonal and solve_pentadiagonal. As this requires up to
3691 5 new 3D-fields, this code is only turned on for the combination of
3692 ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
3693 for singular matrix check (only for TARGET_NEC_SX).
3694 - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
3695 ALLOW_AUTODIFF. This flag now needs to be set outside of
3696 solve_tri/pentadiagonal.F
3697 o pkg/exf:
3698 - fix previous modif in exf_readparms.F (revision 1.66: treatment of
3699 optional namelist EXF_NML_OBCS).
3700 - add many debug-print (to trace down where pkg/cal error msg comes from)
3701 o pkg/mom_vecinv/mom_vi_hdissip.F
3702 - rearrange loops so that vectorization is improved and in particular
3703 the adjoint routine vectorizes. The code is a little longer now, but I
3704 think easier to read.
3705 Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
3706 o pkg/seaice:
3707 - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
3708 o pkg/exch2:
3709 - alternative code (without tile x tile matrix) for cumulated (global) sum;
3710 used as default; keep using matrix version in adjustment.cs-32x32x1.
3711 o tools/build_options:
3712 - after merging some MPI and/or multi-threads specific optfiles so that
3713 the modified default optfile support both built (using genmake2 -mpi
3714 for the MPI built, using genmake2 -omp for OpenMP built),
3715 move now obsolete optfiles to tools/build_options/unsupported/
3716 (add copy of email sent to support list in doc/optfiles_changes.txt)
3717
3718 checkpoint63c (2011/09/28)
3719 o pkg/ebm:
3720 - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
3721 test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
3722 o pkg/seaice (SItracer pickup)
3723 * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
3724 To be done:
3725 - thorough testing of missing fields in S/R seaice_read_pickup
3726 - thorough matching between generic tracers and specific fields used
3727 (e.g. volume-weighted age, area-weighted age, salinity, ...)
3728 o pkg/grdchk:
3729 - all procs calculate and print finite-difference gradient (for testreport)
3730 - change description output used by testreport;
3731 - AD testing: also compare and report Finite-difference gradient;
3732 => update all output_adm*.txt
3733 o test exp. global_ocean_ebm:
3734 - switch back useRealFreshWaterFlux (no problem anymore with run-off);
3735 and turn on exactConserve; update (fwd) output.
3736 o pkg/seaice (LSR):
3737 - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
3738 - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
3739 * identical results with non-CS topology (but save up to half of EXCH calls)
3740 * no much changes in cs-32 verification tests since no ice at face edges
3741 (differences due to convergence criteria, since nb of iterations changed)
3742 * expect some differences on lat-lon-cap grid.
3743 update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
3744 o pkg/exch2:
3745 - add new CPP option to disable Cumul-Sum matrix (to save storage when using
3746 many tiles); until alternative coding is added, just add a stop.
3747 o pkg/kpp:
3748 - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
3749 to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
3750 o optfiles:
3751 - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
3752 into corresponding standard one, which now support different build:
3753 (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
3754 - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
3755 o pkg/obcs (seaice):
3756 - add missing EXCH for uIce,vIce after applying OBCS;
3757 - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
3758 argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
3759 EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
3760 - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
3761 - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
3762 and eedata.mth for MPI and mutlti-threaded testing.
3763 o pkg/flt:
3764 - make FLT EXCH working with multi-threads (and MPI + multi-threads);
3765 - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
3766 - fix pickup and trajectories + profiles output with multi-threads;
3767 - add parameter to select group of fields to write along trajectory and
3768 profile (default unchanged);
3769 - only call PORT_RAND* function when flt_noise <> 0;
3770 - add multi-threaded test for verification exp. flt_example.
3771 o eesupp/src:
3772 - fix S/R ALL_PROC_DIE for MPI+multi-threads.
3773 - USE_OMP_THREADING: check that number of threads (from eedata) matches
3774 actual number (from env.var. setting).
3775 o pkg/ebm:
3776 - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
3777 - add multi-threaded test for verification exp. global_ocean_ebm
3778
3779 checkpoint63b (2011/08/29)
3780 o pkg/ebm:
3781 - fix sign of runoff;
3782 - update directly forcing fields (Qnet,EmPmR) to use standard
3783 external_forcing_surf.F (remove ebm_forcing_surf.F);
3784 - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
3785 - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
3786 and apply relaxation towards corresponding SST field (2-D map or ZonAver).
3787 - update global_ocean_ebm parameters file data and update output (fwd+ad).
3788 o verification/matrix_example:
3789 - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
3790 MPI and mutlti-threaded testing.
3791 o pkg/matrix:
3792 - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
3793 - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
3794 - fix for multi-threaded (remove DATA statement);
3795 - use standard DIFFERENT_MULTIPLE function;
3796 - add MATRIX_OPTIONS.h
3797 o verification/matrix_example:
3798 To allow to split the domain in several tiles, change the domain size
3799 from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
3800 Western side) of land points.
3801 o (*_)write_pickup:
3802 - fix few bugs in mypackage_read/write_pickup.F
3803 - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
3804 array of length 1 (was caught by compiler syntax-check).
3805 o pkg/diagnostics (velocity potential solver):
3806 - fix initialisation of main diagonal matrix (for overlap values)
3807 o tools/build_options:
3808 - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
3809 into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
3810 - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
3811 * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
3812 * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
3813 and use "-devel" testreport option for standard testing on baudelaire.
3814 o pkg/grdchk:
3815 - Assume that all gradient-check position are within the same tile
3816 corresponding to global indices (iGloTile,jGloTile) and that
3817 positions (i,j indices or nbeg) are local to this tile;
3818 - set tile local-indices and proc. number according to tile global-indices;
3819 - remove grdchkwhichproc from namelist (retired param);
3820 - send adjoint gradient to all procs so that all procs print it to STDOUT;
3821 - switch on MPI test for global_ocean.90x40x15 AD test experiment.
3822 o adding package bbl (Bottom Boundary Layer)
3823 description in MITgcm/pkg/bbl/bbl_description.tex
3824 example/test experiment in MITgcm_contrib/bbl
3825 o adjoint verifications
3826 - changed 5 experiments to multi-tiles
3827 * global_ocean.90x40x15
3828 * obcs_ctrl
3829 * offline_exf_seaice
3830 * tutorial_dic_adjoffline
3831 * tutorial_tracer_adjsens
3832 changed reference output for those that crossed tile boundaries
3833 (changed choices of gradient check positions)
3834 - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
3835 - temporary bug fix in grdchk_loc.F for obcs
3836 o genmake2 & testreport
3837 - add target "obj" (just for OBJFILES files) to Makefile;
3838 - add option to specify FEXTRAFLAGS on command line.
3839 o pkg/mypackage:
3840 - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
3841
3842 checkpoint63a (2011/08/02)
3843 o pkg/diagnostics (velocity potential):
3844 - fix velocity-potential calculation when using OBCS: balance net inflow
3845 at each level (new S/R OBCS_DIAG_BALANCE).
3846 - fix some of the problems with OBCS in stream-function calculation.
3847 o pkg/exf/exf_readparms.F
3848 - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
3849 EXF_NML_OBCS) more consistent, so that you need not have these lists
3850 in data.exf when they are not used.
3851 o optim/optim_readdata.F:
3852 - add some output about obcs variables that might help debugging
3853 - add a check about nvarlength
3854 o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
3855 o pkg/diagnostics (velocity potential):
3856 - fix mask for OBCS (still problems in stream-function with OBCS);
3857 - add specific parameter (default = main code CG2D params) for solver;
3858 - in case of poor convergence, use solution corresponding to lowest residual.
3859 o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
3860 adjoint code. In general statements like tmpscal=fld(i,j) are problematic
3861 and should be avoided where possible.
3862 o model/src (rStar):
3863 - include r* effect on reference-state (PhiRef) in totPhiHyd
3864 (so that it's really the potential anomaly at the cell center);
3865 affect solution only if z* with full pressure in EOS.
3866 - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
3867 update output (because of z* in totPhiHyd and viscA4 changes);
3868 - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
3869 @ constant r) until interpolation at constant r is implemented.
3870 o pkg/diagnostics
3871 - fix RCENTER diagnostics in case cell center is not at interface middle
3872 o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
3873 this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
3874 that THETA and SALT are "conservative temperature" and "absolute
3875 salinity"
3876 o pkg/ctrl
3877 - fix computation of endrec in s/r ctrl_init_rec
3878 - ctrl_pack/unpack_*: remove unused variables and some obsolete code
3879 o pkg/seaice/seaice_growth.F
3880 - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
3881 remove then obsolete STORE directives
3882 - fix STORE directives for tice and tices, so that only the
3883 appropriate part of the fields are stored (and not the entire
3884 field); update global_ocean.cs32x15.seaice AD output.
3885 - cosmetic changes: adjust CPP flags and indentation for better
3886 legibilty
3887 o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
3888 Chris Wilson)
3889 o pkg/gmredi:
3890 Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
3891 and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
3892
3893 checkpoint63 (2011/07/11)
3894 o pkg/exch2:
3895 - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
3896 - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
3897 (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
3898 increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
3899 o pkg/diagnostics:
3900 - deal with pairs of post-processed diags which are computed together; in
3901 particular, re-order list of diags within 1 file to save 2nd computation.
3902 - add S/R to compute velocity stream-function (called after velocity-potential
3903 calculation) from divergence free transport -> new diagnostics "PsiVEL".
3904 - add parameter to select grid-point location where PsiVEL == 0.
3905 o eesupp/src:
3906 new S/R to calculate cumulated sum on tiled array, corner grid-cell location
3907 (specific S/R needed with exch2 topology - for now, just print an error msg)
3908 o pkg/shelfice
3909 - Implement friction velocity-dependent transfer coefficients following
3910 Holland and Jenkins, JPO, 1999
3911 Original code by M. Losch with small modifs.
3912 Enable with CPP option SHI_ALLOW_GAMMAFRICT
3913 and runtime flag SHELFICEuseGammaFrict
3914 o verification lab_sea & global_ocean.cs32x15:
3915 - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
3916 does not miss some dependencies (but is slower) and also works with many files
3917 (default makedepend limitation for AD built).
3918 - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
3919 o pkg/diagnostics:
3920 - add run-time parameter "useMissingValue" (def=False) to fill land-point
3921 (i.e., where mask=0) with MissingValue ; used only in MNC output file.
3922 This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
3923 - Extend the use of "missing_value" setting from data.diagnostics for the case
3924 of counter-diagnostics (where fraction-weight is zero). This applies both to
3925 MNC and MDS output files.
3926 o pkg/seaice/seaice_growth.F:
3927 - add 'a priori' cap of latent heat flux based on actual mass considerations
3928 when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
3929 non-legacy seaice_solve4temp.
3930 - add diagnostic of the residual sublimation freshwater flux (the freshwater
3931 flux taken from the ocean if the total actual latent heat fluxes exceed
3932 the maximum)
3933 - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
3934 fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
3935 - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
3936 SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
3937 - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
3938 - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
3939 o verification 1D_ocean_ice_column:
3940 made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
3941 update results
3942 o pkg/diagnostics:
3943 - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
3944 which are not filled-up but computed from other diags ; In this case, the mate
3945 diag points to the primary (filled-up) diag to used for post processing.
3946 - Update Velocity-potential computation using post-processed diag framework.
3947 ==> Change the ordering of fields and time-periods in MDS output file
3948 when using periodic averaging: now writes one time record with the full set
3949 of fields for this time period, then the next time reccord (it used to be
3950 one field with the full set of time records then the next field).
3951 Note: this is now similar to NetCDF (MNC) output file. <==
3952
3953 checkpoint62z (2011/06/21)
3954 o adjoint monitor:
3955 - Add adjoint monitor output for packages exf, seaice
3956 and update relevant testreport output
3957 o pkg/seaice:
3958 - re-order diags inits so that they appear in order in available_diagnostics.log
3959 - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
3960 area/heff/hsnow preceeding thermodynamic growth/melt.
3961 - modified diag: SIdA; output actual effect, as the description states.
3962 - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
3963 - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
3964 (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
3965 and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
3966 - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
3967 - added diagnostics for seaice generic tracers (SItr*).
3968 - added SItrUnit and SItrNameLong run time param (for SItr* diags).
3969 - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
3970 I. Fenty: 18-Jun-2011:
3971 Minor changes to seaice package:
3972 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
3973 added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
3974 - Differentiated "regularization variables" from "floor variables"
3975 * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
3976 * hiceMin became SEAICE_hice_reg (old hiceMin)
3977 (with _reg meaning regularization variable)
3978 - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
3979 so as to ensure energy conservation when going between phases
3980 - A22 was not used anywhere
3981 2) Changed regularization procedure for heffActual and hsnowActual to ensure
3982 well-boundedness and smooth adjoint in seaice_growth.F
3983 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
3984 because the old regularization always set heffActual >= 0.05 cm
3985 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
3986 on AREA when HEFF > 0.
3987 - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
3988 requiring that DISABLE_AREA_FLOOR *not* be defined
3989 Affected verifications:
3990 - 1D_ocean_ice_column (output.txt output_adm.txt)
3991 - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
3992 o pkg/diagnostics:
3993 - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
3994 - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
3995 (was _RL, now integer) with option = 0 to retrieve all levels.
3996 - add pieces of code to compute velocity potential at each level (new diagnostics
3997 PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
3998 for now, using same params as CG2D (target-resisual, max Nb of iter ...).
3999 - fix few issues with counter diagnostics in diagnostics_setdiag.F &
4000 diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
4001 and in diagnostics_fract_fill.F (do not need a valid pointer for the
4002 diagnostics counter-mate); check that definition of counter-diagnostic
4003 includes a valid counter-mate (in diagnostics_set_levels.F).
4004 o model/src (rStar):
4005 - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
4006 affect solution only if z* with full pressure in EOS;
4007 update output of test-exp global_ocean.90x40x15.
4008 o pkg/seaice:
4009 - introduce siEps=1e-5 parameter
4010 - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
4011 - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
4012 - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
4013 For now it covers, and was tested for, ice salinity and age (attached to HEFF),
4014 as well as ice cover age and ridging index (attached to AREA).
4015 For now the run time parameters (in data.seaice/SEAICE_PARM03) are
4016 SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
4017 Up to SItrMaxNum=3 tracers can be used simultaneously.
4018 o pkg/salt_plume:
4019 -introduce SPsalFRAC run time parameter that sets the fraction of the
4020 salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
4021 that gets vertically redistributed (fluxed down) by pkg/salt_plume.
4022 o model debug options:
4023 - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
4024 in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
4025 - Refine debug-msg printing selection (3 new levels):
4026 debugMode : controls printing of debug messages (sequence of S/R calls).
4027 debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
4028 debLevZero = 0 ; /* level of disabled aux. msg printing */
4029 debLevA = 1 ; /* level of minimum aux. msg printing */
4030 debLevB = 2 ; /* level of low aux. print (report read-file opening)*/
4031 debLevC = 3 ; /* level of moderate debug prt (most pkgs debug msg) */
4032 debLevD = 4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
4033 debLevE = 5 ; /* level of extensive debug printing */
4034 New debugLevel default: with default debugMode value (=F),
4035 = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
4036 and if debugMode=T, default debugLevel = 4 (debLevD).
4037 Relation with previous settings:
4038 debLevB (=2) corresponds to former debLevA (=1)
4039 debLevD (=4) corresponds to former debLevB (=2)
4040 Note:
4041 a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
4042 b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
4043 to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
4044 - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
4045 detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
4046 o pkg/obcs:
4047 - change OBCSfixTopo default from True to False (should not change the results);
4048 keep OBCSfixTopo=T in verification-exp. seaice_obcs.
4049 o pkg/thsice:
4050 - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
4051 2nd layer seaice sublimation (unlikely to happen)
4052 - use Interior mask for OBCS in thsice_advection.F (similar to what is
4053 done in gad_advection & seaice_advection).
4054 o adjoint:
4055 bug fix spotted by Gael Forget:
4056 seaice_advection and thsice_advection still had
4057 legacy CPP options to avoid CS corner updates for adjoint
4058 o pkg/seaice:
4059 => Change some of the defaults (2011/05/29):
4060 - change SEAICEuseFluxForm default (from False to True)
4061 - change DIFF1 default (from 0.004 m/s to 0. m/s)
4062 And print warnings if DIFF1 is not set in data.seaice and centered
4063 avection scheme is used without any diffusion.
4064 also:
4065 - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
4066 - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
4067 - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
4068 other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
4069 #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
4070 update results of test exp.:
4071 lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
4072 output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
4073 output_adm.noseaicedyn (SEAICEuseFluxForm=T)
4074 offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
4075 seaice_obcs: output (SEAICEuseFluxForm=T)
4076 and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
4077 for standard fwd & AD lab_sea tests (to keep the same output).
4078 o pkg/seaice/seaice_growth.F:
4079 - use Ian Fenty's capping formulas for actual ice
4080 thickness thoughout EVOLUTION branch.
4081 - put treatment pathological case #2) in CPP brackets
4082 (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
4083 - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
4084 o pkg/seaice:
4085 - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
4086 pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
4087 also pass fac as a param, which can be 1. (to update the tendency
4088 field) or the time step (to update the field itself).
4089 - seaice_advdiff.F: for multidim, call seaice_diffusion with
4090 e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
4091 seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
4092 - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
4093 hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
4094 o pkg/seaice:
4095 diffusion with centered advection scheme (diffus.F & advect.F):
4096 - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
4097 to just compute the laplacian of input-field.
4098 - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
4099 - fix flux-form version in diffus.F to conserve tracer.
4100 update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
4101 machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
4102
4103 checkpoint62y (2011/05/26)
4104 o pkg/seaice:
4105 - seaice_growth.F : in EVOLUTION branch, always include
4106 a_QSWbyATM_cover in qnet (as it should be).
4107 - verification/global_ocean.cs32x15 : update results accordingly
4108 (output.seaice.txt output_adm.seaice.txt).
4109 o pkg/seaice + obcs:
4110 - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
4111 equivalent of assuming no tracer gradient outside the OB region.
4112 update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
4113 - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
4114 after changes above);
4115 - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
4116 only at OB location (instead of over a band of OLx width).
4117 o pkg/seaice:
4118 - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
4119 (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
4120 o pkg/obcs:
4121 - split header file "OBCS.h" into 4 separated files:
4122 OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
4123 Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
4124 (contain no conditional statement which depends on OBCS options).
4125 - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
4126 to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
4127 o ctrl, cost, grdchk & autodiff pkgs:
4128 - make options file more standard (like other {PKG}_OPTIONS.h file but
4129 with AD_CONFIG.h); clean-up some of the included header files.
4130 o pkg/obcs:
4131 - do not mask tracer when applying OB (tracer == 0 could generate problems)
4132 - apply tracer OB values to tracer field only at OB location (instead of
4133 over a band of OLx width)
4134 - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
4135 - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
4136 obcs_apply_tloc.F & obcs_apply_sloc.F
4137 o obcs in model/src:
4138 - call OBCS_APPLY_W only if NonHydrostatic.
4139 - call OBCS_APPLY_ETA only if NonLinFreeSurf.
4140 - reset dEtaHdt and wVel to zero outside OB interior region ;
4141 - leave tracer unchanged outside OB interior region: This has no effect
4142 on the solution but just to prevent unrealistic tracer value outside OB.
4143 - zero out velocity outside OB interior region: This has no effect on
4144 the solution but just to prevent unrealistic velocity outside OB.
4145 o obcs and non-lin free-surf:
4146 move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
4147 and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
4148 + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
4149 this fixes missing EXCH + get consistent eta OB value (+ fix restart).
4150 update results of test-exp. exp4(nlfs).
4151 o exp4 (nlfs) test-exp:
4152 use OBC for Eta at Western & Eastern OB (to test prescribing Eta
4153 with NonLin-FreeSurf); update output.nlfs.txt
4154 o obcs and 2d/3d solver norm:
4155 use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
4156 and outside OB interior region (will allow to place OB further inside the
4157 domain). Depending on the domain, can affects cg2d-Norm (previous
4158 cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
4159 and cg3d-Norm (previous Norm was computed before canceling OB terms),
4160 e.g. in tutorial_plume_on_slope.
4161 - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
4162 o pkg rbcs:
4163 - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
4164 - add capability to apply relaxation to horizontal velocity uVel & vVel.
4165 o pkg/grdchk: add gradient check for control variable xx_shifwflx
4166 o pkg/shelfice/shelfice_init_fixed.F
4167 fix CPP-flag combinations
4168 o pkg/seaice: Merge iceage code of Pierre Rampal
4169 * update/change/correct ice age calculations
4170 * add age updates for pathological cases
4171 Probably needs more testing...
4172
4173 checkpoint62x (2011/05/13)
4174 o pkg/mom_vecinv:
4175 high-order vorticity scheme: use interior masks (maskInW & S)
4176 to zero-out (outside OB) gradient of vorticity.
4177 o verification exp.:
4178 turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
4179 hs94.128x64x5 and seaice_obcs ; update results.
4180 o pkg/obcs:
4181 fix bug in OBeta for YZ sections in obcs_exf_load.F
4182 o pkg/ctrl, pkg/shelfice, and optim:
4183 - add new control variable xx_shifwflx (fresh water flux underneath ice
4184 shelves). This is almost as tedious as obcs-ctrl, because the
4185 variables needs its own mask.
4186 - add a cost function term that penalizes the deviation of xx_shifwflx
4187 from the first guess (zero) in analogy to other control variables
4188 o pkg/shelfice:
4189 - start basic adjoint
4190 o pkg/ctrl:
4191 - remove extra 2D field "for good measure" when initializing in
4192 ctrl_set_globfld_[xy/xz/yz].F
4193 - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
4194 - improve error messages in ctrl_set_unpack_*
4195 o OBC implementation in momentum:
4196 use interior masks (maskInC,W & S) in momentum S/R:
4197 - multiply divergence, tension and some del^i.u or del^j.v by maskInC
4198 - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
4199 - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
4200 - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
4201 Motivation: fix/clean implementation of OBC with biharmonic-viscosity
4202 (and also with Leith/Smagorinsky harmonic-viscosity).
4203 Update output of experiment dome and exp4 (+nlfs).
4204 o exp4 test-exp:
4205 - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
4206 and prescribe time-varying OB (without pkg/exf) for zonal-velocity
4207 at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
4208 time-varying OB at Western-side for wVel (NonHyd); update output.
4209 - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
4210 and biharmonic-viscosity ; also use prescribed time varying OB.
4211 o pkg/obcs:
4212 fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
4213 o model/src:
4214 - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
4215 - initialise startTime & nIter0 with unlikely values: allows to set one
4216 from the other without ambiguity.
4217 o seaice_obcs test-exp.:
4218 add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
4219 o pkg/obcs:
4220 - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
4221 no longer needed with maskInC,W,S in pkg/generic_advdiff.
4222 o pkg/seaice:
4223 - retired SEAICE_SALINITY and SEAICE_salinity in favor of
4224 SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
4225 - fixed bug in the initialization of sea ice salinity variable HSALT
4226 in seaice_init_varia.F (removed dependence on ICE2WATR)
4227 o fizhi-cs test exp.:
4228 switch reference output convention for these 2 non-standard test-exp,
4229 from: pgi 6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
4230 to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
4231 reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
4232 o model/inc:
4233 - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
4234 of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
4235 o pkg/seaice:
4236 - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
4237 o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
4238 - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
4239 and initial HSALT
4240
4241 checkpoint62w (2011/04/26)
4242 o pkg/mom_fluxform:
4243 - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
4244 - use parameter "sideDragFactor" in no-slip BC side-drag part.
4245 - update output of exp. global_ocean.90x40x15
4246 o pkg/mom_vecinv:
4247 mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
4248 o update seaice exp.:
4249 use more consistent parameter values (remove "backward compatability only":
4250 ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
4251 related to thermodynamics seaice. Update output (fwd+AD) of exp.:
4252 1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
4253 o update test-exp global_ocean.90x40x15:
4254 o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
4255 o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
4256 o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
4257 o turn on zStar & viscA4 in standard set-up (dir input/)
4258 and update output files: output.txt & output.dwnslp.txt
4259 o new AD-test experiment: obcs_ctrl
4260 (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
4261 o pkg/dic:
4262 fix two bugs in handling water vapour pressure in carbonate chemistry
4263 and air-sea fluxes. Found by Val Bennington and Galen McKinley
4264 (add DIC Option = WATERVAP_BUG to recover old results)
4265 update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
4266 o adding allowInteriorFreezing option to check for water below freezing point
4267 at depth and bring the negative heat anomaly to the surface level
4268 o pkgs _fields_load:
4269 - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
4270 - use new S/R GET_PERIODIC_INTERVAL in pkgs:
4271 bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
4272 rbcs to get interpolation weights and time reccord number.
4273 - fix multi-threading in aim_fields_load.F
4274 - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
4275 o external_fields_load:
4276 new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
4277 interpolation weights) to use in a periodic time-series ; do not divide by
4278 time-step to convert to integer:
4279 - this fixes case where externForcingPeriod is not multiple of time-step
4280 (Thanks to Christopher L. Wolfe)
4281 - this fixes case where externForcingPeriod is an odd multiple of time-step
4282 (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
4283 store index of time-record which is currently loaded:
4284 - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
4285 - needed for the adjoint but not yet used because of extensive recomputations;
4286 (to be fixed soon)
4287
4288 checkpoint62v (2011/04/02)
4289 o verification/1D_ocean_ice_column added to test Ian Fenty's
4290 pkg/seaice_growth.F modifications for improving sea ice code differentiability
4291 o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
4292 (new velocity statistics after changing maskInW & maskInS definition)
4293 o pkg/generic_advdiff with OBCS:
4294 use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
4295 equivalent to assumption of no tracer gradient outside the OB region.
4296 This will affect the results if using obcs+biharmonic diffusion.
4297 update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
4298 o pkg/obcs:
4299 change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
4300 (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
4301 in Interior region. No impact on solution but affects Velocity monitor stats.
4302 o pkg/ptracers (adjoint)
4303 New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
4304 tape file for each tracer
4305 o model/inc/src and pkg/autodiff: add parameters that allow to turn
4306 of parts of the adjoint code at run time. For now, there are only
4307 useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
4308 parameters are set in data.pkg.
4309 This is the lazy coward's version of doing this, but still useful for
4310 debugging. In order to do it right, everything needs to be moved to
4311 pkg/autodiff.
4312 o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
4313 the end; this fixes the adjoint balancing code for open boundaries.
4314 o pkg/ctrl:
4315 - change behavior of xx_${varname}period to be analogous to exf-conventions:
4316 xx_${varname}period = 0., means time-independent control part
4317 xx_${varname}period = -12., means one-year-periodic monthly control part
4318 - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
4319 clean up ctrl_init a little, remove unused variables
4320 - ctrl_init: fixed the handling of the start/endrec for obcs-variables
4321 - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
4322
4323 checkpoint62u (2011/03/15)
4324 o model/src:
4325 - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
4326 h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
4327 - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
4328 INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
4329 o pkg/ctrl/obcs/ecco:
4330 - remove obsolete, unused, and partially broken code:
4331 ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
4332 ALLOW_CTRL_OBCS_BALANCE
4333 - put a stop statement into ecco/cost_obcsvol.F, but also add
4334 cost_obcsvol to ecco_ad_diff.list
4335 o pkg/ecco: fix counting cost function contributions for obcs (code
4336 by Matt M.) and diffkr for diagnostics
4337 o pkg/ecco, pkg/ctrl, pkg/grdchk:
4338 add cost penalty terms for initial uvel, vvel, eta controls
4339 and I/O for prior error files
4340 o pkg/mdsio:
4341 move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
4342 (new argument) to check for tiled file in mdsioLocalDir : this fix the
4343 restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
4344 o pkg/ctrl:
4345 - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
4346 ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
4347 unused and superfluous variables
4348 - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
4349 o pkg/ecco
4350 - enable adjoint of Stevens OB
4351 o pkg/ctrl/ecco/grdchk:
4352 - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
4353 Fortunately, we do not have any tests for the numerous cpp-flagged
4354 option of "obcs as control parameters" so we will never know
4355 if this is an improvement (but at least now things compile).
4356 - remove an obsolete initialization from ecco_cost_init_barfiles.F
4357 - fix some problems within never used ifdefs to make the code compile
4358 o pkg/obcs:
4359 - Refine Interior mask definition to work with more complex OB (e.g.
4360 if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
4361 read in Interior mask from file. Check if Interior mask is consistent
4362 with OB list of indices.
4363 o pkg/seaice
4364 - beginning code for a seaice tracer package,
4365 but currently only used for seaice age: SEAICE_AGE
4366 SEAICE_num = 4
4367 iTracer = 1: area-weighted ice age
4368 = 2: volume-weighted ice age
4369 = 3, 4: template for one-year vs. multi-year ice
4370 data.seaice has new namelist SEAICE_PARM03 for arrays related to
4371 SEAICE_num
4372
4373 checkpoint62t (2011/03/05)
4374 o pkg/obcs:
4375 - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
4376 then normal component. This ensures that the normal component is set
4377 correctly even when it conficts with tangential setting from an other OB.
4378 Affects results of test-experiment seaice_obcs: update the output.txt
4379 o pkg/obcs:
4380 - add code to monitor statistics of dynamical fields at OB.
4381 - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
4382 - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
4383 - change default: balance the Net inflow through all OB (instead of balancing
4384 each OB separately); keep the old method if setting OBC_balanceFacX < 0.
4385 - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
4386 to match Nortern OB inflow (OBCS_balanceFacN=0).
4387 o pkg/seaice:
4388 - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
4389 o pkg/seaice (seaice_growth v 1.113):
4390 - reverting seaice_growth to v 1.111 in order to have code with exact bit
4391 compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
4392 CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
4393 runtime flag SEAICEareaFormula is kept but is inactive
4394 o model/src:
4395 - add new param to scale curvilinear grid distance and area when using
4396 a different sphere radius from the grid-files.
4397 - test/check multi-threads EXCH applied to local variable (cg2d_x)
4398 o adjoint:
4399 - enable adjoint of Stevens OB
4400 - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
4401 (a bit delicate because of potentially modified adj. common block structure;
4402 current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
4403
4404 checkpoint62s (2011/02/15)
4405 o pkg/seaice (seaice_growth v 1.112):
4406 - introduce SEAICEareaFormula run time parameter, which selects the recipe for
4407 computing the ice cover tendency from effective thickness tendencies. Include
4408 Ian Fenty's formula.
4409 - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
4410 SEAICEareaFormula.
4411 - simplify notations for the various d_HEFF/d_AREA terms.
4412 o pkg/gmredi:
4413 - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
4414 from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
4415 add a verification test-run (front_relax.bvp) to test GM_useBVP.
4416 o pkg/seaice (seaice_growth v 1.111):
4417 - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
4418 - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
4419 also melt ice.
4420 o pkg/seaice:
4421 - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
4422 - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
4423 o pkg/cheapaml:
4424 - from Nico Wienders: New version of this package.
4425 o pkg/flt:
4426 - add CPP options to prevent floats to re-enter the opposite side of
4427 a periodic domain (default: keep periodicity)
4428 o pkg/gmredi:
4429 - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
4430 (needed for multi-dim advection).
4431 - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
4432 o model/src:
4433 - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
4434 o tutorial_tracer_adjsens
4435 - extend to NLFS and replace maskC by hFacC
4436 (change reference output accordingly)
4437
4438 checkpoint62r (2011/01/24)
4439 o testreport:
4440 - add option -deloutp (-do) to remove output file after successful run
4441 - add option -mfile (-mf) for MPI machile-file and for each test-exp,
4442 extract exact list of procs from this file ; adjust COMMAND by
4443 replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
4444 o pkg/ecco: replace old ineffective way of penalizing deviations from
4445 first guess (of obcs) with code by Matt Mazloff
4446 o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
4447 exf/cal
4448 - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
4449 and handle case of obcs?period == 0
4450 Not affected by these changes: There is still an inconsistency in
4451 the computation of start/endrec for the obcs variables for ALLOW_CAL
4452 defined (see comment by Menemenlis, 7-Mar-2003)
4453 - make S/R ctrl_get_gen_rec return something meaningful even if
4454 ALLOW_CAL is not defined
4455 - ctrl_getobcs?: simplify code so that it does not need to use
4456 S/R exf_swapfields
4457 o testreport:
4458 allow to test MPI with different number of processors for each experiment:
4459 create file "SIZE.h.mpi" in each build dir.
4460 Note: update of "-command" argument not yet implemented.
4461 o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
4462 alleviate the need for additional 3D tapes when using
4463 the non-inear free surface in the adjoint. This is done
4464 by adding an 'update' of hfacc etc. to their current
4465 value at the beginning of forward_step.F.
4466 o pkg/seaice
4467 seaice_lsr: move stress-divergence computations out of outer pseudo-
4468 timestepping loop
4469 o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
4470 up, so that the calls of the ctrl_* subroutines are really at the end
4471 of the routine.
4472 o pkg/gmredi:
4473 allow to specify a 2-D horizontal map and a 1-D vertical profil
4474 as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
4475 o pkg/seaice:
4476 move lsr iterations from seaice_dynsolver to seaice_lsr.
4477 o pkg/seaice:
4478 reduce memory footprint of seaice mutldim advection tapes,
4479 by using a 2D tape independent of the generic_advdiff ones,
4480 and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
4481
4482 checkpoint62q (2010/12/29)
4483 o model/src:
4484 - check horizontal grid-spacing for unset or zero/negative values.
4485 - change AD test hs94.1x64x5 to be truly a 2-D set-up.
4486 o pkg/flt:
4487 - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
4488 - precision of input and output files set according to readBinaryPrec
4489 and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
4490 - initial float position from tiled file was not converted to index space
4491 (looks like a bug): fixed to make it similar to initial pos. global file.
4492 o global_ocean.cs32x15:
4493 change SIZE.h of AD set-up to get same tiling as with MPI.
4494 Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
4495 o model/src:
4496