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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2172 by jmc, Thu Jul 16 23:26:38 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/offline:
8      - change (rarely used) offset-iteration parameter to an offset time (in s):
9        can easily recover previous offset-iter effect by setting offset-time
10        (offlineTimeOffset) to offset-iter x deltaToffline;
11      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
12        in KPP as part of surface buoyancy forcing) in offline run.
13      - fix ptracers KPP non-local term in the case where KPP is re-computed.
14    o OpenAD
15      - Adding preliminary ggl90 test to OpenAD verification.
16        Config. with ggl90 currently diverges after 64 time steps
17        so will need more work to become more stable
18      - Adding preliminary kpp test to OpenAD verification.
19        required small tweakes in kpp_routines.F
20      - Merge and update from Krishna Narayanan's contrib area:
21        * Add one variable for preliminary OpenAD DIVA
22        * Add replacement time-stepping for OpenAD DIVA
23        * genmake2 flag -diva (but only for OpenAD; preliminary)
24        * required modifs for OAD_support
25        successful preliminary test for tutorial_global_oce_biogeo/
26    o pkg/seaice:
27      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
28      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
29        delta with a smooth function in s/r seaice_calc_viscosity
30        (no effect on EVP)
31      - rename local suffix "sqr" into "sq" for more consistent variable names
32    o pkg/seaice:
33        add new parameter SEAICE_deltaMin that is used ***only***
34        for regularizing Delta (and nothing else, like the parameter
35        which is also used for all sorts of things SEAICE_EPS).
36        Defaults to SEAICE_EPS for backward compatibility only.
37    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
38        the wrong key by inialising it before use -> fixes a recomputation
39        problem but does not fix the gradient
40    o pkg/layers:
41      - move resetting of flux arrays to outside the iLa loop
42        (this caused layers_diapycnal to not work with more than one layer coord.)
43      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
44    o pkg/layers:
45      - remove from common block 3D layers fields (used to diagnose transport
46        in tracer coords) and declare them as local arrays in layers_calc.F
47    o pkg/seaice:
48      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
49        in lab_sea forward experiment (changes results -> updated)
50      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
51    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
52       computations; for SEAICE_VECTORIZE_LSR
53      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
54        sweep to the outside,
55      - remove store directives and add "CADJ loop sequential" directives
56        in analogy to model/src/solve_tridiagonal.F
57      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
58        boundaries to yield more readable code. This has also the charming side
59        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
60        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
61        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
62        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
63        an additional option)
64       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
65       but the adjoint gradients (which are affected by this change) still explode.
66    o coupler (atm & ocn _compon_interf):
67      - avoid using Exch2 IO mapping if not suitable.
68    
69    checkpoint65m (2015/06/15)
70    o pkg/layers:
71      - clean-up old parameters setting (from Sep 2012):
72        + remove old parameters setting from common block (declared locally);
73        + stop if any old parameter is mixed with new parameters;
74        + check for valid or consistent parameter setting (e.g., layers_name)
75      - check that layers_bounds for Pot.Density are in the right range;
76        this is supposed to catch un-updated setting after recently shifting
77        potential density field "prho" by -1000 (now in "sigma" scale).
78    o pkg/layers:
79      - Added missing call to layers_fill for keeping track of tottend in
80        pkg/diagnostics/diagnostics_fill_state.F
81    o pkg/layers:
82      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
83        of diapycnal fluxes
84    o pkg/layers:
85      - reverted changes to interpolation to previous treatment; there
86        was never actually a problem
87    o pkg/layers:
88      - fix interpolation of layers tracers in the presence of partial cells
89      - add lots of new functionality to compute water mass transformation
90        (enabled by CPP flag LAYERS_THERMODYNAMICS)
91      - add new calls from main code (diags_oceanic_surf_flux.F,
92        thermodynamics.F, impldiff.F) and gad to save the necessary fields
93        for layers_thermodynamics calculations
94    o pkg/ptracers:
95      - add capability of stepping a passive tracer forward without advection
96        by setting PTRACERS_advScheme to 0.
97    o pkg/diagnostics:
98      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
99    o pkg/layers:
100      - shift potential density field "prho" by -1000 for density layer averaging so
101        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
102        Note that density bin boundaries (layers_bounds in data.layers) have
103        to be set accordingly (i.e., shifted, in sigma scale).
104    o pkg/layers:
105      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
106      - fix calculation of layer non-weighted velocity and layer probability
107      - add diagnostics for pot.density used for layer averaging
108    o pkg/seaice:
109      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
110        positiveness, modify a few comments and improve variable names,
111      - the changed computation of deltaC affects most seaice-related
112        experiments at the truncation level.
113        seaice_itd.thermo is affected by far the most, with
114        only 7 digits of agreement remaining; update experiments.
115    
116    checkpoint65l (2015/05/04)
117    o pkg/shelfice:
118      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
119        factor drKp1 to zero where it is negative (ie. do not use
120        SHELFICEBoundaryLayer if hFacC>1)
121      - the same for factor drLoc in shelfice_forcing.F
122    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
123        with modules in ptracers, when using testreport option "-small_f"
124    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
125      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
126    o verification/testreport
127      - add new option -small_f
128        with this option testreport first makes the target small_f (*.f files)
129        before running make (all). This is useful for explicit inlining when
130        all sources need to be full available.
131    o pkg/exf/exf_interp.F:
132        remove previous changes related to reverse (decreasing) input grids latitude
133    
134    checkpoint65k (2015/04/01)
135    o pkg/ecco:
136        fix missing cosphi initialization; use eccoiter in place of optimcycle;
137        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
138        instead of active read/write
139    o pkg/ctrl:
140        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
141        instead of active read/write.
142    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
143        return if .NOT.useAUTODIFF
144    o pkg/seaice: add CPP brackets (cost function related).
145    o model/src:
146        add useAUTODIFF run time switch.
147    o pkg/exf/exf_interp.F:
148        add code to allow input grids with latitude starting in the north (i.e. when
149        j=1 corresponds to northern edge of field); modify global_with_exf to test
150        this feature.
151    o verification/testreport:
152      - replace "grep -A3" with POSIX conformal sed command, because there are
153        implementations of grep that cannot do contextual searches
154      - replace "cat -n" by "nl" (two occurrences), because not all implementations
155        of "cat" have the option "-n"
156    o model/src:
157        add new file gsw_teos10.F that contains 3 functions, more or less a copy
158        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
159        convert from conservative to potential temperature. For now they are not
160        called anywhere.
161    o pkg/ggl90: make "useIDEMIX" useful
162      - re-organize code in s/r ggl90_calc a little to move computations that
163        are different for idemix into separate loops (changes verification
164        experiment idemix at truncation level, 12 digits remain -> updated)
165      - requires 2 new 2D fields KappaM, verticalShear
166      - make hFacI and recip_hFacI local 3D variables that are passed to
167        s/r ggl90_idemix
168      - fix and improve some comments
169    
170    checkpoint65j (2015/02/25)
171    o pkg/openad
172      - synchronize seawater.F with version in model/src: replace routine
173        body of sw_temp by calling sw_ptmp and fix/add a few comments.
174    o pkg/mnc:
175      - change default value of pickup_read/write_mnc params to FALSE
176        (since few features are missing in reading MNC pickup files).
177    o model/src:
178      - change default (background) vertical diffusivity for salt to be the
179        temperature (background) vertical diffusivity.
180      - change background vertical diffusivity in vertical mixing pkgs ggl90,
181        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
182        This makes ptracers default diffusivity (that uses salt diffKr) more
183        consistent with vertical mixing schemes.
184    o verification/testreport:
185      - fix typo in "-pcls" option ;
186      - put temp files in /tmp (instead of in local dir)
187      - add option "-ncad" to use genmake2 new option "-nocat4ad"
188      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
189    o pkg/ggl90 (idemix code):
190      - apply few fixes ; add some missing "_d 0" ; update output of exp.
191        global_ocean.90x40x15.idemix
192    o OpenAD
193      - enable active file I/O and begin removal of work-around code
194        for OpenAD for handling control variables (memory vs. active files)
195      - new CPP options file OPENAD_OPTIONS.h
196      - revert to genarr2d gradient check for hs94.1x64x5
197      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
198      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
199    o tools/genmake2:
200      - add option for an alternative Makefile (from Martin) where multiple
201        source files are sent to TAF (instead of all in one file).
202    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
203      - code provided by Carsten Eden as an extension of ggl90
204      - so far the code is turned on within ggl90 by setting a CPP-flag at
205        compile time; a runtime flag implementation is not yet complete
206      - tested in new verification experiment global_ocean.90x40x15.idemix
207    o verification:
208      - reduce length of the AD test run by half for experiments
209        global_ocean.cs32x15 (std + thsice) and isomip
210      - enable active file I/O for OpenAD, adjust verifications accordingly
211      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
212    o verification/testreport:
213      - fix two non-POSIX sed statements so that there are no error messages
214        on Mac OS X
215      - replace hostname -s with hostname | sed 's/\..*$//'
216    o model/src/seawater.F:
217      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
218        (following the matlab code), which would have avoided the bug caught
219        by Matt (see below) in the first place
220    o pkg/shelfice:
221      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
222        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
223      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
224        ice-shelf case (i.e., within surface level).
225      - add config summary in shelfice_check.F
226      - remove global variable recip_SHELFICElatentHeat and replace by a local
227        variable recip_latentHeat
228      - introduce diagnostics for friction velocity uStar (in case of
229        SHELFICEuseGammaFrict)
230      - change verification experiment isomip.htd:
231        + start from pickup (as input_ad at nIter0=8640)
232        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
233        + test SHELFICEuseGammaFrict = .TRUE.
234        + test SHELFICEadvDiffHeatFlux = .TRUE.
235    o model/src:
236      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
237        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
238        update output of experiments global_with_exf.yearly and isomip (all 6).
239    o pkg/shelfice:
240      - change setting of kTopC to also be zero where there is no ice-shelf.
241      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
242        ice-shelf is.
243      - first attempt to get RealFreshWaterFlux effects: for now, only without
244        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
245    o pkg/seaice: add the option to prescribe a fixed thickness PDF
246      for thermodynamic calculations
247      - because of divisions of the type 7/7 not exactly equal to 1, this change
248        affects results of some verification experiments by up to 4 digits:
249        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
250        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
251        adjoint: lab_sea, lab_sea.noseaicedyn
252        -> updated
253    
254    checkpoint65i (2015/01/23)
255    o model/src:
256      - change units of frictionHeating field from W to W/m^2
257      - fix bug in frictional heating from stratospheric drag in
258        S/R ATM_PHYS_TENDENCY_APPLY_V
259      - with synchronous time-stepping: move resetting to zero of frictionHeating
260        field from load_fields_driver.F to thermodynamics.F ;
261      - add diagnostics for frictional heating.
262    o model/src & gmredi K3D:
263      - add frictionHeating field to pickup-files (for synchronous time-stepping)
264      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
265      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
266        and name in pickup file).
267      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
268    o model/src:
269      - move (from ini_forcing.F) initialisation of all arrays in header file
270        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
271        (since Nov 2012) with option selectAddFluid=1.
272    o pkg/shelfice:
273      - change units (+ document) of newly added field "shelfIceMassDynTendency"
274      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
275    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
276    o pkg/seaice: two new runtime parameters:
277      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
278        long overdue
279      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
280        parameterization of tensil stress for fast ice (does not do anything yet)
281    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
282        for LSR: move checking overlaps out of JFNK-if-block
283    o pkg/atm_phys:
284      - move copy of grid and dynamical fields out of atm_phys_driver.F into
285        new S/R ATM_PHYS_DYN2PHYS.
286      - fix level height for Linear Free-Surf case (to be consistent with
287        fixed-in-time pressure levels).
288    o pkg/mom_common (bottomdrag):
289      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
290        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
291        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
292    o pkg/shelfice (u/v_drag):
293      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
294      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
295        (now similar to shelfice_u_drag.F)
296      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
297        from mom_vecinv.F (similar to mom_fluxform calls).
298    o pkg/mom_common (bottomdrag):
299      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
300      - add options for alternative discretisation of velocity norm in quadratic
301        bottom drag: averaging of grid-cell-center KE to U.point and V.point
302        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
303        improves when averaging only the other component (e.g. vVel for U bottom
304        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
305      - add options (bottomVisc_pCell) to account for partial-cell in bottom
306        friction (no-slip BC) thus getting the true distance from the bottom;
307        off by default since this also reduces model stability (explicit bottom
308        friction). Changes produce different machine truncation with linear-drag
309        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
310        front_relax (bvp & mxl, 10 & 11 digits).
311    o model/src & mom pkgs:
312      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
313        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
314      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
315        just copy level Nr value to level Nr+1.
316    o doc:
317      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
318    o pkg/streamice:
319      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
320        SHELFICE.h: move array shelficemass to init_varia, initialise
321        from array shelficemassinit, which is set in init_fixed and
322        has option to be set from file; introduce array
323        shelficeMassDynTend array, set thru file in init_fixed
324      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
325        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
326        pkg/streamice
327      - shelfice_thermodynamics.F: call shelfice_step_icemass if
328        SHELFICEMassStepping = .true.
329      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
330    
331    checkpoint65h (2014/12/17)
332    o verification/global_ocean.90x40x15, global_ocean_ebm:
333      - update to generic controls.
334    o pkg/ctrl:
335      - ctrl_map_ini_genarr.F: test for igen>0
336      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
337      - move gentim2d part of ctrl_map_ini_genarr.F to
338        new separate routine : ctrl_map_ini_gentim2d.F
339      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
340        add time variable weights and cyclic controls (time mean,
341        seasonal cycle, etc) capabilities to gentim2d
342    o pkg/ecco:
343      - move reading of error, conversion to weights from
344        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
345    o global_oce_llc90, cs32:
346      - activte sbo.
347      - CTRL_SIZE.h : add maxCtrlProc.
348      - activate the new genctrl capabilities.
349      - update following reorganization of global_oce_input_fields.tar.gz  
350    o pkg/ctrl/ctrl_ad_diff.list:
351      - add missing ctrl_init_rec.f
352    o tools/OAD_support/keepOriginal:
353      - add ctrl_init_rec.F
354    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
355      - avoid recomputations of xx_gentim2d_dummy.
356    o momentum diagnostics:
357      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
358        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
359    o pkg/seaice/seaice_lsr.F:
360      - fix computation of BU/BV, make sure they are non-zero, only necessary
361        for cubed sphere exchanges and SEAICE_OLx/y>0.
362        This makes calling s/r fill_cs_corner_rl obsolete (removed).
363    o verification/global_ocean.cs32x15/input.seaice
364      - add test for strong implicit coupling and restricted addtive Schwarz
365        methods for LSR
366      - update results/output.seaice.txt
367    o verification/tutorial_global_oce_biogeo:
368      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
369        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
370        update output_adm,_oadm,_tlm.txt
371    o pkg/dic:
372      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
373      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
374        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
375    o verification/tutorial_global_oce_biogeo:
376      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
377        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
378        update output_adm,_oadm,_tlm.txt
379    o eesupp/src:
380      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
381        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
382    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
383      LSR (following Hutchings et al. 2004)
384      - introduce zetaZ as a global variable (requires adjustments in
385        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
386        in seaice_calc_viscosities.F
387      - new flag SEAICEuseStrImpCpl (default off)
388      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
389        momentum equations
390      - JFNK-solver (preconditioner) adjusted to allow using this method
391        (where it does not have any positive effect)
392    o pkg/seaice
393      - add overlap for restrictive additive Schwartz method also to LSR, but
394        turn it off by default (because it only seems to work for non-cubed
395        sphere/llc topologies)
396    o pkg/autodiff
397      - add extra exchanges in addummy_in_steppging also for mnc output
398    o pkg/seaice:
399      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
400        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
401    o pkg/obcs:
402      - add option to specify domain-connected piece Id along OB though files
403        (for now, only used to diagnose PhiVel; default =1 -> global correction)
404      - modify obcs_diag_balance.F to process each connected-part separately;
405        exclude OB where Id = 0 but keep the full divergence there (-> constant
406        Psi along this portion of OB and all inflow derived from grad(Phi))
407      - add example of OB-conect files in verification/so_box_biogeo/input.
408    o pkg/diagnostics:
409      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
410      a) use non zero matrix element across OB and solve for Phi 1 grid point
411         outside OB (i.e, where tracer OBCS are applied).
412      b) global imbalance of inFlow/outFlow across OB: instead of modifying
413         velocity across OB, spread it uniformly along the OB in the RHS.
414    
415    checkpoint65g (2014/11/19)
416    o pkg/diagnostcis:
417      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
418    o pkg/my82,pp81,kl10:
419      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
420        field diffKr as background diffusivity to set minimum diffusivity value.
421    o pkg/seaice:
422      - add new parameter SEAICEuseEVPrev (for revisited EVP by
423        Bouillon et al 2013)
424      - add SEAICE_evpAlpha/Beta to namelist
425      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
426        involve trivial re-ordering of divisions/multiplications that should not
427        have any effects, but ... they do change the results of lab_sea.hb87 so
428        that only 2 digits of agreement remain, in line with the general
429        instability/fragility of the evp-code. For now, I do not care and just
430        update the verification experiment
431    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
432      - remove xx_genarr2d_numsmooth etc
433      - use xx_genarr2d_preproc etc instead
434      - carry out smooth_correl2D at initialization stage rather than during
435        time stepping.
436      - get smoothOpNb from xx_gentim2d_preproc
437    o global_oce_cs32 :
438      - add test of generic ecco capabilities.
439    o pkg/exf/exf_getsurfacefluxes.F :
440      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
441    o pkg/ctrl,ecco :
442      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
443        is defined.
444    o pkg/seaice: add diagnostics for Delta (deformation parameter)
445    o model/src:
446      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
447        diffusivity (background) is specified but ignored.
448    o verification:
449      - in testreport, convert hostname to lower case for default output dir name
450    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
451    o pkg/dic: add modifications from Hajoon:
452      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
453      - light attenuation: add self-shading effect by climatological Chlorophyll
454        (read from file).
455    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
456        compiles when SEAICE_ALLOW_DYNAMICS is undefined
457    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
458        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
459        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
460        approach where CPP_OPTIONS.h includes an omnipotent
461        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
462    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
463        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
464    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
465        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
466        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
467    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
468      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
469      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
470      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
471      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
472    o pkg/ctrl,ecco,exf :
473      - remove variables associated with NON-generic costs,
474        unless ECCO_CTRL_DEPRECATED is defined.
475      - remove NON-generic NON-obcs controls,
476        unless ECCO_CTRL_DEPRECATED is defined.
477    o pkg/ctrl : added ctrl_local_params.h
478    o pkg/ecco : added ecco_local_params.h
479    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
480        experiments, which will progressively be removed once the
481        experiments are revised to use only generic controls/costs.
482    
483    checkpoint65f (2014/10/13)
484    o pkg/ctrl, ecco, seaice : minor changes in headers
485    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
486        cost function and control capabilities added since checkpoint65c.
487    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
488    o pkg/ecco: increase modularity and improve logic
489      - ecco_toolbox.F (new) : basic operations that are often used,
490        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
491        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
492      - cost_gencal.F (new) : determine filnames and records.
493      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
494      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
495        and exploit the above functions leading to more compact code.
496      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
497      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
498        using_ers, using_gfo, using_mdt is now only defined within gencost)
499    o pkg/ecco: extend generic cost capabilities
500      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
501        capabilities via gencost_preproc (+ _c,_i,_r related params),
502        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
503        gencost_outputlevel arguments to cost_generic
504      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
505        and active_read, making room for gencost_preproc to take effect.
506        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
507      - pkg/ecco/cost_generic.F :
508        compute and store misfit maks*(model-data) in localdif that is
509        then used in cost and for output, output misfit if outlev.GT.0
510      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
511        rather gencost_barfile for deciding whether to write barfile
512      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
513      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
514        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
515      - pkg/ecco/ecco_summary.F : report gencost variables
516      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
517    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
518    o pkg/ecco: internal re-organization
519      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
520        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
521        mv relevant variables definition from ecco_cost.h to ecco.h,
522        make sure gencost routines only include ecco.h)
523      - throughout : add missing CCP switches, rm unused variables,
524        and rm un-necessary CPP switches
525      - throughout gencost routines : replace modelstartdate with
526        gencost_startdate when needed
527      - cost_bp_read.F : use arguments, instead of common blocs
528        so that it can be used also by (new) cost_gencost_bpv4.F
529      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
530      - ecco_phys.F : compute etanFull
531      - ecco_readparms.F : rename using_topex as using_tpj, add
532        bpv4-grace to gencost list, initialize added parameters
533      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
534    
535    checkpoint65e (2014/09/28)
536    o pkg/obcs:
537      - replaced the just-added CPP options with run-time variables
538        (see pkg/obcs/OBCS_PARAMS.h for details)
539    o pkg/obcs:
540      - add additional CPP options for sponge boundary layers
541        (see pkg/obcs/OBCS_OPTIONS.h for details)
542    o pkg/atm_phys:
543      - implement simple (obliquity only, assuming circular planet orbit)
544        seasonal cycle for incoming insolation ; used when run-time parameter
545        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
546    o pkg/exf, pkg/ecco, pkg/ctrl:
547      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
548      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
549      - implement gentim2d for xx_tauu, xx_tauv
550    o pkg/ctrl, pkg/ecco :
551      - fix and complement the generic controls implementation
552    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
553        pkg/shelfice/shelfice_thermodynamics.F,
554        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
555        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
556      - add weight in CTRL_GET_GEN calls
557    o pkg/ctrl :
558      - ctrl_get_gen.F : add weight as input parameter, and apply
559        it directly rather than using smooth_correl2Dw (to be retired).
560      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
561    o pkg/ctrl :
562      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
563        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
564      - re-activate ctrl_summary (call in ctrl_init.F)
565    o pkg/ctrl/ctrl_cost_gen.F :
566      - fix CCP brackets, remove un-necessary myiter, mytime
567    o pkg/ecco, pkg/ctrl :
568      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
569      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
570      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
571      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
572    
573    checkpoint65d (2014/09/15)
574    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
575      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
576        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
577    o pkg/ctrl/ctrl_map_ini_genarr.F :
578      - remove compilation failure
579      - replace hard coded example
580      - use ctrl_map_ini_gen2D, 3D
581    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
582      - on/off switch based upon xx_genarr2d_weight,3d
583    o src/packages_init_variables.F :
584      - regroup pkg/estimation calls
585      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
586        (moved to ctrl_init_variables)
587    o cost/cost_init_varia.F :
588      - remove ecco_cost_init_varia
589        (moved to ecco_init_varia)
590    o ctrl/ctrl_init_variables.F :
591      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
592      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
593    o ctrl/ctrl_map_ini.F :
594      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
595        (moved to ctrl_init_variables)
596    o ctrl/ctrl_map_ini_ecco.F :
597      - remove ECCO_PHYS (mv to ecco_init_varia)
598      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
599    o ecco/ecco_ad_diff.list :
600      - add ecco_init_varia.f
601    o ecco/ecco_init_varia.F
602      - new routine
603    o pkg/streamice:
604      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
605        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
606      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
607    o pkg/generic_advdiff:
608      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
609    o pkg/exf:
610      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
611         xxg_precip capability
612      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
613    o pkg/ctrl:
614      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
615    o model/src/load_fields_driver.F :
616      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
617        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
618    o OpenAD verification experiments:
619      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
620        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
621        for now, only in pkgs used in OpenAD verification experiments.
622      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
623        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
624        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
625        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
626    o OpenAD verification tests:
627      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
628      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
629        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
630      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
631        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
632    o model/src & generic_advdiff:
633      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
634        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
635        dynamics requires valid tracer forcing only over tile interior but, for
636        some diagnostics, may need to extend it over 1 point in tile halo region.
637      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
638        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
639        setting in temp/salt/ptracer_integrate.F
640    o pkg/dic:
641      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
642        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
643        in gchem_forcing_sep.F
644    o pkg/autodiff & obcs:
645      - add storage of current OB values for U & V (was already done for T & S).
646    
647    checkpoint65c (2014/08/30)
648    o pkg/dic:
649      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
650        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
651        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
652    o verification:
653      - new experiment testing OBCS and DIC pkgs, using params & output from
654        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
655        passage: take OBCS from the last year of a 2 yrs simulation and initial
656        conditions from t=1.yr while keeping the same forcing.
657    o model/src:
658      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
659        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
660    o pkg/diagnostics (Stats-Diags):
661      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
662        a) refine region where stats are computed, excluding where arrhFac=0 ;
663        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
664        c) extend regional stats over the region edges (for U or V pt location).
665    o pkg/gchem:
666      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
667        pkg/dic is currently changing/updating ptracers values beyond the OB).
668    o verification (hs94):
669      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
670        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
671        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
672        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
673    o pkg/ptracers:
674      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
675        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
676      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
677        with AB-2 code (so that it get tested).
678    o model/src:
679      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
680        with AB-2 code (previously only available with AB-3 code).
681        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
682        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
683        there, by calling CYCLE_AB_TRACER).
684    o pkg/generic_advdiff:
685      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
686        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
687        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
688        S/R temp/salt/ptracers_integrate.F
689    o model/src & pkg/ptracers:
690      - remove common block variables gT,gS (in DYNVARS.h), except when
691         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
692      - remove common block variable gPtr.
693    o model/src & pkgs:
694      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
695         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
696         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
697         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
698      + change accordingly all calling S/R.
699      - use local temperature/salinity/ptracer tendency array (without bi,bj)
700        in S/R temp/salt/ptracers_integrate.F
701    o pkg/seaice:
702      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
703        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
704      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
705        in seaice_lsr
706      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
707        in s/r seaice_lsr_calc_coeffs
708    o pkg/mdsio:
709      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
710        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
711        too long (e.g., > MAX_LEN_FNAM/2 )
712    
713    checkpoint65b (2014/08/12)
714    o pkg/matrix:
715      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
716    o model/src:
717      - fix initialisation of geothermalFile; compile geothermal-flux code in
718        natl_box verification experiment.
719    o model/src & pkg/down_slope:
720      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
721      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
722        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
723        results at machine truncation level: update output of experiments
724        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
725    o pkg/diagnostics (Stats-Diags):
726      - do not cumulate the full volume when DIAGNOSTICS_FILL is
727        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
728        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
729        times (but Min,Max and StD are still wrong).
730    o model/src:
731      - add geothermal flux forcing: read in ini_forcing.F as time-constant
732        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
733    o model/src:
734      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
735        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
736        arrays are already updated while adjustments (filters, conv.adjustment) are
737        still applied later, in S/R TRACERS_CORRECTION_STEP.
738    o model/src:
739      - store in common bloc array "rhoInSitu" the virtual potential temperature
740        anomaly that is used to compute geopotential: this make the atmos code
741        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
742    o pkg/seaice/seaice_lsr.F
743      - rename integer variable ilcall to ipass (that's what it is called
744        in the residual diagnostics
745      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
746        default) for improved non-linear convergence of the first few steps
747      - adjust a few comments and add new ones to explain some of the store
748        directives
749    o pkg/generic_advdiff (& ptracers):
750      - re-work the code to check for valid advection scheme and for minimum
751        size of overlap (now stored in local common bloc in gad_advscheme.F)
752    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
753      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
754      - add an auxilliary variable "bet" and fix store directives and keys in
755        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
756        less exact gradients in my tests); but there are still
757        recomputation warning (although gradients are sort of OK), when
758        SEAICE_LSR_VECTORIZE is not defined, so this flag and
759        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
760      - update verification experiments lab_sea.
761      - change some comments in S/R seaice_calc_viscosities
762    o model/src:
763      - if staggerTimeStep=T, always apply exchange to velocity field in
764        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
765        (independent of using multi-dim advection or not); no effect on FWD run
766        but affects AD results (at machine truncation level): update output of
767        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
768        and isomip (oad: 12.d).
769    o pkg/generic_advdiff:
770      - stop if doAB_onGtGs is set to FALSE but ignored
771      - refine warning related to stability of tracer time-stepping
772        regarding internal wave dynamics.
773      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
774        on staggerTimeStep & implicitIntGravWave (will now get a warning
775        if potentially unstable).
776    o pkg/kl10:
777      - add new pkg "kl10" for mixing due to internal wave breaking, from
778        http://www.sciencedirect.com/science/article/pii/S1463500310000144
779        (contribution from Jody Klymak), tested in verification experiment
780        verification/internal_wave/input.kl10/
781    o isomip experiment:
782      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
783        (input.htd) and update the output.
784    o cd_code experiments:
785      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
786        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
787        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
788        update the corresponding output.
789    o pkg/seaice:
790      - reduce the number of include files and store directives in
791        S/R seaice_lsr_tridiagu/v
792      - change the order of loops in one case in S/R seaice_lsr_tridiagv
793        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
794        get rid off one store directive (a TAF bug?)
795      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
796        S/R seaice_lsr_tridiagv to change the loop range for consistency
797      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
798      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
799        S/R seaice_lsr_tridiagu/v (requires update of
800        offline_exf_seaice/input.dyn_jfnk)
801    
802    checkpoint65a (2014/07/27)
803    o model/src:
804      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
805        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
806        (topo in p-coords, ice-shelf in z-coords); update output of experiments
807        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
808    o model/src:
809      - collect momentum forcing tendency into local 2-D array (passed as argument
810        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
811        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
812        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
813      - collect T & S forcing tendency into local 2-D array (passed as argument to
814        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
815        affects results at machine truncation level (e.g., ocean: if using
816        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
817        correction due to vertical advection).
818      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
819        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
820        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
821        obcs_ctrl (ad & fwd grd @ 12 & 7).
822    o pkg/ptracers & diagnostics:
823      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
824        title (to avoid some unexpected truncation); sort out ptracers diags units.
825      - collect ptracer forcing tendency into local 2-D array (passed as argument
826        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
827    
828    checkpoint65 (2014/07/18)
829    o pkg/fizhi:
830      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
831        affects results at machine truncation level. Update output of experiments
832        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
833    o pkg/seaice: more clean up
834      - rename TAF common block tapes to be more consistent and remove
835        unnecessary duplicates
836      - add store directives to remove more recomputations, but use smaller
837        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
838        The idea behind this flag is to reduce the memory footprint when the
839        adjoint of the LSR is not required. As of now, defining the flag
840        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
841        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
842        For experiment offline_exf_seaice, this means on a linux box with gfortran
843        nearly a factor of 10 (but keep in mind there is mostly seaice code in
844        this experiment):
845        > size mitgcmuv_ad
846        text    data        bss     dec        hex
847        5100659 1216  220458952  225560827  d71c8fb
848        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
849        but only a moderate increase of 36% for global_ocean.cs32x15:
850        text    data        bss     dec        hex
851        6695027 1648 1014578664 1021275339 3cdf6ccb
852        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
853      - note: there are still recomputations in global_ocean.cs32x15 and
854        offline_exf_seaice and the gradient agreement changes (gets a
855        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
856      - in general, the AD gradients still are wrong
857    o OpenAD
858      - clean up code_oad/ directories somewhat by moving files
859        dontCompile, dontTransform, keepOriginal to OAD_support/
860    o model/src:
861      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
862        (not currently tested): add dissipation terms before NLFS rescaling of
863        tendencies (previously done after).
864    o pkg/diagnostics:
865      - write stats-diags in ascii file with more digits (same as in monitor).
866    o pkg/down_slope:
867      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
868        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
869    o model/src:
870      - new file "apply_forcing.F" containing all the code previously in
871        external_forcing.F, but with new argument list: pass, as new argument,
872        the current level tendency array to update (instead of a direct update
873        of the common bloc array). Change the corresponding calls.
874      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
875        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
876    o pkg/seaice/seaice_lsr, a little bit of clean up
877      - rearrange some code blocks, so that now all calculations for
878        setting up the right-hand-sides done within one single block
879        (I find that easier to read and understand)
880      - rearrange freedrift-code to reduce the number of ifdefs
881      - adjust some indentations and comments
882    
883    checkpoint64z (2014/07/10)
884    o model/src and several pkgs:
885      - change argument list of all S/R called from external_forcing.F and
886        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
887        to pass, as argument, the current level tendency array to update
888        (instead of a direct update of the common bloc array).
889      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
890      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
891    o pkg/seaice/seaice_lsr.F
892      - always initialize local arrays in seaice_lsr_tridiagu/v
893      - add more local tapes to seaice_lsr_tridiagu/v
894      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
895        keep it in bi/bj loop; this seems to be essential
896      - gradients are still wrong but only by 4-7 orders of magnitude
897        instead of 15 orders of magnitude, lab_sea improves a little
898    o pkg/seaice
899      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
900        generates unnecessary code in seaice_lsr_ad
901      - add more store directives in seaice_lsr to avoid unnecessary code
902        in seaice_lsr_ad
903      - exclude some residual computations in seaice_lsr when
904        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
905        in seaice_lsr_ad
906      - add more storing, a new tape (model/src/the_main_loop.F) and
907        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
908        and klockey should be checked by a specialist)
909      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
910        and update lab_sea after previous changes in pkg/seaice below
911    o pkg/autodiff:
912      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
913        viscFacInAd : run time parameters allowing for adjoint switches
914        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
915    o pkg/ecco:
916      - introduce cost_gencost_boxmean.F that computes a box mean
917        temperature (for use in adjoint sensitivity studies).
918    o model/src/set_defaults.F : initialize viscFacAdj to 1.
919    o pkg/mom_common/mom_calc_visc.F:
920      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
921    o pkg/seaice/seaice_summary.F:
922      - statement for SEAICEadjMODE now in autodiff_readparms.F
923    o pkg/seaice:
924      - remove some store directives and add new ones in an effort to get
925        finally rid off the recomputation warnings. This is successful
926        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
927        defined (i.e. no extensive recomputation warnings left), but there
928        are still too many recomputations on the solver iteration level
929      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
930      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
931        SEAICE_SIZE.h
932      - add a store directive in S/R seaice_calc_viscosities
933    o pkg/seaice (ITD code):
934      - fix definition of Hlimit for multi-threaded case
935      - use double precision arithmetic to compute Hlimit: this affects results;
936        update output of experiment seaice_itd.
937    o replace content of verification/seaice_itd
938      - instead of a 1D column use the configuration of offline_exf_seaice
939        to test the ice thickness distribution code with ridging
940      - this is a first shot at this experiment
941      - change of some defaults of ridging parameters SEAICEhStar (from
942        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
943        and lot of new comments.
944    
945    checkpoint64y (2014/06/20)
946    o pkg/seaice/seaice_reg_ridge.F:
947      - modify the regularization of very small volumes of ice; only check
948        total volume HEFF, and do not apply correction to individual ice
949        classes because that leads to funny patterns in the heat and fw-fluxes
950        into the ocean. Adjust seaice_itd/results/output.txt
951      - replace nITD by SEAICE_multDim in loop-ranges
952    o pkg/exf:
953      - add code to process the case field period = -12. with UV interpolation.
954      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
955        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
956    o verification/global_with_exf:
957      - switch all fields period to -12. (was previously untested) in input/data.exf
958        (but keep secondary test ".yearly" unchanged); update the reference output.
959    o pkg/cal:
960      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
961    o pkg/exf:
962      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
963        to replace logical switch "exf_verbose"
964      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
965    o pkg/sbo:
966      - update from Katherine Quinn: evaluate mass directly from density and SSH
967        (budget using Finite Volume method) instead of from bottom pressure.
968      - allow testreport to collect few selected SBO output ; tested in exp.
969        global_ocean.90x40x15 (after updating the results, to include SBO output).
970      - fix some multi-threading issues (in output part).
971    o model/src & most packages:
972      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
973      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
974        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
975        "data.{pkg}" exist ; and leave the S/R (return) just after.
976      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
977        + call LAND_READPARMS from packages_readparms.F
978    o pkg/seaice:
979      - remove code that resets useThSice in S/R seaice_readparms and
980        replace it by a warning in S/R seaice_check
981      - remove parameter MULTDIM, replace with nITD and runtime
982        parameter SEAICE_multDim (still hard-wired to nITD if
983        SEAICE_ITD is defined)
984    
985    checkpoint64x (2014/05/24)
986    o verification/lab_sea:
987      - update adjoint and TLM output following changes to pkg/salt_plume
988      - un-do the update after putting back local recip_Cp in few places.
989    o pkg/salt_plume: modifications by An Nguyen:
990      - add capability to do brine rejection (salt-plume) as function of
991        volume+tracers (instead of only salinity tracer).
992      - conserve volume by exchanging volume from each kLev to above to
993        accommodate in-coming brine volume
994      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
995      - switch KPP surf buoyancy due to brine forcing to 3-d
996        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
997      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
998      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
999        in East/West Arctic.
1000    o pkg/sbo:
1001      - incorporate modifications from Katherine Quinn to enable the use of sbo
1002        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1003        output for future testreport verification (unfinished).
1004    o pkg/atm_phys:
1005      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1006        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1007        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1008    o pkg/seaice
1009      seaice_calc_ice_strength.F: modify expression to avoid divisions
1010        (affects truncation)
1011      seaice_do_ridging.F: clean up the insectarium
1012      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1013      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1014      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1015      - add some debugging information and error messages (warnings)
1016    o model/src: modifications relatd to atmosphere p*:
1017      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1018      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1019        of vertical profile tRef in geopotential background and anomaly.
1020      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1021        and pkg/atm_phys.
1022      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1023        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1024    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1025    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1026        not used right now, but can be used in BGC packages to fix conservation.
1027    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1028        other packages too.
1029    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1030        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1031    o model/src:
1032      - since we have several heat capacity (even in model/src), define "recip_Cp"
1033        as local variable (no longer in common block) to avoid any confusion.
1034      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1035    o pkg/exf:
1036      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1037        air density as function of air Temp, Humidity and atm pressure.
1038    
1039    checkpoint64w (2014/05/02)
1040    o verification:
1041      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1042        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1043        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1044        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1045        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1046    o model/src: for atmosphere in p* coords:
1047      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1048      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1049        but not yet activated.
1050    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1051      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1052      - this changes the results (but not for any verification experiment, because
1053        none tests this), but avoids having an extra field in the restart files
1054    o pkg/seaice: remove global variable TICE (not needed)
1055      - replace by TICES or local variable where necessary (cost_seaice_test,
1056        seaice_diagnostics_state)
1057      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1058      - use specific read/write routines for reading and writing individual leves
1059        of a multilevel field
1060    o pkg/ctrl & model/inc:
1061      - move additional anomaly fields of control vars (related to options:
1062         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1063        from DYNVARS.h into new header file: CTRL_FIELDS.h
1064    o pkg/seaice: some small modifications to the ridging code
1065      - make fw2ObyRidge a global variable and add the freshwater flux to
1066        seaice_growth
1067      - pass actual thickness from seaice_prepare_ridging, so that it is
1068        computed only in one place and compute it in the same way as in
1069        seaice_growth
1070      - initialise more fields in seaice_do_ridging that where cause floating
1071        point exceptions over land
1072  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1073    - move most of "PART 1" of S/R seaice_growth into a new and separate    - move most of "PART 1" of S/R seaice_growth into a new and separate
1074      S/R seaice_reg_ridge that will both regularize the state variable after      S/R seaice_reg_ridge that will both regularize the state variable after
1075      advection call the actual ridging routine;      advection call the actual ridging routine;
1076    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1077      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1078    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1079    - clean up remaining part 1 of seaice_growth in an attempt to make it    - clean up remaining part 1 of seaice_growth in an attempt to make it
1080      more readable (this is probably subjective)      more readable (this is probably subjective)
1081    - call seaice_itd_redist once in the initialisation phase to have the initial    - call seaice_itd_redist once in the initialisation phase to have the initial
1082      conditions in the correct category      conditions in the correct category
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