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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2168 by heimbach, Thu Jul 2 15:59:16 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 OpenAD
8     - Adding preliminary ggl90 test to OpenAD verification.
9       Config. with ggl90 currently diverges after 64 time steps
10       so will need more work to become more stable
11    o pkg/seaice:
12     - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
13     - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
14       delta with a smooth function in s/r seaice_calc_viscosity
15       (no effect on EVP)
16     - rename local suffix "sqr" into "sq" for more consistent variable names
17    o pkg/seaice: add new parameter SEAICE_deltaMin that is used ***only***
18      for regularizing Delta (and nothing else, like the parameter
19      which is also used for all sorts of things SEAICE_EPS). Defaults to
20      SEAICE_EPS for backward compatibility only.
21    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
22      the wrong key by inialising it before use -> fixes a recomputation
23      problem but does not fix the gradient
24    o pkg/layers:
25      - move resetting of flux arrays to outside the iLa loop
26        (this caused layers_diapycnal to not work with more than one layer coord.)
27      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
28    o pkg/layers:
29      - remove from common block 3D layers fields (used to diagnose transport
30        in tracer coords) and declare them as local arrays in layers_calc.F
31    o pkg/seaice:
32      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
33        in lab_sea forward experiment (changes results -> updated)
34      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
35    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
36      computations; for SEAICE_VECTORIZE_LSR
37      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
38        sweep to the outside,
39      - remove store directives and add "CADJ loop sequential" directives
40        in analogy to model/src/solve_tridiagonal.F
41      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
42        boundaries to yield more readable code. This has also the charming side
43        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
44        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
45        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
46        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
47        an additional option)
48       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
49       but the adjoint gradients (which are affected by this change) still explode.
50    o coupler (atm & ocn _compon_interf):
51      - avoid using Exch2 IO mapping if not suitable.
52    
53    checkpoint65m (2015/06/15)
54    o pkg/layers:
55      - clean-up old parameters setting (from Sep 2012):
56        + remove old parameters setting from common block (declared locally);
57        + stop if any old parameter is mixed with new parameters;
58        + check for valid or consistent parameter setting (e.g., layers_name)
59      - check that layers_bounds for Pot.Density are in the right range;
60        this is supposed to catch un-updated setting after recently shifting
61        potential density field "prho" by -1000 (now in "sigma" scale).
62    o pkg/layers:
63      - Added missing call to layers_fill for keeping track of tottend in
64        pkg/diagnostics/diagnostics_fill_state.F
65    o pkg/layers:
66      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
67        of diapycnal fluxes
68    o pkg/layers:
69      - reverted changes to interpolation to previous treatment; there
70        was never actually a problem
71    o pkg/layers:
72      - fix interpolation of layers tracers in the presence of partial cells
73      - add lots of new functionality to compute water mass transformation
74        (enabled by CPP flag LAYERS_THERMODYNAMICS)
75      - add new calls from main code (diags_oceanic_surf_flux.F,
76        thermodynamics.F, impldiff.F) and gad to save the necessary fields
77        for layers_thermodynamics calculations
78    o pkg/ptracers:
79      - add capability of stepping a passive tracer forward without advection
80        by setting PTRACERS_advScheme to 0.
81    o pkg/diagnostics:
82      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
83    o pkg/layers:
84      - shift potential density field "prho" by -1000 for density layer averaging so
85        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
86        Note that density bin boundaries (layers_bounds in data.layers) have
87        to be set accordingly (i.e., shifted, in sigma scale).
88    o pkg/layers:
89      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
90      - fix calculation of layer non-weighted velocity and layer probability
91      - add diagnostics for pot.density used for layer averaging
92    o pkg/seaice:
93      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
94        positiveness, modify a few comments and improve variable names,
95      - the changed computation of deltaC affects most seaice-related
96        experiments at the truncation level.
97        seaice_itd.thermo is affected by far the most, with
98        only 7 digits of agreement remaining; update experiments.
99    
100    checkpoint65l (2015/05/04)
101    o pkg/shelfice:
102      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
103        factor drKp1 to zero where it is negative (ie. do not use
104        SHELFICEBoundaryLayer if hFacC>1)
105      - the same for factor drLoc in shelfice_forcing.F
106    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
107        with modules in ptracers, when using testreport option "-small_f"
108    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
109      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
110    o verification/testreport
111      - add new option -small_f
112        with this option testreport first makes the target small_f (*.f files)
113        before running make (all). This is useful for explicit inlining when
114        all sources need to be full available.
115    o pkg/exf/exf_interp.F:
116        remove previous changes related to reverse (decreasing) input grids latitude
117    
118    checkpoint65k (2015/04/01)
119    o pkg/ecco:
120        fix missing cosphi initialization; use eccoiter in place of optimcycle;
121        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
122        instead of active read/write
123    o pkg/ctrl:
124        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
125        instead of active read/write.
126    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
127        return if .NOT.useAUTODIFF
128    o pkg/seaice: add CPP brackets (cost function related).
129    o model/src:
130        add useAUTODIFF run time switch.
131    o pkg/exf/exf_interp.F:
132        add code to allow input grids with latitude starting in the north (i.e. when
133        j=1 corresponds to northern edge of field); modify global_with_exf to test
134        this feature.
135    o verification/testreport:
136      - replace "grep -A3" with POSIX conformal sed command, because there are
137        implementations of grep that cannot do contextual searches
138      - replace "cat -n" by "nl" (two occurrences), because not all implementations
139        of "cat" have the option "-n"
140    o model/src:
141        add new file gsw_teos10.F that contains 3 functions, more or less a copy
142        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
143        convert from conservative to potential temperature. For now they are not
144        called anywhere.
145    o pkg/ggl90: make "useIDEMIX" useful
146      - re-organize code in s/r ggl90_calc a little to move computations that
147        are different for idemix into separate loops (changes verification
148        experiment idemix at truncation level, 12 digits remain -> updated)
149      - requires 2 new 2D fields KappaM, verticalShear
150      - make hFacI and recip_hFacI local 3D variables that are passed to
151        s/r ggl90_idemix
152      - fix and improve some comments
153    
154    checkpoint65j (2015/02/25)
155    o pkg/openad
156      - synchronize seawater.F with version in model/src: replace routine
157        body of sw_temp by calling sw_ptmp and fix/add a few comments.
158    o pkg/mnc:
159      - change default value of pickup_read/write_mnc params to FALSE
160        (since few features are missing in reading MNC pickup files).
161    o model/src:
162      - change default (background) vertical diffusivity for salt to be the
163        temperature (background) vertical diffusivity.
164      - change background vertical diffusivity in vertical mixing pkgs ggl90,
165        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
166        This makes ptracers default diffusivity (that uses salt diffKr) more
167        consistent with vertical mixing schemes.
168    o verification/testreport:
169      - fix typo in "-pcls" option ;
170      - put temp files in /tmp (instead of in local dir)
171      - add option "-ncad" to use genmake2 new option "-nocat4ad"
172      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
173    o pkg/ggl90 (idemix code):
174      - apply few fixes ; add some missing "_d 0" ; update output of exp.
175        global_ocean.90x40x15.idemix
176    o OpenAD
177      - enable active file I/O and begin removal of work-around code
178        for OpenAD for handling control variables (memory vs. active files)
179      - new CPP options file OPENAD_OPTIONS.h
180      - revert to genarr2d gradient check for hs94.1x64x5
181      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
182      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
183    o tools/genmake2:
184      - add option for an alternative Makefile (from Martin) where multiple
185        source files are sent to TAF (instead of all in one file).
186    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
187      - code provided by Carsten Eden as an extension of ggl90
188      - so far the code is turned on within ggl90 by setting a CPP-flag at
189        compile time; a runtime flag implementation is not yet complete
190      - tested in new verification experiment global_ocean.90x40x15.idemix
191    o verification:
192      - reduce length of the AD test run by half for experiments
193        global_ocean.cs32x15 (std + thsice) and isomip
194      - enable active file I/O for OpenAD, adjust verifications accordingly
195      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
196    o verification/testreport:
197      - fix two non-POSIX sed statements so that there are no error messages
198        on Mac OS X
199      - replace hostname -s with hostname | sed 's/\..*$//'
200    o model/src/seawater.F:
201      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
202        (following the matlab code), which would have avoided the bug caught
203        by Matt (see below) in the first place
204    o pkg/shelfice:
205      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
206        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
207      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
208        ice-shelf case (i.e., within surface level).
209      - add config summary in shelfice_check.F
210      - remove global variable recip_SHELFICElatentHeat and replace by a local
211        variable recip_latentHeat
212      - introduce diagnostics for friction velocity uStar (in case of
213        SHELFICEuseGammaFrict)
214      - change verification experiment isomip.htd:
215        + start from pickup (as input_ad at nIter0=8640)
216        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
217        + test SHELFICEuseGammaFrict = .TRUE.
218        + test SHELFICEadvDiffHeatFlux = .TRUE.
219    o model/src:
220      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
221        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
222        update output of experiments global_with_exf.yearly and isomip (all 6).
223    o pkg/shelfice:
224      - change setting of kTopC to also be zero where there is no ice-shelf.
225      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
226        ice-shelf is.
227      - first attempt to get RealFreshWaterFlux effects: for now, only without
228        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
229    o pkg/seaice: add the option to prescribe a fixed thickness PDF
230      for thermodynamic calculations
231      - because of divisions of the type 7/7 not exactly equal to 1, this change
232        affects results of some verification experiments by up to 4 digits:
233        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
234        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
235        adjoint: lab_sea, lab_sea.noseaicedyn
236        -> updated
237    
238    checkpoint65i (2015/01/23)
239    o model/src:
240      - change units of frictionHeating field from W to W/m^2
241      - fix bug in frictional heating from stratospheric drag in
242        S/R ATM_PHYS_TENDENCY_APPLY_V
243      - with synchronous time-stepping: move resetting to zero of frictionHeating
244        field from load_fields_driver.F to thermodynamics.F ;
245      - add diagnostics for frictional heating.
246    o model/src & gmredi K3D:
247      - add frictionHeating field to pickup-files (for synchronous time-stepping)
248      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
249      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
250        and name in pickup file).
251      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
252    o model/src:
253      - move (from ini_forcing.F) initialisation of all arrays in header file
254        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
255        (since Nov 2012) with option selectAddFluid=1.
256    o pkg/shelfice:
257      - change units (+ document) of newly added field "shelfIceMassDynTendency"
258      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
259    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
260    o pkg/seaice: two new runtime parameters:
261      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
262        long overdue
263      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
264        parameterization of tensil stress for fast ice (does not do anything yet)
265    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
266        for LSR: move checking overlaps out of JFNK-if-block
267    o pkg/atm_phys:
268      - move copy of grid and dynamical fields out of atm_phys_driver.F into
269        new S/R ATM_PHYS_DYN2PHYS.
270      - fix level height for Linear Free-Surf case (to be consistent with
271        fixed-in-time pressure levels).
272    o pkg/mom_common (bottomdrag):
273      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
274        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
275        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
276    o pkg/shelfice (u/v_drag):
277      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
278      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
279        (now similar to shelfice_u_drag.F)
280      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
281        from mom_vecinv.F (similar to mom_fluxform calls).
282    o pkg/mom_common (bottomdrag):
283      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
284      - add options for alternative discretisation of velocity norm in quadratic
285        bottom drag: averaging of grid-cell-center KE to U.point and V.point
286        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
287        improves when averaging only the other component (e.g. vVel for U bottom
288        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
289      - add options (bottomVisc_pCell) to account for partial-cell in bottom
290        friction (no-slip BC) thus getting the true distance from the bottom;
291        off by default since this also reduces model stability (explicit bottom
292        friction). Changes produce different machine truncation with linear-drag
293        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
294        front_relax (bvp & mxl, 10 & 11 digits).
295    o model/src & mom pkgs:
296      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
297        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
298      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
299        just copy level Nr value to level Nr+1.
300    o doc:
301      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
302    o pkg/streamice:
303      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
304        SHELFICE.h: move array shelficemass to init_varia, initialise
305        from array shelficemassinit, which is set in init_fixed and
306        has option to be set from file; introduce array
307        shelficeMassDynTend array, set thru file in init_fixed
308      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
309        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
310        pkg/streamice
311      - shelfice_thermodynamics.F: call shelfice_step_icemass if
312        SHELFICEMassStepping = .true.
313      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
314    
315    checkpoint65h (2014/12/17)
316    o verification/global_ocean.90x40x15, global_ocean_ebm:
317      - update to generic controls.
318    o pkg/ctrl:
319      - ctrl_map_ini_genarr.F: test for igen>0
320      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
321      - move gentim2d part of ctrl_map_ini_genarr.F to
322        new separate routine : ctrl_map_ini_gentim2d.F
323      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
324        add time variable weights and cyclic controls (time mean,
325        seasonal cycle, etc) capabilities to gentim2d
326    o pkg/ecco:
327      - move reading of error, conversion to weights from
328        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
329    o global_oce_llc90, cs32:
330      - activte sbo.
331      - CTRL_SIZE.h : add maxCtrlProc.
332      - activate the new genctrl capabilities.
333      - update following reorganization of global_oce_input_fields.tar.gz  
334    o pkg/ctrl/ctrl_ad_diff.list:
335      - add missing ctrl_init_rec.f
336    o tools/OAD_support/keepOriginal:
337      - add ctrl_init_rec.F
338    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
339      - avoid recomputations of xx_gentim2d_dummy.
340    o momentum diagnostics:
341      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
342        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
343    o pkg/seaice/seaice_lsr.F:
344      - fix computation of BU/BV, make sure they are non-zero, only necessary
345        for cubed sphere exchanges and SEAICE_OLx/y>0.
346        This makes calling s/r fill_cs_corner_rl obsolete (removed).
347    o verification/global_ocean.cs32x15/input.seaice
348      - add test for strong implicit coupling and restricted addtive Schwarz
349        methods for LSR
350      - update results/output.seaice.txt
351    o verification/tutorial_global_oce_biogeo:
352      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
353        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
354        update output_adm,_oadm,_tlm.txt
355    o pkg/dic:
356      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
357      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
358        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
359    o verification/tutorial_global_oce_biogeo:
360      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
361        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
362        update output_adm,_oadm,_tlm.txt
363    o eesupp/src:
364      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
365        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
366    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
367      LSR (following Hutchings et al. 2004)
368      - introduce zetaZ as a global variable (requires adjustments in
369        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
370        in seaice_calc_viscosities.F
371      - new flag SEAICEuseStrImpCpl (default off)
372      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
373        momentum equations
374      - JFNK-solver (preconditioner) adjusted to allow using this method
375        (where it does not have any positive effect)
376    o pkg/seaice
377      - add overlap for restrictive additive Schwartz method also to LSR, but
378        turn it off by default (because it only seems to work for non-cubed
379        sphere/llc topologies)
380    o pkg/autodiff
381      - add extra exchanges in addummy_in_steppging also for mnc output
382    o pkg/seaice:
383      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
384        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
385    o pkg/obcs:
386      - add option to specify domain-connected piece Id along OB though files
387        (for now, only used to diagnose PhiVel; default =1 -> global correction)
388      - modify obcs_diag_balance.F to process each connected-part separately;
389        exclude OB where Id = 0 but keep the full divergence there (-> constant
390        Psi along this portion of OB and all inflow derived from grad(Phi))
391      - add example of OB-conect files in verification/so_box_biogeo/input.
392    o pkg/diagnostics:
393      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
394      a) use non zero matrix element across OB and solve for Phi 1 grid point
395         outside OB (i.e, where tracer OBCS are applied).
396      b) global imbalance of inFlow/outFlow across OB: instead of modifying
397         velocity across OB, spread it uniformly along the OB in the RHS.
398    
399    checkpoint65g (2014/11/19)
400    o pkg/diagnostcis:
401      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
402    o pkg/my82,pp81,kl10:
403      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
404        field diffKr as background diffusivity to set minimum diffusivity value.
405    o pkg/seaice:
406      - add new parameter SEAICEuseEVPrev (for revisited EVP by
407        Bouillon et al 2013)
408      - add SEAICE_evpAlpha/Beta to namelist
409      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
410        involve trivial re-ordering of divisions/multiplications that should not
411        have any effects, but ... they do change the results of lab_sea.hb87 so
412        that only 2 digits of agreement remain, in line with the general
413        instability/fragility of the evp-code. For now, I do not care and just
414        update the verification experiment
415    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
416      - remove xx_genarr2d_numsmooth etc
417      - use xx_genarr2d_preproc etc instead
418      - carry out smooth_correl2D at initialization stage rather than during
419        time stepping.
420      - get smoothOpNb from xx_gentim2d_preproc
421    o global_oce_cs32 :
422      - add test of generic ecco capabilities.
423    o pkg/exf/exf_getsurfacefluxes.F :
424      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
425    o pkg/ctrl,ecco :
426      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
427        is defined.
428    o pkg/seaice: add diagnostics for Delta (deformation parameter)
429    o model/src:
430      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
431        diffusivity (background) is specified but ignored.
432    o verification:
433      - in testreport, convert hostname to lower case for default output dir name
434    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
435    o pkg/dic: add modifications from Hajoon:
436      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
437      - light attenuation: add self-shading effect by climatological Chlorophyll
438        (read from file).
439    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
440        compiles when SEAICE_ALLOW_DYNAMICS is undefined
441    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
442        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
443        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
444        approach where CPP_OPTIONS.h includes an omnipotent
445        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
446    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
447        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
448    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
449        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
450        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
451    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
452      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
453      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
454      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
455      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
456    o pkg/ctrl,ecco,exf :
457      - remove variables associated with NON-generic costs,
458        unless ECCO_CTRL_DEPRECATED is defined.
459      - remove NON-generic NON-obcs controls,
460        unless ECCO_CTRL_DEPRECATED is defined.
461    o pkg/ctrl : added ctrl_local_params.h
462    o pkg/ecco : added ecco_local_params.h
463    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
464        experiments, which will progressively be removed once the
465        experiments are revised to use only generic controls/costs.
466    
467    checkpoint65f (2014/10/13)
468    o pkg/ctrl, ecco, seaice : minor changes in headers
469    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
470        cost function and control capabilities added since checkpoint65c.
471    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
472    o pkg/ecco: increase modularity and improve logic
473      - ecco_toolbox.F (new) : basic operations that are often used,
474        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
475        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
476      - cost_gencal.F (new) : determine filnames and records.
477      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
478      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
479        and exploit the above functions leading to more compact code.
480      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
481      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
482        using_ers, using_gfo, using_mdt is now only defined within gencost)
483    o pkg/ecco: extend generic cost capabilities
484      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
485        capabilities via gencost_preproc (+ _c,_i,_r related params),
486        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
487        gencost_outputlevel arguments to cost_generic
488      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
489        and active_read, making room for gencost_preproc to take effect.
490        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
491      - pkg/ecco/cost_generic.F :
492        compute and store misfit maks*(model-data) in localdif that is
493        then used in cost and for output, output misfit if outlev.GT.0
494      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
495        rather gencost_barfile for deciding whether to write barfile
496      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
497      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
498        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
499      - pkg/ecco/ecco_summary.F : report gencost variables
500      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
501    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
502    o pkg/ecco: internal re-organization
503      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
504        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
505        mv relevant variables definition from ecco_cost.h to ecco.h,
506        make sure gencost routines only include ecco.h)
507      - throughout : add missing CCP switches, rm unused variables,
508        and rm un-necessary CPP switches
509      - throughout gencost routines : replace modelstartdate with
510        gencost_startdate when needed
511      - cost_bp_read.F : use arguments, instead of common blocs
512        so that it can be used also by (new) cost_gencost_bpv4.F
513      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
514      - ecco_phys.F : compute etanFull
515      - ecco_readparms.F : rename using_topex as using_tpj, add
516        bpv4-grace to gencost list, initialize added parameters
517      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
518    
519    checkpoint65e (2014/09/28)
520    o pkg/obcs:
521      - replaced the just-added CPP options with run-time variables
522        (see pkg/obcs/OBCS_PARAMS.h for details)
523    o pkg/obcs:
524      - add additional CPP options for sponge boundary layers
525        (see pkg/obcs/OBCS_OPTIONS.h for details)
526    o pkg/atm_phys:
527      - implement simple (obliquity only, assuming circular planet orbit)
528        seasonal cycle for incoming insolation ; used when run-time parameter
529        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
530    o pkg/exf, pkg/ecco, pkg/ctrl:
531      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
532      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
533      - implement gentim2d for xx_tauu, xx_tauv
534    o pkg/ctrl, pkg/ecco :
535      - fix and complement the generic controls implementation
536    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
537        pkg/shelfice/shelfice_thermodynamics.F,
538        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
539        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
540      - add weight in CTRL_GET_GEN calls
541    o pkg/ctrl :
542      - ctrl_get_gen.F : add weight as input parameter, and apply
543        it directly rather than using smooth_correl2Dw (to be retired).
544      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
545    o pkg/ctrl :
546      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
547        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
548      - re-activate ctrl_summary (call in ctrl_init.F)
549    o pkg/ctrl/ctrl_cost_gen.F :
550      - fix CCP brackets, remove un-necessary myiter, mytime
551    o pkg/ecco, pkg/ctrl :
552      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
553      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
554      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
555      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
556    
557    checkpoint65d (2014/09/15)
558    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
559      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
560        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
561    o pkg/ctrl/ctrl_map_ini_genarr.F :
562      - remove compilation failure
563      - replace hard coded example
564      - use ctrl_map_ini_gen2D, 3D
565    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
566      - on/off switch based upon xx_genarr2d_weight,3d
567    o src/packages_init_variables.F :
568      - regroup pkg/estimation calls
569      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
570        (moved to ctrl_init_variables)
571    o cost/cost_init_varia.F :
572      - remove ecco_cost_init_varia
573        (moved to ecco_init_varia)
574    o ctrl/ctrl_init_variables.F :
575      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
576      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
577    o ctrl/ctrl_map_ini.F :
578      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
579        (moved to ctrl_init_variables)
580    o ctrl/ctrl_map_ini_ecco.F :
581      - remove ECCO_PHYS (mv to ecco_init_varia)
582      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
583    o ecco/ecco_ad_diff.list :
584      - add ecco_init_varia.f
585    o ecco/ecco_init_varia.F
586      - new routine
587    o pkg/streamice:
588      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
589        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
590      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
591    o pkg/generic_advdiff:
592      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
593    o pkg/exf:
594      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
595         xxg_precip capability
596      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
597    o pkg/ctrl:
598      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
599    o model/src/load_fields_driver.F :
600      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
601        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
602    o OpenAD verification experiments:
603      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
604        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
605        for now, only in pkgs used in OpenAD verification experiments.
606      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
607        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
608        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
609        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
610    o OpenAD verification tests:
611      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
612      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
613        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
614      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
615        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
616    o model/src & generic_advdiff:
617      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
618        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
619        dynamics requires valid tracer forcing only over tile interior but, for
620        some diagnostics, may need to extend it over 1 point in tile halo region.
621      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
622        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
623        setting in temp/salt/ptracer_integrate.F
624    o pkg/dic:
625      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
626        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
627        in gchem_forcing_sep.F
628    o pkg/autodiff & obcs:
629      - add storage of current OB values for U & V (was already done for T & S).
630    
631    checkpoint65c (2014/08/30)
632    o pkg/dic:
633      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
634        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
635        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
636    o verification:
637      - new experiment testing OBCS and DIC pkgs, using params & output from
638        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
639        passage: take OBCS from the last year of a 2 yrs simulation and initial
640        conditions from t=1.yr while keeping the same forcing.
641    o model/src:
642      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
643        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
644    o pkg/diagnostics (Stats-Diags):
645      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
646        a) refine region where stats are computed, excluding where arrhFac=0 ;
647        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
648        c) extend regional stats over the region edges (for U or V pt location).
649    o pkg/gchem:
650      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
651        pkg/dic is currently changing/updating ptracers values beyond the OB).
652    o verification (hs94):
653      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
654        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
655        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
656        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
657    o pkg/ptracers:
658      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
659        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
660      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
661        with AB-2 code (so that it get tested).
662    o model/src:
663      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
664        with AB-2 code (previously only available with AB-3 code).
665        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
666        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
667        there, by calling CYCLE_AB_TRACER).
668    o pkg/generic_advdiff:
669      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
670        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
671        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
672        S/R temp/salt/ptracers_integrate.F
673    o model/src & pkg/ptracers:
674      - remove common block variables gT,gS (in DYNVARS.h), except when
675         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
676      - remove common block variable gPtr.
677    o model/src & pkgs:
678      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
679         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
680         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
681         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
682      + change accordingly all calling S/R.
683      - use local temperature/salinity/ptracer tendency array (without bi,bj)
684        in S/R temp/salt/ptracers_integrate.F
685    o pkg/seaice:
686      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
687        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
688      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
689        in seaice_lsr
690      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
691        in s/r seaice_lsr_calc_coeffs
692    o pkg/mdsio:
693      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
694        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
695        too long (e.g., > MAX_LEN_FNAM/2 )
696    
697    checkpoint65b (2014/08/12)
698    o pkg/matrix:
699      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
700    o model/src:
701      - fix initialisation of geothermalFile; compile geothermal-flux code in
702        natl_box verification experiment.
703    o model/src & pkg/down_slope:
704      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
705      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
706        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
707        results at machine truncation level: update output of experiments
708        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
709    o pkg/diagnostics (Stats-Diags):
710      - do not cumulate the full volume when DIAGNOSTICS_FILL is
711        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
712        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
713        times (but Min,Max and StD are still wrong).
714    o model/src:
715      - add geothermal flux forcing: read in ini_forcing.F as time-constant
716        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
717    o model/src:
718      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
719        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
720        arrays are already updated while adjustments (filters, conv.adjustment) are
721        still applied later, in S/R TRACERS_CORRECTION_STEP.
722    o model/src:
723      - store in common bloc array "rhoInSitu" the virtual potential temperature
724        anomaly that is used to compute geopotential: this make the atmos code
725        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
726    o pkg/seaice/seaice_lsr.F
727      - rename integer variable ilcall to ipass (that's what it is called
728        in the residual diagnostics
729      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
730        default) for improved non-linear convergence of the first few steps
731      - adjust a few comments and add new ones to explain some of the store
732        directives
733    o pkg/generic_advdiff (& ptracers):
734      - re-work the code to check for valid advection scheme and for minimum
735        size of overlap (now stored in local common bloc in gad_advscheme.F)
736    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
737      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
738      - add an auxilliary variable "bet" and fix store directives and keys in
739        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
740        less exact gradients in my tests); but there are still
741        recomputation warning (although gradients are sort of OK), when
742        SEAICE_LSR_VECTORIZE is not defined, so this flag and
743        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
744      - update verification experiments lab_sea.
745      - change some comments in S/R seaice_calc_viscosities
746    o model/src:
747      - if staggerTimeStep=T, always apply exchange to velocity field in
748        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
749        (independent of using multi-dim advection or not); no effect on FWD run
750        but affects AD results (at machine truncation level): update output of
751        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
752        and isomip (oad: 12.d).
753    o pkg/generic_advdiff:
754      - stop if doAB_onGtGs is set to FALSE but ignored
755      - refine warning related to stability of tracer time-stepping
756        regarding internal wave dynamics.
757      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
758        on staggerTimeStep & implicitIntGravWave (will now get a warning
759        if potentially unstable).
760    o pkg/kl10:
761      - add new pkg "kl10" for mixing due to internal wave breaking, from
762        http://www.sciencedirect.com/science/article/pii/S1463500310000144
763        (contribution from Jody Klymak), tested in verification experiment
764        verification/internal_wave/input.kl10/
765    o isomip experiment:
766      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
767        (input.htd) and update the output.
768    o cd_code experiments:
769      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
770        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
771        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
772        update the corresponding output.
773    o pkg/seaice:
774      - reduce the number of include files and store directives in
775        S/R seaice_lsr_tridiagu/v
776      - change the order of loops in one case in S/R seaice_lsr_tridiagv
777        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
778        get rid off one store directive (a TAF bug?)
779      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
780        S/R seaice_lsr_tridiagv to change the loop range for consistency
781      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
782      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
783        S/R seaice_lsr_tridiagu/v (requires update of
784        offline_exf_seaice/input.dyn_jfnk)
785    
786    checkpoint65a (2014/07/27)
787    o model/src:
788      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
789        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
790        (topo in p-coords, ice-shelf in z-coords); update output of experiments
791        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
792    o model/src:
793      - collect momentum forcing tendency into local 2-D array (passed as argument
794        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
795        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
796        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
797      - collect T & S forcing tendency into local 2-D array (passed as argument to
798        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
799        affects results at machine truncation level (e.g., ocean: if using
800        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
801        correction due to vertical advection).
802      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
803        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
804        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
805        obcs_ctrl (ad & fwd grd @ 12 & 7).
806    o pkg/ptracers & diagnostics:
807      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
808        title (to avoid some unexpected truncation); sort out ptracers diags units.
809      - collect ptracer forcing tendency into local 2-D array (passed as argument
810        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
811    
812    checkpoint65 (2014/07/18)
813    o pkg/fizhi:
814      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
815        affects results at machine truncation level. Update output of experiments
816        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
817    o pkg/seaice: more clean up
818      - rename TAF common block tapes to be more consistent and remove
819        unnecessary duplicates
820      - add store directives to remove more recomputations, but use smaller
821        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
822        The idea behind this flag is to reduce the memory footprint when the
823        adjoint of the LSR is not required. As of now, defining the flag
824        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
825        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
826        For experiment offline_exf_seaice, this means on a linux box with gfortran
827        nearly a factor of 10 (but keep in mind there is mostly seaice code in
828        this experiment):
829        > size mitgcmuv_ad
830        text    data        bss     dec        hex
831        5100659 1216  220458952  225560827  d71c8fb
832        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
833        but only a moderate increase of 36% for global_ocean.cs32x15:
834        text    data        bss     dec        hex
835        6695027 1648 1014578664 1021275339 3cdf6ccb
836        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
837      - note: there are still recomputations in global_ocean.cs32x15 and
838        offline_exf_seaice and the gradient agreement changes (gets a
839        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
840      - in general, the AD gradients still are wrong
841    o OpenAD
842      - clean up code_oad/ directories somewhat by moving files
843        dontCompile, dontTransform, keepOriginal to OAD_support/
844    o model/src:
845      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
846        (not currently tested): add dissipation terms before NLFS rescaling of
847        tendencies (previously done after).
848    o pkg/diagnostics:
849      - write stats-diags in ascii file with more digits (same as in monitor).
850    o pkg/down_slope:
851      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
852        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
853    o model/src:
854      - new file "apply_forcing.F" containing all the code previously in
855        external_forcing.F, but with new argument list: pass, as new argument,
856        the current level tendency array to update (instead of a direct update
857        of the common bloc array). Change the corresponding calls.
858      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
859        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
860    o pkg/seaice/seaice_lsr, a little bit of clean up
861      - rearrange some code blocks, so that now all calculations for
862        setting up the right-hand-sides done within one single block
863        (I find that easier to read and understand)
864      - rearrange freedrift-code to reduce the number of ifdefs
865      - adjust some indentations and comments
866    
867    checkpoint64z (2014/07/10)
868    o model/src and several pkgs:
869      - change argument list of all S/R called from external_forcing.F and
870        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
871        to pass, as argument, the current level tendency array to update
872        (instead of a direct update of the common bloc array).
873      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
874      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
875    o pkg/seaice/seaice_lsr.F
876      - always initialize local arrays in seaice_lsr_tridiagu/v
877      - add more local tapes to seaice_lsr_tridiagu/v
878      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
879        keep it in bi/bj loop; this seems to be essential
880      - gradients are still wrong but only by 4-7 orders of magnitude
881        instead of 15 orders of magnitude, lab_sea improves a little
882    o pkg/seaice
883      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
884        generates unnecessary code in seaice_lsr_ad
885      - add more store directives in seaice_lsr to avoid unnecessary code
886        in seaice_lsr_ad
887      - exclude some residual computations in seaice_lsr when
888        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
889        in seaice_lsr_ad
890      - add more storing, a new tape (model/src/the_main_loop.F) and
891        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
892        and klockey should be checked by a specialist)
893      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
894        and update lab_sea after previous changes in pkg/seaice below
895    o pkg/autodiff:
896      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
897        viscFacInAd : run time parameters allowing for adjoint switches
898        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
899    o pkg/ecco:
900      - introduce cost_gencost_boxmean.F that computes a box mean
901        temperature (for use in adjoint sensitivity studies).
902    o model/src/set_defaults.F : initialize viscFacAdj to 1.
903    o pkg/mom_common/mom_calc_visc.F:
904      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
905    o pkg/seaice/seaice_summary.F:
906      - statement for SEAICEadjMODE now in autodiff_readparms.F
907    o pkg/seaice:
908      - remove some store directives and add new ones in an effort to get
909        finally rid off the recomputation warnings. This is successful
910        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
911        defined (i.e. no extensive recomputation warnings left), but there
912        are still too many recomputations on the solver iteration level
913      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
914      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
915        SEAICE_SIZE.h
916      - add a store directive in S/R seaice_calc_viscosities
917    o pkg/seaice (ITD code):
918      - fix definition of Hlimit for multi-threaded case
919      - use double precision arithmetic to compute Hlimit: this affects results;
920        update output of experiment seaice_itd.
921    o replace content of verification/seaice_itd
922      - instead of a 1D column use the configuration of offline_exf_seaice
923        to test the ice thickness distribution code with ridging
924      - this is a first shot at this experiment
925      - change of some defaults of ridging parameters SEAICEhStar (from
926        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
927        and lot of new comments.
928    
929    checkpoint64y (2014/06/20)
930    o pkg/seaice/seaice_reg_ridge.F:
931      - modify the regularization of very small volumes of ice; only check
932        total volume HEFF, and do not apply correction to individual ice
933        classes because that leads to funny patterns in the heat and fw-fluxes
934        into the ocean. Adjust seaice_itd/results/output.txt
935      - replace nITD by SEAICE_multDim in loop-ranges
936    o pkg/exf:
937      - add code to process the case field period = -12. with UV interpolation.
938      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
939        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
940    o verification/global_with_exf:
941      - switch all fields period to -12. (was previously untested) in input/data.exf
942        (but keep secondary test ".yearly" unchanged); update the reference output.
943    o pkg/cal:
944      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
945    o pkg/exf:
946      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
947        to replace logical switch "exf_verbose"
948      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
949    o pkg/sbo:
950      - update from Katherine Quinn: evaluate mass directly from density and SSH
951        (budget using Finite Volume method) instead of from bottom pressure.
952      - allow testreport to collect few selected SBO output ; tested in exp.
953        global_ocean.90x40x15 (after updating the results, to include SBO output).
954      - fix some multi-threading issues (in output part).
955    o model/src & most packages:
956      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
957      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
958        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
959        "data.{pkg}" exist ; and leave the S/R (return) just after.
960      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
961        + call LAND_READPARMS from packages_readparms.F
962    o pkg/seaice:
963      - remove code that resets useThSice in S/R seaice_readparms and
964        replace it by a warning in S/R seaice_check
965      - remove parameter MULTDIM, replace with nITD and runtime
966        parameter SEAICE_multDim (still hard-wired to nITD if
967        SEAICE_ITD is defined)
968    
969    checkpoint64x (2014/05/24)
970    o verification/lab_sea:
971      - update adjoint and TLM output following changes to pkg/salt_plume
972      - un-do the update after putting back local recip_Cp in few places.
973    o pkg/salt_plume: modifications by An Nguyen:
974      - add capability to do brine rejection (salt-plume) as function of
975        volume+tracers (instead of only salinity tracer).
976      - conserve volume by exchanging volume from each kLev to above to
977        accommodate in-coming brine volume
978      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
979      - switch KPP surf buoyancy due to brine forcing to 3-d
980        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
981      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
982      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
983        in East/West Arctic.
984    o pkg/sbo:
985      - incorporate modifications from Katherine Quinn to enable the use of sbo
986        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
987        output for future testreport verification (unfinished).
988    o pkg/atm_phys:
989      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
990        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
991        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
992    o pkg/seaice
993      seaice_calc_ice_strength.F: modify expression to avoid divisions
994        (affects truncation)
995      seaice_do_ridging.F: clean up the insectarium
996      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
997      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
998      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
999      - add some debugging information and error messages (warnings)
1000    o model/src: modifications relatd to atmosphere p*:
1001      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1002      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1003        of vertical profile tRef in geopotential background and anomaly.
1004      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1005        and pkg/atm_phys.
1006      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1007        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1008    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1009    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1010        not used right now, but can be used in BGC packages to fix conservation.
1011    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1012        other packages too.
1013    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1014        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1015    o model/src:
1016      - since we have several heat capacity (even in model/src), define "recip_Cp"
1017        as local variable (no longer in common block) to avoid any confusion.
1018      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1019    o pkg/exf:
1020      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1021        air density as function of air Temp, Humidity and atm pressure.
1022    
1023    checkpoint64w (2014/05/02)
1024    o verification:
1025      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1026        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1027        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1028        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1029        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1030    o model/src: for atmosphere in p* coords:
1031      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1032      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1033        but not yet activated.
1034    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1035      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1036      - this changes the results (but not for any verification experiment, because
1037        none tests this), but avoids having an extra field in the restart files
1038    o pkg/seaice: remove global variable TICE (not needed)
1039      - replace by TICES or local variable where necessary (cost_seaice_test,
1040        seaice_diagnostics_state)
1041      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1042      - use specific read/write routines for reading and writing individual leves
1043        of a multilevel field
1044    o pkg/ctrl & model/inc:
1045      - move additional anomaly fields of control vars (related to options:
1046         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1047        from DYNVARS.h into new header file: CTRL_FIELDS.h
1048    o pkg/seaice: some small modifications to the ridging code
1049      - make fw2ObyRidge a global variable and add the freshwater flux to
1050        seaice_growth
1051      - pass actual thickness from seaice_prepare_ridging, so that it is
1052        computed only in one place and compute it in the same way as in
1053        seaice_growth
1054      - initialise more fields in seaice_do_ridging that where cause floating
1055        point exceptions over land
1056  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1057    - 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
1058      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
1059      advection call the actual ridging routine;      advection call the actual ridging routine;
1060    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1061      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1062    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1063    - 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
1064      more readable (this is probably subjective)      more readable (this is probably subjective)
1065    - 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
1066      conditions in the correct category      conditions in the correct category
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