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revision 1.1994 by mlosch, Mon May 12 14:15:52 2014 UTC revision 1.2195 by dimitri, Mon Nov 2 21:27:41 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/seaice/seaice_do_ridging.F: clean up the insectarium  o pkg/shelfice:
8      - add SHELFICETransCoeffTFile for initializing spatially varying
9        heat and salt transfer coefficients
10    o pkg/atm_compon_interf & ocn_compon_interf:
11      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
12        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
13      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
14    o pkg/atm_ocn_coupler:
15      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
16    o pkg/rbcs:
17      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
18        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
19      - add a short report (to STDOUT) about RBCS-mask settings.
20    
21    checkpoint65p (2015/10/23)
22    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
23        there is no adjoint test for EVP, we don't know what it does to the adjoint
24        solution, but at least there are no more recomputation warnings left
25    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
26        a chance of giving the same results as a fully converged VP (JFNK) solver
27    o tools/adjoint_options/adjoint_diva:
28      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
29    o pkg/streamice:
30      - spotted bug in streamice_driving_stress using dyG where should have been dxG
31    o pkg/exf:
32      - remove STOP statement that prevented to use wind or (wind-)stress
33        interpolation for constant-in-time forcing fields (wind/stress period = 0).
34    o pkg/seaice:
35      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
36        5 additionals 2D fields and 6 new store directives
37      - change logic in seaice_readparms.F: EVP code can now be turned on in
38        various ways, setting SEAICE_deltaTev is no longer required,
39        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
40        or SEAICEaEVPcoeff
41    o pkg/shelfice/shelfice_thermodynamics.F
42      - redefining uLoc/vLoc to u/v, instead of 2u/v
43    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
44      - this is an intermediate state of a truely converging EVP that has
45        the potential of outperforming implicit VP methods, I do not recommend
46        using it yet.
47      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
48        and all parameters are hardwired
49      - for convergence it still requires very smooth regularisations, that means,
50        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
51        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
52        specific averaging appears to be required, still subject to tuning
53      - still needs cleaning and I need to turn parameter into runtime parameters
54      - add code to compute and print residuals of iteration, compile with
55        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
56    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
57      that entered with r1.54 on Sep04, 2015, -> update results
58    
59    checkpoint65o (2015/09/14)
60    o pkg/mom_vecinv & mom_common:
61      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
62        called from there.
63      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
64        allows to use Vector-Invariant form in deep atmos and anelastic formulation
65    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
66      and Koenig-Beatty+Holland (2012)
67      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
68      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
69      - requires an extra input argument for S/R seaice_calc_viscosities
70      - tensileStrength's depth dependence is different from Itkin et al. (2015)
71        (to be changed and played with, for now exponential)
72    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
73      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
74        by AREA according to Connelly et al. (2004), JPO.
75      - For EVP and the LSR solver, the implicit part of the drag term is
76        the only non-zero term in the denominator when there is no ice (which
77        prevented running the model with zero ice-ocean drag). If
78        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
79        (or zero main diagonals BU/BV) which need to be caught. A practical
80        consequence is that for open water, the momentum equation reduce
81        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
82        they happen to be zero, often leading to a non-zero solution over
83        open water.
84    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
85        efficient EVP method.
86      - introduce area-weighted averages for e12 (analogously to
87        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
88        remain, but also changing the order of terms in the previous average
89        changed the results as much) -> update experiment
90      - add SEAICE_DELTA_SMOOTHREG code
91      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
92        TEM-code
93      - adjust loop bounds so that only required fields are computed
94      - add new averaging code for zetaZ/deltaZ (again similar to
95        seaice_calc_viscosities.F), inactive by default for now (will change
96        results again), but will replace old code eventually
97    o eesupp/src:
98      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
99        to always cumulate tile local-sum in the same order
100        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
101        Still uses MPI_Allreduce (like standard code) but on array of tiles
102        and should be faster than GLOBAL_SUM_SEND_RECV code.
103      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
104        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
105      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
106         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
107         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
108         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
109         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
110    
111    checkpoint65n (2015/07/29)
112    o pkg/thsice:
113      - add a warning when used with pkg/aim but without updating SST
114        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
115    o pkg/offline:
116      - change where Offline-Fields are loaded, from load_fields_driver.F to
117        directly within FORWARD_STEP, just after updating iter number and time;
118      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
119        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
120       These changes allow:
121        a) to recover exactly on-line results using deltaToffline=deltaTClock,
122        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
123        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
124        time-step, both with GM & KPP files and with recomputing these fields;
125        b) no needs to switch on staggerTimeStep anymore;
126        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
127      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
128    o pkg/offline:
129      - change (rarely used) offset-iteration parameter to an offset time (in s):
130        can easily recover previous offset-iter effect by setting offset-time
131        (offlineTimeOffset) to offset-iter x deltaToffline;
132      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
133        in KPP as part of surface buoyancy forcing) in offline run.
134      - fix ptracers KPP non-local term in the case where KPP is re-computed.
135    o OpenAD
136      - Adding preliminary ggl90 test to OpenAD verification.
137        Config. with ggl90 currently diverges after 64 time steps
138        so will need more work to become more stable
139      - Adding preliminary kpp test to OpenAD verification.
140        required small tweakes in kpp_routines.F
141      - Merge and update from Krishna Narayanan's contrib area:
142        * Add one variable for preliminary OpenAD DIVA
143        * Add replacement time-stepping for OpenAD DIVA
144        * genmake2 flag -diva (but only for OpenAD; preliminary)
145        * required modifs for OAD_support
146        successful preliminary test for tutorial_global_oce_biogeo/
147    o pkg/seaice:
148      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
149      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
150        delta with a smooth function in s/r seaice_calc_viscosity
151        (no effect on EVP)
152      - rename local suffix "sqr" into "sq" for more consistent variable names
153    o pkg/seaice:
154        add new parameter SEAICE_deltaMin that is used ***only***
155        for regularizing Delta (and nothing else, like the parameter
156        which is also used for all sorts of things SEAICE_EPS).
157        Defaults to SEAICE_EPS for backward compatibility only.
158    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
159        the wrong key by inialising it before use -> fixes a recomputation
160        problem but does not fix the gradient
161    o pkg/layers:
162      - move resetting of flux arrays to outside the iLa loop
163        (this caused layers_diapycnal to not work with more than one layer coord.)
164      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
165    o pkg/layers:
166      - remove from common block 3D layers fields (used to diagnose transport
167        in tracer coords) and declare them as local arrays in layers_calc.F
168    o pkg/seaice:
169      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
170        in lab_sea forward experiment (changes results -> updated)
171      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
172    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
173       computations; for SEAICE_VECTORIZE_LSR
174      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
175        sweep to the outside,
176      - remove store directives and add "CADJ loop sequential" directives
177        in analogy to model/src/solve_tridiagonal.F
178      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
179        boundaries to yield more readable code. This has also the charming side
180        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
181        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
182        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
183        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
184        an additional option)
185       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
186       but the adjoint gradients (which are affected by this change) still explode.
187    o coupler (atm & ocn _compon_interf):
188      - avoid using Exch2 IO mapping if not suitable.
189    
190    checkpoint65m (2015/06/15)
191    o pkg/layers:
192      - clean-up old parameters setting (from Sep 2012):
193        + remove old parameters setting from common block (declared locally);
194        + stop if any old parameter is mixed with new parameters;
195        + check for valid or consistent parameter setting (e.g., layers_name)
196      - check that layers_bounds for Pot.Density are in the right range;
197        this is supposed to catch un-updated setting after recently shifting
198        potential density field "prho" by -1000 (now in "sigma" scale).
199    o pkg/layers:
200      - Added missing call to layers_fill for keeping track of tottend in
201        pkg/diagnostics/diagnostics_fill_state.F
202    o pkg/layers:
203      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
204        of diapycnal fluxes
205    o pkg/layers:
206      - reverted changes to interpolation to previous treatment; there
207        was never actually a problem
208    o pkg/layers:
209      - fix interpolation of layers tracers in the presence of partial cells
210      - add lots of new functionality to compute water mass transformation
211        (enabled by CPP flag LAYERS_THERMODYNAMICS)
212      - add new calls from main code (diags_oceanic_surf_flux.F,
213        thermodynamics.F, impldiff.F) and gad to save the necessary fields
214        for layers_thermodynamics calculations
215    o pkg/ptracers:
216      - add capability of stepping a passive tracer forward without advection
217        by setting PTRACERS_advScheme to 0.
218    o pkg/diagnostics:
219      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
220    o pkg/layers:
221      - shift potential density field "prho" by -1000 for density layer averaging so
222        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
223        Note that density bin boundaries (layers_bounds in data.layers) have
224        to be set accordingly (i.e., shifted, in sigma scale).
225    o pkg/layers:
226      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
227      - fix calculation of layer non-weighted velocity and layer probability
228      - add diagnostics for pot.density used for layer averaging
229    o pkg/seaice:
230      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
231        positiveness, modify a few comments and improve variable names,
232      - the changed computation of deltaC affects most seaice-related
233        experiments at the truncation level.
234        seaice_itd.thermo is affected by far the most, with
235        only 7 digits of agreement remaining; update experiments.
236    
237    checkpoint65l (2015/05/04)
238    o pkg/shelfice:
239      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
240        factor drKp1 to zero where it is negative (ie. do not use
241        SHELFICEBoundaryLayer if hFacC>1)
242      - the same for factor drLoc in shelfice_forcing.F
243    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
244        with modules in ptracers, when using testreport option "-small_f"
245    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
246      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
247    o verification/testreport
248      - add new option -small_f
249        with this option testreport first makes the target small_f (*.f files)
250        before running make (all). This is useful for explicit inlining when
251        all sources need to be full available.
252    o pkg/exf/exf_interp.F:
253        remove previous changes related to reverse (decreasing) input grids latitude
254    
255    checkpoint65k (2015/04/01)
256    o pkg/ecco:
257        fix missing cosphi initialization; use eccoiter in place of optimcycle;
258        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
259        instead of active read/write
260    o pkg/ctrl:
261        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
262        instead of active read/write.
263    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
264        return if .NOT.useAUTODIFF
265    o pkg/seaice: add CPP brackets (cost function related).
266    o model/src:
267        add useAUTODIFF run time switch.
268    o pkg/exf/exf_interp.F:
269        add code to allow input grids with latitude starting in the north (i.e. when
270        j=1 corresponds to northern edge of field); modify global_with_exf to test
271        this feature.
272    o verification/testreport:
273      - replace "grep -A3" with POSIX conformal sed command, because there are
274        implementations of grep that cannot do contextual searches
275      - replace "cat -n" by "nl" (two occurrences), because not all implementations
276        of "cat" have the option "-n"
277    o model/src:
278        add new file gsw_teos10.F that contains 3 functions, more or less a copy
279        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
280        convert from conservative to potential temperature. For now they are not
281        called anywhere.
282    o pkg/ggl90: make "useIDEMIX" useful
283      - re-organize code in s/r ggl90_calc a little to move computations that
284        are different for idemix into separate loops (changes verification
285        experiment idemix at truncation level, 12 digits remain -> updated)
286      - requires 2 new 2D fields KappaM, verticalShear
287      - make hFacI and recip_hFacI local 3D variables that are passed to
288        s/r ggl90_idemix
289      - fix and improve some comments
290    
291    checkpoint65j (2015/02/25)
292    o pkg/openad
293      - synchronize seawater.F with version in model/src: replace routine
294        body of sw_temp by calling sw_ptmp and fix/add a few comments.
295    o pkg/mnc:
296      - change default value of pickup_read/write_mnc params to FALSE
297        (since few features are missing in reading MNC pickup files).
298    o model/src:
299      - change default (background) vertical diffusivity for salt to be the
300        temperature (background) vertical diffusivity.
301      - change background vertical diffusivity in vertical mixing pkgs ggl90,
302        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
303        This makes ptracers default diffusivity (that uses salt diffKr) more
304        consistent with vertical mixing schemes.
305    o verification/testreport:
306      - fix typo in "-pcls" option ;
307      - put temp files in /tmp (instead of in local dir)
308      - add option "-ncad" to use genmake2 new option "-nocat4ad"
309      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
310    o pkg/ggl90 (idemix code):
311      - apply few fixes ; add some missing "_d 0" ; update output of exp.
312        global_ocean.90x40x15.idemix
313    o OpenAD
314      - enable active file I/O and begin removal of work-around code
315        for OpenAD for handling control variables (memory vs. active files)
316      - new CPP options file OPENAD_OPTIONS.h
317      - revert to genarr2d gradient check for hs94.1x64x5
318      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
319      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
320    o tools/genmake2:
321      - add option for an alternative Makefile (from Martin) where multiple
322        source files are sent to TAF (instead of all in one file).
323    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
324      - code provided by Carsten Eden as an extension of ggl90
325      - so far the code is turned on within ggl90 by setting a CPP-flag at
326        compile time; a runtime flag implementation is not yet complete
327      - tested in new verification experiment global_ocean.90x40x15.idemix
328    o verification:
329      - reduce length of the AD test run by half for experiments
330        global_ocean.cs32x15 (std + thsice) and isomip
331      - enable active file I/O for OpenAD, adjust verifications accordingly
332      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
333    o verification/testreport:
334      - fix two non-POSIX sed statements so that there are no error messages
335        on Mac OS X
336      - replace hostname -s with hostname | sed 's/\..*$//'
337    o model/src/seawater.F:
338      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
339        (following the matlab code), which would have avoided the bug caught
340        by Matt (see below) in the first place
341    o pkg/shelfice:
342      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
343        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
344      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
345        ice-shelf case (i.e., within surface level).
346      - add config summary in shelfice_check.F
347      - remove global variable recip_SHELFICElatentHeat and replace by a local
348        variable recip_latentHeat
349      - introduce diagnostics for friction velocity uStar (in case of
350        SHELFICEuseGammaFrict)
351      - change verification experiment isomip.htd:
352        + start from pickup (as input_ad at nIter0=8640)
353        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
354        + test SHELFICEuseGammaFrict = .TRUE.
355        + test SHELFICEadvDiffHeatFlux = .TRUE.
356    o model/src:
357      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
358        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
359        update output of experiments global_with_exf.yearly and isomip (all 6).
360    o pkg/shelfice:
361      - change setting of kTopC to also be zero where there is no ice-shelf.
362      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
363        ice-shelf is.
364      - first attempt to get RealFreshWaterFlux effects: for now, only without
365        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
366    o pkg/seaice: add the option to prescribe a fixed thickness PDF
367      for thermodynamic calculations
368      - because of divisions of the type 7/7 not exactly equal to 1, this change
369        affects results of some verification experiments by up to 4 digits:
370        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
371        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
372        adjoint: lab_sea, lab_sea.noseaicedyn
373        -> updated
374    
375    checkpoint65i (2015/01/23)
376    o model/src:
377      - change units of frictionHeating field from W to W/m^2
378      - fix bug in frictional heating from stratospheric drag in
379        S/R ATM_PHYS_TENDENCY_APPLY_V
380      - with synchronous time-stepping: move resetting to zero of frictionHeating
381        field from load_fields_driver.F to thermodynamics.F ;
382      - add diagnostics for frictional heating.
383    o model/src & gmredi K3D:
384      - add frictionHeating field to pickup-files (for synchronous time-stepping)
385      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
386      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
387        and name in pickup file).
388      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
389    o model/src:
390      - move (from ini_forcing.F) initialisation of all arrays in header file
391        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
392        (since Nov 2012) with option selectAddFluid=1.
393    o pkg/shelfice:
394      - change units (+ document) of newly added field "shelfIceMassDynTendency"
395      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
396    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
397    o pkg/seaice: two new runtime parameters:
398      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
399        long overdue
400      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
401        parameterization of tensil stress for fast ice (does not do anything yet)
402    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
403        for LSR: move checking overlaps out of JFNK-if-block
404    o pkg/atm_phys:
405      - move copy of grid and dynamical fields out of atm_phys_driver.F into
406        new S/R ATM_PHYS_DYN2PHYS.
407      - fix level height for Linear Free-Surf case (to be consistent with
408        fixed-in-time pressure levels).
409    o pkg/mom_common (bottomdrag):
410      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
411        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
412        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
413    o pkg/shelfice (u/v_drag):
414      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
415      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
416        (now similar to shelfice_u_drag.F)
417      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
418        from mom_vecinv.F (similar to mom_fluxform calls).
419    o pkg/mom_common (bottomdrag):
420      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
421      - add options for alternative discretisation of velocity norm in quadratic
422        bottom drag: averaging of grid-cell-center KE to U.point and V.point
423        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
424        improves when averaging only the other component (e.g. vVel for U bottom
425        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
426      - add options (bottomVisc_pCell) to account for partial-cell in bottom
427        friction (no-slip BC) thus getting the true distance from the bottom;
428        off by default since this also reduces model stability (explicit bottom
429        friction). Changes produce different machine truncation with linear-drag
430        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
431        front_relax (bvp & mxl, 10 & 11 digits).
432    o model/src & mom pkgs:
433      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
434        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
435      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
436        just copy level Nr value to level Nr+1.
437    o doc:
438      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
439    o pkg/streamice:
440      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
441        SHELFICE.h: move array shelficemass to init_varia, initialise
442        from array shelficemassinit, which is set in init_fixed and
443        has option to be set from file; introduce array
444        shelficeMassDynTend array, set thru file in init_fixed
445      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
446        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
447        pkg/streamice
448      - shelfice_thermodynamics.F: call shelfice_step_icemass if
449        SHELFICEMassStepping = .true.
450      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
451    
452    checkpoint65h (2014/12/17)
453    o verification/global_ocean.90x40x15, global_ocean_ebm:
454      - update to generic controls.
455    o pkg/ctrl:
456      - ctrl_map_ini_genarr.F: test for igen>0
457      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
458      - move gentim2d part of ctrl_map_ini_genarr.F to
459        new separate routine : ctrl_map_ini_gentim2d.F
460      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
461        add time variable weights and cyclic controls (time mean,
462        seasonal cycle, etc) capabilities to gentim2d
463    o pkg/ecco:
464      - move reading of error, conversion to weights from
465        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
466    o global_oce_llc90, cs32:
467      - activte sbo.
468      - CTRL_SIZE.h : add maxCtrlProc.
469      - activate the new genctrl capabilities.
470      - update following reorganization of global_oce_input_fields.tar.gz  
471    o pkg/ctrl/ctrl_ad_diff.list:
472      - add missing ctrl_init_rec.f
473    o tools/OAD_support/keepOriginal:
474      - add ctrl_init_rec.F
475    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
476      - avoid recomputations of xx_gentim2d_dummy.
477    o momentum diagnostics:
478      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
479        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
480    o pkg/seaice/seaice_lsr.F:
481      - fix computation of BU/BV, make sure they are non-zero, only necessary
482        for cubed sphere exchanges and SEAICE_OLx/y>0.
483        This makes calling s/r fill_cs_corner_rl obsolete (removed).
484    o verification/global_ocean.cs32x15/input.seaice
485      - add test for strong implicit coupling and restricted addtive Schwarz
486        methods for LSR
487      - update results/output.seaice.txt
488    o verification/tutorial_global_oce_biogeo:
489      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
490        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
491        update output_adm,_oadm,_tlm.txt
492    o pkg/dic:
493      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
494      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
495        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
496    o verification/tutorial_global_oce_biogeo:
497      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
498        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
499        update output_adm,_oadm,_tlm.txt
500    o eesupp/src:
501      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
502        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
503    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
504      LSR (following Hutchings et al. 2004)
505      - introduce zetaZ as a global variable (requires adjustments in
506        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
507        in seaice_calc_viscosities.F
508      - new flag SEAICEuseStrImpCpl (default off)
509      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
510        momentum equations
511      - JFNK-solver (preconditioner) adjusted to allow using this method
512        (where it does not have any positive effect)
513    o pkg/seaice
514      - add overlap for restrictive additive Schwartz method also to LSR, but
515        turn it off by default (because it only seems to work for non-cubed
516        sphere/llc topologies)
517    o pkg/autodiff
518      - add extra exchanges in addummy_in_steppging also for mnc output
519    o pkg/seaice:
520      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
521        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
522    o pkg/obcs:
523      - add option to specify domain-connected piece Id along OB though files
524        (for now, only used to diagnose PhiVel; default =1 -> global correction)
525      - modify obcs_diag_balance.F to process each connected-part separately;
526        exclude OB where Id = 0 but keep the full divergence there (-> constant
527        Psi along this portion of OB and all inflow derived from grad(Phi))
528      - add example of OB-conect files in verification/so_box_biogeo/input.
529    o pkg/diagnostics:
530      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
531      a) use non zero matrix element across OB and solve for Phi 1 grid point
532         outside OB (i.e, where tracer OBCS are applied).
533      b) global imbalance of inFlow/outFlow across OB: instead of modifying
534         velocity across OB, spread it uniformly along the OB in the RHS.
535    
536    checkpoint65g (2014/11/19)
537    o pkg/diagnostcis:
538      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
539    o pkg/my82,pp81,kl10:
540      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
541        field diffKr as background diffusivity to set minimum diffusivity value.
542    o pkg/seaice:
543      - add new parameter SEAICEuseEVPrev (for revisited EVP by
544        Bouillon et al 2013)
545      - add SEAICE_evpAlpha/Beta to namelist
546      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
547        involve trivial re-ordering of divisions/multiplications that should not
548        have any effects, but ... they do change the results of lab_sea.hb87 so
549        that only 2 digits of agreement remain, in line with the general
550        instability/fragility of the evp-code. For now, I do not care and just
551        update the verification experiment
552    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
553      - remove xx_genarr2d_numsmooth etc
554      - use xx_genarr2d_preproc etc instead
555      - carry out smooth_correl2D at initialization stage rather than during
556        time stepping.
557      - get smoothOpNb from xx_gentim2d_preproc
558    o global_oce_cs32 :
559      - add test of generic ecco capabilities.
560    o pkg/exf/exf_getsurfacefluxes.F :
561      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
562    o pkg/ctrl,ecco :
563      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
564        is defined.
565    o pkg/seaice: add diagnostics for Delta (deformation parameter)
566    o model/src:
567      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
568        diffusivity (background) is specified but ignored.
569    o verification:
570      - in testreport, convert hostname to lower case for default output dir name
571    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
572    o pkg/dic: add modifications from Hajoon:
573      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
574      - light attenuation: add self-shading effect by climatological Chlorophyll
575        (read from file).
576    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
577        compiles when SEAICE_ALLOW_DYNAMICS is undefined
578    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
579        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
580        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
581        approach where CPP_OPTIONS.h includes an omnipotent
582        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
583    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
584        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
585    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
586        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
587        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
588    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
589      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
590      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
591      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
592      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
593    o pkg/ctrl,ecco,exf :
594      - remove variables associated with NON-generic costs,
595        unless ECCO_CTRL_DEPRECATED is defined.
596      - remove NON-generic NON-obcs controls,
597        unless ECCO_CTRL_DEPRECATED is defined.
598    o pkg/ctrl : added ctrl_local_params.h
599    o pkg/ecco : added ecco_local_params.h
600    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
601        experiments, which will progressively be removed once the
602        experiments are revised to use only generic controls/costs.
603    
604    checkpoint65f (2014/10/13)
605    o pkg/ctrl, ecco, seaice : minor changes in headers
606    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
607        cost function and control capabilities added since checkpoint65c.
608    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
609    o pkg/ecco: increase modularity and improve logic
610      - ecco_toolbox.F (new) : basic operations that are often used,
611        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
612        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
613      - cost_gencal.F (new) : determine filnames and records.
614      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
615      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
616        and exploit the above functions leading to more compact code.
617      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
618      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
619        using_ers, using_gfo, using_mdt is now only defined within gencost)
620    o pkg/ecco: extend generic cost capabilities
621      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
622        capabilities via gencost_preproc (+ _c,_i,_r related params),
623        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
624        gencost_outputlevel arguments to cost_generic
625      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
626        and active_read, making room for gencost_preproc to take effect.
627        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
628      - pkg/ecco/cost_generic.F :
629        compute and store misfit maks*(model-data) in localdif that is
630        then used in cost and for output, output misfit if outlev.GT.0
631      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
632        rather gencost_barfile for deciding whether to write barfile
633      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
634      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
635        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
636      - pkg/ecco/ecco_summary.F : report gencost variables
637      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
638    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
639    o pkg/ecco: internal re-organization
640      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
641        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
642        mv relevant variables definition from ecco_cost.h to ecco.h,
643        make sure gencost routines only include ecco.h)
644      - throughout : add missing CCP switches, rm unused variables,
645        and rm un-necessary CPP switches
646      - throughout gencost routines : replace modelstartdate with
647        gencost_startdate when needed
648      - cost_bp_read.F : use arguments, instead of common blocs
649        so that it can be used also by (new) cost_gencost_bpv4.F
650      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
651      - ecco_phys.F : compute etanFull
652      - ecco_readparms.F : rename using_topex as using_tpj, add
653        bpv4-grace to gencost list, initialize added parameters
654      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
655    
656    checkpoint65e (2014/09/28)
657    o pkg/obcs:
658      - replaced the just-added CPP options with run-time variables
659        (see pkg/obcs/OBCS_PARAMS.h for details)
660    o pkg/obcs:
661      - add additional CPP options for sponge boundary layers
662        (see pkg/obcs/OBCS_OPTIONS.h for details)
663    o pkg/atm_phys:
664      - implement simple (obliquity only, assuming circular planet orbit)
665        seasonal cycle for incoming insolation ; used when run-time parameter
666        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
667    o pkg/exf, pkg/ecco, pkg/ctrl:
668      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
669      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
670      - implement gentim2d for xx_tauu, xx_tauv
671    o pkg/ctrl, pkg/ecco :
672      - fix and complement the generic controls implementation
673    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
674        pkg/shelfice/shelfice_thermodynamics.F,
675        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
676        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
677      - add weight in CTRL_GET_GEN calls
678    o pkg/ctrl :
679      - ctrl_get_gen.F : add weight as input parameter, and apply
680        it directly rather than using smooth_correl2Dw (to be retired).
681      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
682    o pkg/ctrl :
683      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
684        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
685      - re-activate ctrl_summary (call in ctrl_init.F)
686    o pkg/ctrl/ctrl_cost_gen.F :
687      - fix CCP brackets, remove un-necessary myiter, mytime
688    o pkg/ecco, pkg/ctrl :
689      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
690      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
691      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
692      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
693    
694    checkpoint65d (2014/09/15)
695    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
696      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
697        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
698    o pkg/ctrl/ctrl_map_ini_genarr.F :
699      - remove compilation failure
700      - replace hard coded example
701      - use ctrl_map_ini_gen2D, 3D
702    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
703      - on/off switch based upon xx_genarr2d_weight,3d
704    o src/packages_init_variables.F :
705      - regroup pkg/estimation calls
706      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
707        (moved to ctrl_init_variables)
708    o cost/cost_init_varia.F :
709      - remove ecco_cost_init_varia
710        (moved to ecco_init_varia)
711    o ctrl/ctrl_init_variables.F :
712      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
713      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
714    o ctrl/ctrl_map_ini.F :
715      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
716        (moved to ctrl_init_variables)
717    o ctrl/ctrl_map_ini_ecco.F :
718      - remove ECCO_PHYS (mv to ecco_init_varia)
719      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
720    o ecco/ecco_ad_diff.list :
721      - add ecco_init_varia.f
722    o ecco/ecco_init_varia.F
723      - new routine
724    o pkg/streamice:
725      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
726        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
727      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
728    o pkg/generic_advdiff:
729      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
730    o pkg/exf:
731      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
732         xxg_precip capability
733      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
734    o pkg/ctrl:
735      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
736    o model/src/load_fields_driver.F :
737      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
738        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
739    o OpenAD verification experiments:
740      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
741        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
742        for now, only in pkgs used in OpenAD verification experiments.
743      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
744        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
745        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
746        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
747    o OpenAD verification tests:
748      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
749      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
750        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
751      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
752        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
753    o model/src & generic_advdiff:
754      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
755        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
756        dynamics requires valid tracer forcing only over tile interior but, for
757        some diagnostics, may need to extend it over 1 point in tile halo region.
758      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
759        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
760        setting in temp/salt/ptracer_integrate.F
761    o pkg/dic:
762      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
763        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
764        in gchem_forcing_sep.F
765    o pkg/autodiff & obcs:
766      - add storage of current OB values for U & V (was already done for T & S).
767    
768    checkpoint65c (2014/08/30)
769    o pkg/dic:
770      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
771        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
772        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
773    o verification:
774      - new experiment testing OBCS and DIC pkgs, using params & output from
775        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
776        passage: take OBCS from the last year of a 2 yrs simulation and initial
777        conditions from t=1.yr while keeping the same forcing.
778    o model/src:
779      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
780        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
781    o pkg/diagnostics (Stats-Diags):
782      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
783        a) refine region where stats are computed, excluding where arrhFac=0 ;
784        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
785        c) extend regional stats over the region edges (for U or V pt location).
786    o pkg/gchem:
787      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
788        pkg/dic is currently changing/updating ptracers values beyond the OB).
789    o verification (hs94):
790      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
791        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
792        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
793        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
794    o pkg/ptracers:
795      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
796        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
797      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
798        with AB-2 code (so that it get tested).
799    o model/src:
800      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
801        with AB-2 code (previously only available with AB-3 code).
802        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
803        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
804        there, by calling CYCLE_AB_TRACER).
805    o pkg/generic_advdiff:
806      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
807        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
808        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
809        S/R temp/salt/ptracers_integrate.F
810    o model/src & pkg/ptracers:
811      - remove common block variables gT,gS (in DYNVARS.h), except when
812         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
813      - remove common block variable gPtr.
814    o model/src & pkgs:
815      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
816         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
817         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
818         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
819      + change accordingly all calling S/R.
820      - use local temperature/salinity/ptracer tendency array (without bi,bj)
821        in S/R temp/salt/ptracers_integrate.F
822    o pkg/seaice:
823      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
824        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
825      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
826        in seaice_lsr
827      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
828        in s/r seaice_lsr_calc_coeffs
829    o pkg/mdsio:
830      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
831        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
832        too long (e.g., > MAX_LEN_FNAM/2 )
833    
834    checkpoint65b (2014/08/12)
835    o pkg/matrix:
836      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
837    o model/src:
838      - fix initialisation of geothermalFile; compile geothermal-flux code in
839        natl_box verification experiment.
840    o model/src & pkg/down_slope:
841      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
842      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
843        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
844        results at machine truncation level: update output of experiments
845        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
846    o pkg/diagnostics (Stats-Diags):
847      - do not cumulate the full volume when DIAGNOSTICS_FILL is
848        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
849        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
850        times (but Min,Max and StD are still wrong).
851    o model/src:
852      - add geothermal flux forcing: read in ini_forcing.F as time-constant
853        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
854    o model/src:
855      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
856        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
857        arrays are already updated while adjustments (filters, conv.adjustment) are
858        still applied later, in S/R TRACERS_CORRECTION_STEP.
859    o model/src:
860      - store in common bloc array "rhoInSitu" the virtual potential temperature
861        anomaly that is used to compute geopotential: this make the atmos code
862        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
863    o pkg/seaice/seaice_lsr.F
864      - rename integer variable ilcall to ipass (that's what it is called
865        in the residual diagnostics
866      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
867        default) for improved non-linear convergence of the first few steps
868      - adjust a few comments and add new ones to explain some of the store
869        directives
870    o pkg/generic_advdiff (& ptracers):
871      - re-work the code to check for valid advection scheme and for minimum
872        size of overlap (now stored in local common bloc in gad_advscheme.F)
873    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
874      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
875      - add an auxilliary variable "bet" and fix store directives and keys in
876        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
877        less exact gradients in my tests); but there are still
878        recomputation warning (although gradients are sort of OK), when
879        SEAICE_LSR_VECTORIZE is not defined, so this flag and
880        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
881      - update verification experiments lab_sea.
882      - change some comments in S/R seaice_calc_viscosities
883    o model/src:
884      - if staggerTimeStep=T, always apply exchange to velocity field in
885        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
886        (independent of using multi-dim advection or not); no effect on FWD run
887        but affects AD results (at machine truncation level): update output of
888        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
889        and isomip (oad: 12.d).
890    o pkg/generic_advdiff:
891      - stop if doAB_onGtGs is set to FALSE but ignored
892      - refine warning related to stability of tracer time-stepping
893        regarding internal wave dynamics.
894      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
895        on staggerTimeStep & implicitIntGravWave (will now get a warning
896        if potentially unstable).
897    o pkg/kl10:
898      - add new pkg "kl10" for mixing due to internal wave breaking, from
899        http://www.sciencedirect.com/science/article/pii/S1463500310000144
900        (contribution from Jody Klymak), tested in verification experiment
901        verification/internal_wave/input.kl10/
902    o isomip experiment:
903      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
904        (input.htd) and update the output.
905    o cd_code experiments:
906      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
907        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
908        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
909        update the corresponding output.
910    o pkg/seaice:
911      - reduce the number of include files and store directives in
912        S/R seaice_lsr_tridiagu/v
913      - change the order of loops in one case in S/R seaice_lsr_tridiagv
914        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
915        get rid off one store directive (a TAF bug?)
916      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
917        S/R seaice_lsr_tridiagv to change the loop range for consistency
918      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
919      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
920        S/R seaice_lsr_tridiagu/v (requires update of
921        offline_exf_seaice/input.dyn_jfnk)
922    
923    checkpoint65a (2014/07/27)
924    o model/src:
925      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
926        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
927        (topo in p-coords, ice-shelf in z-coords); update output of experiments
928        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
929    o model/src:
930      - collect momentum forcing tendency into local 2-D array (passed as argument
931        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
932        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
933        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
934      - collect T & S forcing tendency into local 2-D array (passed as argument to
935        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
936        affects results at machine truncation level (e.g., ocean: if using
937        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
938        correction due to vertical advection).
939      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
940        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
941        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
942        obcs_ctrl (ad & fwd grd @ 12 & 7).
943    o pkg/ptracers & diagnostics:
944      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
945        title (to avoid some unexpected truncation); sort out ptracers diags units.
946      - collect ptracer forcing tendency into local 2-D array (passed as argument
947        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
948    
949    checkpoint65 (2014/07/18)
950    o pkg/fizhi:
951      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
952        affects results at machine truncation level. Update output of experiments
953        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
954    o pkg/seaice: more clean up
955      - rename TAF common block tapes to be more consistent and remove
956        unnecessary duplicates
957      - add store directives to remove more recomputations, but use smaller
958        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
959        The idea behind this flag is to reduce the memory footprint when the
960        adjoint of the LSR is not required. As of now, defining the flag
961        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
962        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
963        For experiment offline_exf_seaice, this means on a linux box with gfortran
964        nearly a factor of 10 (but keep in mind there is mostly seaice code in
965        this experiment):
966        > size mitgcmuv_ad
967        text    data        bss     dec        hex
968        5100659 1216  220458952  225560827  d71c8fb
969        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
970        but only a moderate increase of 36% for global_ocean.cs32x15:
971        text    data        bss     dec        hex
972        6695027 1648 1014578664 1021275339 3cdf6ccb
973        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
974      - note: there are still recomputations in global_ocean.cs32x15 and
975        offline_exf_seaice and the gradient agreement changes (gets a
976        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
977      - in general, the AD gradients still are wrong
978    o OpenAD
979      - clean up code_oad/ directories somewhat by moving files
980        dontCompile, dontTransform, keepOriginal to OAD_support/
981    o model/src:
982      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
983        (not currently tested): add dissipation terms before NLFS rescaling of
984        tendencies (previously done after).
985    o pkg/diagnostics:
986      - write stats-diags in ascii file with more digits (same as in monitor).
987    o pkg/down_slope:
988      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
989        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
990    o model/src:
991      - new file "apply_forcing.F" containing all the code previously in
992        external_forcing.F, but with new argument list: pass, as new argument,
993        the current level tendency array to update (instead of a direct update
994        of the common bloc array). Change the corresponding calls.
995      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
996        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
997    o pkg/seaice/seaice_lsr, a little bit of clean up
998      - rearrange some code blocks, so that now all calculations for
999        setting up the right-hand-sides done within one single block
1000        (I find that easier to read and understand)
1001      - rearrange freedrift-code to reduce the number of ifdefs
1002      - adjust some indentations and comments
1003    
1004    checkpoint64z (2014/07/10)
1005    o model/src and several pkgs:
1006      - change argument list of all S/R called from external_forcing.F and
1007        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1008        to pass, as argument, the current level tendency array to update
1009        (instead of a direct update of the common bloc array).
1010      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1011      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1012    o pkg/seaice/seaice_lsr.F
1013      - always initialize local arrays in seaice_lsr_tridiagu/v
1014      - add more local tapes to seaice_lsr_tridiagu/v
1015      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1016        keep it in bi/bj loop; this seems to be essential
1017      - gradients are still wrong but only by 4-7 orders of magnitude
1018        instead of 15 orders of magnitude, lab_sea improves a little
1019    o pkg/seaice
1020      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1021        generates unnecessary code in seaice_lsr_ad
1022      - add more store directives in seaice_lsr to avoid unnecessary code
1023        in seaice_lsr_ad
1024      - exclude some residual computations in seaice_lsr when
1025        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1026        in seaice_lsr_ad
1027      - add more storing, a new tape (model/src/the_main_loop.F) and
1028        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1029        and klockey should be checked by a specialist)
1030      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1031        and update lab_sea after previous changes in pkg/seaice below
1032    o pkg/autodiff:
1033      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1034        viscFacInAd : run time parameters allowing for adjoint switches
1035        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1036    o pkg/ecco:
1037      - introduce cost_gencost_boxmean.F that computes a box mean
1038        temperature (for use in adjoint sensitivity studies).
1039    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1040    o pkg/mom_common/mom_calc_visc.F:
1041      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1042    o pkg/seaice/seaice_summary.F:
1043      - statement for SEAICEadjMODE now in autodiff_readparms.F
1044    o pkg/seaice:
1045      - remove some store directives and add new ones in an effort to get
1046        finally rid off the recomputation warnings. This is successful
1047        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1048        defined (i.e. no extensive recomputation warnings left), but there
1049        are still too many recomputations on the solver iteration level
1050      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1051      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1052        SEAICE_SIZE.h
1053      - add a store directive in S/R seaice_calc_viscosities
1054    o pkg/seaice (ITD code):
1055      - fix definition of Hlimit for multi-threaded case
1056      - use double precision arithmetic to compute Hlimit: this affects results;
1057        update output of experiment seaice_itd.
1058    o replace content of verification/seaice_itd
1059      - instead of a 1D column use the configuration of offline_exf_seaice
1060        to test the ice thickness distribution code with ridging
1061      - this is a first shot at this experiment
1062      - change of some defaults of ridging parameters SEAICEhStar (from
1063        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1064        and lot of new comments.
1065    
1066    checkpoint64y (2014/06/20)
1067    o pkg/seaice/seaice_reg_ridge.F:
1068      - modify the regularization of very small volumes of ice; only check
1069        total volume HEFF, and do not apply correction to individual ice
1070        classes because that leads to funny patterns in the heat and fw-fluxes
1071        into the ocean. Adjust seaice_itd/results/output.txt
1072      - replace nITD by SEAICE_multDim in loop-ranges
1073    o pkg/exf:
1074      - add code to process the case field period = -12. with UV interpolation.
1075      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1076        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1077    o verification/global_with_exf:
1078      - switch all fields period to -12. (was previously untested) in input/data.exf
1079        (but keep secondary test ".yearly" unchanged); update the reference output.
1080    o pkg/cal:
1081      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1082    o pkg/exf:
1083      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1084        to replace logical switch "exf_verbose"
1085      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1086    o pkg/sbo:
1087      - update from Katherine Quinn: evaluate mass directly from density and SSH
1088        (budget using Finite Volume method) instead of from bottom pressure.
1089      - allow testreport to collect few selected SBO output ; tested in exp.
1090        global_ocean.90x40x15 (after updating the results, to include SBO output).
1091      - fix some multi-threading issues (in output part).
1092    o model/src & most packages:
1093      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1094      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1095        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1096        "data.{pkg}" exist ; and leave the S/R (return) just after.
1097      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1098        + call LAND_READPARMS from packages_readparms.F
1099    o pkg/seaice:
1100      - remove code that resets useThSice in S/R seaice_readparms and
1101        replace it by a warning in S/R seaice_check
1102      - remove parameter MULTDIM, replace with nITD and runtime
1103        parameter SEAICE_multDim (still hard-wired to nITD if
1104        SEAICE_ITD is defined)
1105    
1106    checkpoint64x (2014/05/24)
1107    o verification/lab_sea:
1108      - update adjoint and TLM output following changes to pkg/salt_plume
1109      - un-do the update after putting back local recip_Cp in few places.
1110    o pkg/salt_plume: modifications by An Nguyen:
1111      - add capability to do brine rejection (salt-plume) as function of
1112        volume+tracers (instead of only salinity tracer).
1113      - conserve volume by exchanging volume from each kLev to above to
1114        accommodate in-coming brine volume
1115      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1116      - switch KPP surf buoyancy due to brine forcing to 3-d
1117        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1118      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1119      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1120        in East/West Arctic.
1121    o pkg/sbo:
1122      - incorporate modifications from Katherine Quinn to enable the use of sbo
1123        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1124        output for future testreport verification (unfinished).
1125    o pkg/atm_phys:
1126      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1127        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1128        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1129    o pkg/seaice
1130      seaice_calc_ice_strength.F: modify expression to avoid divisions
1131        (affects truncation)
1132      seaice_do_ridging.F: clean up the insectarium
1133    - fix a bug that was compensated by areaScaling (-> remove areaScaling code)    - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1134    - added SEAICEsnowFracRidge to redistributed snow (2nd bug)    - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1135    - set closing/openingRate to zero where no extra iteration is need (3rd bug)    - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1136    - add some debugging information and error messages (warnings)    - add some debugging information and error messages (warnings)
1137  o model/src: modifications relatd to atmosphere p*:  o model/src: modifications relatd to atmosphere p*:
1138    - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)    - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1139    - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead    - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
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