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revision 1.2005 by jmc, Fri Jun 6 21:17:12 2014 UTC revision 1.2193 by jmc, Sun Oct 25 16:34:11 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/rbcs:
8      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
9        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
10      - add a short report (to STDOUT) about RBCS-mask settings.
11    
12    checkpoint65p (2015/10/23)
13    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
14        there is no adjoint test for EVP, we don't know what it does to the adjoint
15        solution, but at least there are no more recomputation warnings left
16    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
17        a chance of giving the same results as a fully converged VP (JFNK) solver
18    o tools/adjoint_options/adjoint_diva:
19      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
20    o pkg/streamice:
21      - spotted bug in streamice_driving_stress using dyG where should have been dxG
22    o pkg/exf:
23      - remove STOP statement that prevented to use wind or (wind-)stress
24        interpolation for constant-in-time forcing fields (wind/stress period = 0).
25    o pkg/seaice:
26      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
27        5 additionals 2D fields and 6 new store directives
28      - change logic in seaice_readparms.F: EVP code can now be turned on in
29        various ways, setting SEAICE_deltaTev is no longer required,
30        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
31        or SEAICEaEVPcoeff
32    o pkg/shelfice/shelfice_thermodynamics.F
33      - redefining uLoc/vLoc to u/v, instead of 2u/v
34    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
35      - this is an intermediate state of a truely converging EVP that has
36        the potential of outperforming implicit VP methods, I do not recommend
37        using it yet.
38      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
39        and all parameters are hardwired
40      - for convergence it still requires very smooth regularisations, that means,
41        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
42        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
43        specific averaging appears to be required, still subject to tuning
44      - still needs cleaning and I need to turn parameter into runtime parameters
45      - add code to compute and print residuals of iteration, compile with
46        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
47    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
48      that entered with r1.54 on Sep04, 2015, -> update results
49    
50    checkpoint65o (2015/09/14)
51    o pkg/mom_vecinv & mom_common:
52      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
53        called from there.
54      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
55        allows to use Vector-Invariant form in deep atmos and anelastic formulation
56    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
57      and Koenig-Beatty+Holland (2012)
58      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
59      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
60      - requires an extra input argument for S/R seaice_calc_viscosities
61      - tensileStrength's depth dependence is different from Itkin et al. (2015)
62        (to be changed and played with, for now exponential)
63    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
64      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
65        by AREA according to Connelly et al. (2004), JPO.
66      - For EVP and the LSR solver, the implicit part of the drag term is
67        the only non-zero term in the denominator when there is no ice (which
68        prevented running the model with zero ice-ocean drag). If
69        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
70        (or zero main diagonals BU/BV) which need to be caught. A practical
71        consequence is that for open water, the momentum equation reduce
72        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
73        they happen to be zero, often leading to a non-zero solution over
74        open water.
75    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
76        efficient EVP method.
77      - introduce area-weighted averages for e12 (analogously to
78        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
79        remain, but also changing the order of terms in the previous average
80        changed the results as much) -> update experiment
81      - add SEAICE_DELTA_SMOOTHREG code
82      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
83        TEM-code
84      - adjust loop bounds so that only required fields are computed
85      - add new averaging code for zetaZ/deltaZ (again similar to
86        seaice_calc_viscosities.F), inactive by default for now (will change
87        results again), but will replace old code eventually
88    o eesupp/src:
89      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
90        to always cumulate tile local-sum in the same order
91        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
92        Still uses MPI_Allreduce (like standard code) but on array of tiles
93        and should be faster than GLOBAL_SUM_SEND_RECV code.
94      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
95        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
96      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
97         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
98         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
99         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
100         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
101    
102    checkpoint65n (2015/07/29)
103    o pkg/thsice:
104      - add a warning when used with pkg/aim but without updating SST
105        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
106    o pkg/offline:
107      - change where Offline-Fields are loaded, from load_fields_driver.F to
108        directly within FORWARD_STEP, just after updating iter number and time;
109      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
110        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
111       These changes allow:
112        a) to recover exactly on-line results using deltaToffline=deltaTClock,
113        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
114        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
115        time-step, both with GM & KPP files and with recomputing these fields;
116        b) no needs to switch on staggerTimeStep anymore;
117        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
118      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
119    o pkg/offline:
120      - change (rarely used) offset-iteration parameter to an offset time (in s):
121        can easily recover previous offset-iter effect by setting offset-time
122        (offlineTimeOffset) to offset-iter x deltaToffline;
123      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
124        in KPP as part of surface buoyancy forcing) in offline run.
125      - fix ptracers KPP non-local term in the case where KPP is re-computed.
126    o OpenAD
127      - Adding preliminary ggl90 test to OpenAD verification.
128        Config. with ggl90 currently diverges after 64 time steps
129        so will need more work to become more stable
130      - Adding preliminary kpp test to OpenAD verification.
131        required small tweakes in kpp_routines.F
132      - Merge and update from Krishna Narayanan's contrib area:
133        * Add one variable for preliminary OpenAD DIVA
134        * Add replacement time-stepping for OpenAD DIVA
135        * genmake2 flag -diva (but only for OpenAD; preliminary)
136        * required modifs for OAD_support
137        successful preliminary test for tutorial_global_oce_biogeo/
138    o pkg/seaice:
139      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
140      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
141        delta with a smooth function in s/r seaice_calc_viscosity
142        (no effect on EVP)
143      - rename local suffix "sqr" into "sq" for more consistent variable names
144    o pkg/seaice:
145        add new parameter SEAICE_deltaMin that is used ***only***
146        for regularizing Delta (and nothing else, like the parameter
147        which is also used for all sorts of things SEAICE_EPS).
148        Defaults to SEAICE_EPS for backward compatibility only.
149    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
150        the wrong key by inialising it before use -> fixes a recomputation
151        problem but does not fix the gradient
152    o pkg/layers:
153      - move resetting of flux arrays to outside the iLa loop
154        (this caused layers_diapycnal to not work with more than one layer coord.)
155      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
156    o pkg/layers:
157      - remove from common block 3D layers fields (used to diagnose transport
158        in tracer coords) and declare them as local arrays in layers_calc.F
159    o pkg/seaice:
160      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
161        in lab_sea forward experiment (changes results -> updated)
162      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
163    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
164       computations; for SEAICE_VECTORIZE_LSR
165      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
166        sweep to the outside,
167      - remove store directives and add "CADJ loop sequential" directives
168        in analogy to model/src/solve_tridiagonal.F
169      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
170        boundaries to yield more readable code. This has also the charming side
171        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
172        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
173        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
174        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
175        an additional option)
176       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
177       but the adjoint gradients (which are affected by this change) still explode.
178    o coupler (atm & ocn _compon_interf):
179      - avoid using Exch2 IO mapping if not suitable.
180    
181    checkpoint65m (2015/06/15)
182    o pkg/layers:
183      - clean-up old parameters setting (from Sep 2012):
184        + remove old parameters setting from common block (declared locally);
185        + stop if any old parameter is mixed with new parameters;
186        + check for valid or consistent parameter setting (e.g., layers_name)
187      - check that layers_bounds for Pot.Density are in the right range;
188        this is supposed to catch un-updated setting after recently shifting
189        potential density field "prho" by -1000 (now in "sigma" scale).
190    o pkg/layers:
191      - Added missing call to layers_fill for keeping track of tottend in
192        pkg/diagnostics/diagnostics_fill_state.F
193    o pkg/layers:
194      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
195        of diapycnal fluxes
196    o pkg/layers:
197      - reverted changes to interpolation to previous treatment; there
198        was never actually a problem
199    o pkg/layers:
200      - fix interpolation of layers tracers in the presence of partial cells
201      - add lots of new functionality to compute water mass transformation
202        (enabled by CPP flag LAYERS_THERMODYNAMICS)
203      - add new calls from main code (diags_oceanic_surf_flux.F,
204        thermodynamics.F, impldiff.F) and gad to save the necessary fields
205        for layers_thermodynamics calculations
206    o pkg/ptracers:
207      - add capability of stepping a passive tracer forward without advection
208        by setting PTRACERS_advScheme to 0.
209    o pkg/diagnostics:
210      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
211    o pkg/layers:
212      - shift potential density field "prho" by -1000 for density layer averaging so
213        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
214        Note that density bin boundaries (layers_bounds in data.layers) have
215        to be set accordingly (i.e., shifted, in sigma scale).
216    o pkg/layers:
217      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
218      - fix calculation of layer non-weighted velocity and layer probability
219      - add diagnostics for pot.density used for layer averaging
220    o pkg/seaice:
221      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
222        positiveness, modify a few comments and improve variable names,
223      - the changed computation of deltaC affects most seaice-related
224        experiments at the truncation level.
225        seaice_itd.thermo is affected by far the most, with
226        only 7 digits of agreement remaining; update experiments.
227    
228    checkpoint65l (2015/05/04)
229    o pkg/shelfice:
230      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
231        factor drKp1 to zero where it is negative (ie. do not use
232        SHELFICEBoundaryLayer if hFacC>1)
233      - the same for factor drLoc in shelfice_forcing.F
234    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
235        with modules in ptracers, when using testreport option "-small_f"
236    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
237      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
238    o verification/testreport
239      - add new option -small_f
240        with this option testreport first makes the target small_f (*.f files)
241        before running make (all). This is useful for explicit inlining when
242        all sources need to be full available.
243    o pkg/exf/exf_interp.F:
244        remove previous changes related to reverse (decreasing) input grids latitude
245    
246    checkpoint65k (2015/04/01)
247    o pkg/ecco:
248        fix missing cosphi initialization; use eccoiter in place of optimcycle;
249        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
250        instead of active read/write
251    o pkg/ctrl:
252        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
253        instead of active read/write.
254    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
255        return if .NOT.useAUTODIFF
256    o pkg/seaice: add CPP brackets (cost function related).
257    o model/src:
258        add useAUTODIFF run time switch.
259    o pkg/exf/exf_interp.F:
260        add code to allow input grids with latitude starting in the north (i.e. when
261        j=1 corresponds to northern edge of field); modify global_with_exf to test
262        this feature.
263    o verification/testreport:
264      - replace "grep -A3" with POSIX conformal sed command, because there are
265        implementations of grep that cannot do contextual searches
266      - replace "cat -n" by "nl" (two occurrences), because not all implementations
267        of "cat" have the option "-n"
268    o model/src:
269        add new file gsw_teos10.F that contains 3 functions, more or less a copy
270        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
271        convert from conservative to potential temperature. For now they are not
272        called anywhere.
273    o pkg/ggl90: make "useIDEMIX" useful
274      - re-organize code in s/r ggl90_calc a little to move computations that
275        are different for idemix into separate loops (changes verification
276        experiment idemix at truncation level, 12 digits remain -> updated)
277      - requires 2 new 2D fields KappaM, verticalShear
278      - make hFacI and recip_hFacI local 3D variables that are passed to
279        s/r ggl90_idemix
280      - fix and improve some comments
281    
282    checkpoint65j (2015/02/25)
283    o pkg/openad
284      - synchronize seawater.F with version in model/src: replace routine
285        body of sw_temp by calling sw_ptmp and fix/add a few comments.
286    o pkg/mnc:
287      - change default value of pickup_read/write_mnc params to FALSE
288        (since few features are missing in reading MNC pickup files).
289    o model/src:
290      - change default (background) vertical diffusivity for salt to be the
291        temperature (background) vertical diffusivity.
292      - change background vertical diffusivity in vertical mixing pkgs ggl90,
293        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
294        This makes ptracers default diffusivity (that uses salt diffKr) more
295        consistent with vertical mixing schemes.
296    o verification/testreport:
297      - fix typo in "-pcls" option ;
298      - put temp files in /tmp (instead of in local dir)
299      - add option "-ncad" to use genmake2 new option "-nocat4ad"
300      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
301    o pkg/ggl90 (idemix code):
302      - apply few fixes ; add some missing "_d 0" ; update output of exp.
303        global_ocean.90x40x15.idemix
304    o OpenAD
305      - enable active file I/O and begin removal of work-around code
306        for OpenAD for handling control variables (memory vs. active files)
307      - new CPP options file OPENAD_OPTIONS.h
308      - revert to genarr2d gradient check for hs94.1x64x5
309      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
310      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
311    o tools/genmake2:
312      - add option for an alternative Makefile (from Martin) where multiple
313        source files are sent to TAF (instead of all in one file).
314    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
315      - code provided by Carsten Eden as an extension of ggl90
316      - so far the code is turned on within ggl90 by setting a CPP-flag at
317        compile time; a runtime flag implementation is not yet complete
318      - tested in new verification experiment global_ocean.90x40x15.idemix
319    o verification:
320      - reduce length of the AD test run by half for experiments
321        global_ocean.cs32x15 (std + thsice) and isomip
322      - enable active file I/O for OpenAD, adjust verifications accordingly
323      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
324    o verification/testreport:
325      - fix two non-POSIX sed statements so that there are no error messages
326        on Mac OS X
327      - replace hostname -s with hostname | sed 's/\..*$//'
328    o model/src/seawater.F:
329      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
330        (following the matlab code), which would have avoided the bug caught
331        by Matt (see below) in the first place
332    o pkg/shelfice:
333      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
334        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
335      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
336        ice-shelf case (i.e., within surface level).
337      - add config summary in shelfice_check.F
338      - remove global variable recip_SHELFICElatentHeat and replace by a local
339        variable recip_latentHeat
340      - introduce diagnostics for friction velocity uStar (in case of
341        SHELFICEuseGammaFrict)
342      - change verification experiment isomip.htd:
343        + start from pickup (as input_ad at nIter0=8640)
344        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
345        + test SHELFICEuseGammaFrict = .TRUE.
346        + test SHELFICEadvDiffHeatFlux = .TRUE.
347    o model/src:
348      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
349        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
350        update output of experiments global_with_exf.yearly and isomip (all 6).
351    o pkg/shelfice:
352      - change setting of kTopC to also be zero where there is no ice-shelf.
353      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
354        ice-shelf is.
355      - first attempt to get RealFreshWaterFlux effects: for now, only without
356        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
357    o pkg/seaice: add the option to prescribe a fixed thickness PDF
358      for thermodynamic calculations
359      - because of divisions of the type 7/7 not exactly equal to 1, this change
360        affects results of some verification experiments by up to 4 digits:
361        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
362        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
363        adjoint: lab_sea, lab_sea.noseaicedyn
364        -> updated
365    
366    checkpoint65i (2015/01/23)
367    o model/src:
368      - change units of frictionHeating field from W to W/m^2
369      - fix bug in frictional heating from stratospheric drag in
370        S/R ATM_PHYS_TENDENCY_APPLY_V
371      - with synchronous time-stepping: move resetting to zero of frictionHeating
372        field from load_fields_driver.F to thermodynamics.F ;
373      - add diagnostics for frictional heating.
374    o model/src & gmredi K3D:
375      - add frictionHeating field to pickup-files (for synchronous time-stepping)
376      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
377      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
378        and name in pickup file).
379      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
380    o model/src:
381      - move (from ini_forcing.F) initialisation of all arrays in header file
382        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
383        (since Nov 2012) with option selectAddFluid=1.
384    o pkg/shelfice:
385      - change units (+ document) of newly added field "shelfIceMassDynTendency"
386      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
387    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
388    o pkg/seaice: two new runtime parameters:
389      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
390        long overdue
391      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
392        parameterization of tensil stress for fast ice (does not do anything yet)
393    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
394        for LSR: move checking overlaps out of JFNK-if-block
395    o pkg/atm_phys:
396      - move copy of grid and dynamical fields out of atm_phys_driver.F into
397        new S/R ATM_PHYS_DYN2PHYS.
398      - fix level height for Linear Free-Surf case (to be consistent with
399        fixed-in-time pressure levels).
400    o pkg/mom_common (bottomdrag):
401      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
402        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
403        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
404    o pkg/shelfice (u/v_drag):
405      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
406      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
407        (now similar to shelfice_u_drag.F)
408      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
409        from mom_vecinv.F (similar to mom_fluxform calls).
410    o pkg/mom_common (bottomdrag):
411      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
412      - add options for alternative discretisation of velocity norm in quadratic
413        bottom drag: averaging of grid-cell-center KE to U.point and V.point
414        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
415        improves when averaging only the other component (e.g. vVel for U bottom
416        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
417      - add options (bottomVisc_pCell) to account for partial-cell in bottom
418        friction (no-slip BC) thus getting the true distance from the bottom;
419        off by default since this also reduces model stability (explicit bottom
420        friction). Changes produce different machine truncation with linear-drag
421        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
422        front_relax (bvp & mxl, 10 & 11 digits).
423    o model/src & mom pkgs:
424      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
425        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
426      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
427        just copy level Nr value to level Nr+1.
428    o doc:
429      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
430    o pkg/streamice:
431      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
432        SHELFICE.h: move array shelficemass to init_varia, initialise
433        from array shelficemassinit, which is set in init_fixed and
434        has option to be set from file; introduce array
435        shelficeMassDynTend array, set thru file in init_fixed
436      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
437        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
438        pkg/streamice
439      - shelfice_thermodynamics.F: call shelfice_step_icemass if
440        SHELFICEMassStepping = .true.
441      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
442    
443    checkpoint65h (2014/12/17)
444    o verification/global_ocean.90x40x15, global_ocean_ebm:
445      - update to generic controls.
446    o pkg/ctrl:
447      - ctrl_map_ini_genarr.F: test for igen>0
448      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
449      - move gentim2d part of ctrl_map_ini_genarr.F to
450        new separate routine : ctrl_map_ini_gentim2d.F
451      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
452        add time variable weights and cyclic controls (time mean,
453        seasonal cycle, etc) capabilities to gentim2d
454    o pkg/ecco:
455      - move reading of error, conversion to weights from
456        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
457    o global_oce_llc90, cs32:
458      - activte sbo.
459      - CTRL_SIZE.h : add maxCtrlProc.
460      - activate the new genctrl capabilities.
461      - update following reorganization of global_oce_input_fields.tar.gz  
462    o pkg/ctrl/ctrl_ad_diff.list:
463      - add missing ctrl_init_rec.f
464    o tools/OAD_support/keepOriginal:
465      - add ctrl_init_rec.F
466    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
467      - avoid recomputations of xx_gentim2d_dummy.
468    o momentum diagnostics:
469      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
470        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
471    o pkg/seaice/seaice_lsr.F:
472      - fix computation of BU/BV, make sure they are non-zero, only necessary
473        for cubed sphere exchanges and SEAICE_OLx/y>0.
474        This makes calling s/r fill_cs_corner_rl obsolete (removed).
475    o verification/global_ocean.cs32x15/input.seaice
476      - add test for strong implicit coupling and restricted addtive Schwarz
477        methods for LSR
478      - update results/output.seaice.txt
479    o verification/tutorial_global_oce_biogeo:
480      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
481        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
482        update output_adm,_oadm,_tlm.txt
483    o pkg/dic:
484      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
485      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
486        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
487    o verification/tutorial_global_oce_biogeo:
488      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
489        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
490        update output_adm,_oadm,_tlm.txt
491    o eesupp/src:
492      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
493        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
494    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
495      LSR (following Hutchings et al. 2004)
496      - introduce zetaZ as a global variable (requires adjustments in
497        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
498        in seaice_calc_viscosities.F
499      - new flag SEAICEuseStrImpCpl (default off)
500      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
501        momentum equations
502      - JFNK-solver (preconditioner) adjusted to allow using this method
503        (where it does not have any positive effect)
504    o pkg/seaice
505      - add overlap for restrictive additive Schwartz method also to LSR, but
506        turn it off by default (because it only seems to work for non-cubed
507        sphere/llc topologies)
508    o pkg/autodiff
509      - add extra exchanges in addummy_in_steppging also for mnc output
510    o pkg/seaice:
511      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
512        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
513    o pkg/obcs:
514      - add option to specify domain-connected piece Id along OB though files
515        (for now, only used to diagnose PhiVel; default =1 -> global correction)
516      - modify obcs_diag_balance.F to process each connected-part separately;
517        exclude OB where Id = 0 but keep the full divergence there (-> constant
518        Psi along this portion of OB and all inflow derived from grad(Phi))
519      - add example of OB-conect files in verification/so_box_biogeo/input.
520    o pkg/diagnostics:
521      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
522      a) use non zero matrix element across OB and solve for Phi 1 grid point
523         outside OB (i.e, where tracer OBCS are applied).
524      b) global imbalance of inFlow/outFlow across OB: instead of modifying
525         velocity across OB, spread it uniformly along the OB in the RHS.
526    
527    checkpoint65g (2014/11/19)
528    o pkg/diagnostcis:
529      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
530    o pkg/my82,pp81,kl10:
531      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
532        field diffKr as background diffusivity to set minimum diffusivity value.
533    o pkg/seaice:
534      - add new parameter SEAICEuseEVPrev (for revisited EVP by
535        Bouillon et al 2013)
536      - add SEAICE_evpAlpha/Beta to namelist
537      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
538        involve trivial re-ordering of divisions/multiplications that should not
539        have any effects, but ... they do change the results of lab_sea.hb87 so
540        that only 2 digits of agreement remain, in line with the general
541        instability/fragility of the evp-code. For now, I do not care and just
542        update the verification experiment
543    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
544      - remove xx_genarr2d_numsmooth etc
545      - use xx_genarr2d_preproc etc instead
546      - carry out smooth_correl2D at initialization stage rather than during
547        time stepping.
548      - get smoothOpNb from xx_gentim2d_preproc
549    o global_oce_cs32 :
550      - add test of generic ecco capabilities.
551    o pkg/exf/exf_getsurfacefluxes.F :
552      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
553    o pkg/ctrl,ecco :
554      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
555        is defined.
556    o pkg/seaice: add diagnostics for Delta (deformation parameter)
557    o model/src:
558      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
559        diffusivity (background) is specified but ignored.
560    o verification:
561      - in testreport, convert hostname to lower case for default output dir name
562    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
563    o pkg/dic: add modifications from Hajoon:
564      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
565      - light attenuation: add self-shading effect by climatological Chlorophyll
566        (read from file).
567    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
568        compiles when SEAICE_ALLOW_DYNAMICS is undefined
569    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
570        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
571        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
572        approach where CPP_OPTIONS.h includes an omnipotent
573        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
574    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
575        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
576    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
577        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
578        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
579    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
580      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
581      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
582      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
583      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
584    o pkg/ctrl,ecco,exf :
585      - remove variables associated with NON-generic costs,
586        unless ECCO_CTRL_DEPRECATED is defined.
587      - remove NON-generic NON-obcs controls,
588        unless ECCO_CTRL_DEPRECATED is defined.
589    o pkg/ctrl : added ctrl_local_params.h
590    o pkg/ecco : added ecco_local_params.h
591    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
592        experiments, which will progressively be removed once the
593        experiments are revised to use only generic controls/costs.
594    
595    checkpoint65f (2014/10/13)
596    o pkg/ctrl, ecco, seaice : minor changes in headers
597    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
598        cost function and control capabilities added since checkpoint65c.
599    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
600    o pkg/ecco: increase modularity and improve logic
601      - ecco_toolbox.F (new) : basic operations that are often used,
602        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
603        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
604      - cost_gencal.F (new) : determine filnames and records.
605      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
606      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
607        and exploit the above functions leading to more compact code.
608      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
609      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
610        using_ers, using_gfo, using_mdt is now only defined within gencost)
611    o pkg/ecco: extend generic cost capabilities
612      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
613        capabilities via gencost_preproc (+ _c,_i,_r related params),
614        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
615        gencost_outputlevel arguments to cost_generic
616      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
617        and active_read, making room for gencost_preproc to take effect.
618        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
619      - pkg/ecco/cost_generic.F :
620        compute and store misfit maks*(model-data) in localdif that is
621        then used in cost and for output, output misfit if outlev.GT.0
622      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
623        rather gencost_barfile for deciding whether to write barfile
624      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
625      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
626        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
627      - pkg/ecco/ecco_summary.F : report gencost variables
628      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
629    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
630    o pkg/ecco: internal re-organization
631      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
632        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
633        mv relevant variables definition from ecco_cost.h to ecco.h,
634        make sure gencost routines only include ecco.h)
635      - throughout : add missing CCP switches, rm unused variables,
636        and rm un-necessary CPP switches
637      - throughout gencost routines : replace modelstartdate with
638        gencost_startdate when needed
639      - cost_bp_read.F : use arguments, instead of common blocs
640        so that it can be used also by (new) cost_gencost_bpv4.F
641      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
642      - ecco_phys.F : compute etanFull
643      - ecco_readparms.F : rename using_topex as using_tpj, add
644        bpv4-grace to gencost list, initialize added parameters
645      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
646    
647    checkpoint65e (2014/09/28)
648    o pkg/obcs:
649      - replaced the just-added CPP options with run-time variables
650        (see pkg/obcs/OBCS_PARAMS.h for details)
651    o pkg/obcs:
652      - add additional CPP options for sponge boundary layers
653        (see pkg/obcs/OBCS_OPTIONS.h for details)
654    o pkg/atm_phys:
655      - implement simple (obliquity only, assuming circular planet orbit)
656        seasonal cycle for incoming insolation ; used when run-time parameter
657        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
658    o pkg/exf, pkg/ecco, pkg/ctrl:
659      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
660      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
661      - implement gentim2d for xx_tauu, xx_tauv
662    o pkg/ctrl, pkg/ecco :
663      - fix and complement the generic controls implementation
664    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
665        pkg/shelfice/shelfice_thermodynamics.F,
666        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
667        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
668      - add weight in CTRL_GET_GEN calls
669    o pkg/ctrl :
670      - ctrl_get_gen.F : add weight as input parameter, and apply
671        it directly rather than using smooth_correl2Dw (to be retired).
672      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
673    o pkg/ctrl :
674      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
675        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
676      - re-activate ctrl_summary (call in ctrl_init.F)
677    o pkg/ctrl/ctrl_cost_gen.F :
678      - fix CCP brackets, remove un-necessary myiter, mytime
679    o pkg/ecco, pkg/ctrl :
680      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
681      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
682      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
683      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
684    
685    checkpoint65d (2014/09/15)
686    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
687      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
688        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
689    o pkg/ctrl/ctrl_map_ini_genarr.F :
690      - remove compilation failure
691      - replace hard coded example
692      - use ctrl_map_ini_gen2D, 3D
693    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
694      - on/off switch based upon xx_genarr2d_weight,3d
695    o src/packages_init_variables.F :
696      - regroup pkg/estimation calls
697      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
698        (moved to ctrl_init_variables)
699    o cost/cost_init_varia.F :
700      - remove ecco_cost_init_varia
701        (moved to ecco_init_varia)
702    o ctrl/ctrl_init_variables.F :
703      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
704      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
705    o ctrl/ctrl_map_ini.F :
706      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
707        (moved to ctrl_init_variables)
708    o ctrl/ctrl_map_ini_ecco.F :
709      - remove ECCO_PHYS (mv to ecco_init_varia)
710      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
711    o ecco/ecco_ad_diff.list :
712      - add ecco_init_varia.f
713    o ecco/ecco_init_varia.F
714      - new routine
715    o pkg/streamice:
716      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
717        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
718      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
719    o pkg/generic_advdiff:
720      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
721    o pkg/exf:
722      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
723         xxg_precip capability
724      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
725    o pkg/ctrl:
726      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
727    o model/src/load_fields_driver.F :
728      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
729        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
730    o OpenAD verification experiments:
731      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
732        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
733        for now, only in pkgs used in OpenAD verification experiments.
734      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
735        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
736        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
737        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
738    o OpenAD verification tests:
739      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
740      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
741        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
742      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
743        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
744    o model/src & generic_advdiff:
745      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
746        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
747        dynamics requires valid tracer forcing only over tile interior but, for
748        some diagnostics, may need to extend it over 1 point in tile halo region.
749      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
750        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
751        setting in temp/salt/ptracer_integrate.F
752    o pkg/dic:
753      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
754        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
755        in gchem_forcing_sep.F
756    o pkg/autodiff & obcs:
757      - add storage of current OB values for U & V (was already done for T & S).
758    
759    checkpoint65c (2014/08/30)
760    o pkg/dic:
761      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
762        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
763        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
764    o verification:
765      - new experiment testing OBCS and DIC pkgs, using params & output from
766        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
767        passage: take OBCS from the last year of a 2 yrs simulation and initial
768        conditions from t=1.yr while keeping the same forcing.
769    o model/src:
770      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
771        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
772    o pkg/diagnostics (Stats-Diags):
773      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
774        a) refine region where stats are computed, excluding where arrhFac=0 ;
775        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
776        c) extend regional stats over the region edges (for U or V pt location).
777    o pkg/gchem:
778      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
779        pkg/dic is currently changing/updating ptracers values beyond the OB).
780    o verification (hs94):
781      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
782        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
783        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
784        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
785    o pkg/ptracers:
786      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
787        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
788      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
789        with AB-2 code (so that it get tested).
790    o model/src:
791      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
792        with AB-2 code (previously only available with AB-3 code).
793        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
794        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
795        there, by calling CYCLE_AB_TRACER).
796    o pkg/generic_advdiff:
797      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
798        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
799        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
800        S/R temp/salt/ptracers_integrate.F
801    o model/src & pkg/ptracers:
802      - remove common block variables gT,gS (in DYNVARS.h), except when
803         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
804      - remove common block variable gPtr.
805    o model/src & pkgs:
806      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
807         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
808         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
809         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
810      + change accordingly all calling S/R.
811      - use local temperature/salinity/ptracer tendency array (without bi,bj)
812        in S/R temp/salt/ptracers_integrate.F
813    o pkg/seaice:
814      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
815        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
816      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
817        in seaice_lsr
818      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
819        in s/r seaice_lsr_calc_coeffs
820    o pkg/mdsio:
821      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
822        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
823        too long (e.g., > MAX_LEN_FNAM/2 )
824    
825    checkpoint65b (2014/08/12)
826    o pkg/matrix:
827      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
828    o model/src:
829      - fix initialisation of geothermalFile; compile geothermal-flux code in
830        natl_box verification experiment.
831    o model/src & pkg/down_slope:
832      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
833      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
834        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
835        results at machine truncation level: update output of experiments
836        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
837    o pkg/diagnostics (Stats-Diags):
838      - do not cumulate the full volume when DIAGNOSTICS_FILL is
839        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
840        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
841        times (but Min,Max and StD are still wrong).
842    o model/src:
843      - add geothermal flux forcing: read in ini_forcing.F as time-constant
844        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
845    o model/src:
846      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
847        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
848        arrays are already updated while adjustments (filters, conv.adjustment) are
849        still applied later, in S/R TRACERS_CORRECTION_STEP.
850    o model/src:
851      - store in common bloc array "rhoInSitu" the virtual potential temperature
852        anomaly that is used to compute geopotential: this make the atmos code
853        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
854    o pkg/seaice/seaice_lsr.F
855      - rename integer variable ilcall to ipass (that's what it is called
856        in the residual diagnostics
857      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
858        default) for improved non-linear convergence of the first few steps
859      - adjust a few comments and add new ones to explain some of the store
860        directives
861    o pkg/generic_advdiff (& ptracers):
862      - re-work the code to check for valid advection scheme and for minimum
863        size of overlap (now stored in local common bloc in gad_advscheme.F)
864    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
865      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
866      - add an auxilliary variable "bet" and fix store directives and keys in
867        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
868        less exact gradients in my tests); but there are still
869        recomputation warning (although gradients are sort of OK), when
870        SEAICE_LSR_VECTORIZE is not defined, so this flag and
871        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
872      - update verification experiments lab_sea.
873      - change some comments in S/R seaice_calc_viscosities
874    o model/src:
875      - if staggerTimeStep=T, always apply exchange to velocity field in
876        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
877        (independent of using multi-dim advection or not); no effect on FWD run
878        but affects AD results (at machine truncation level): update output of
879        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
880        and isomip (oad: 12.d).
881    o pkg/generic_advdiff:
882      - stop if doAB_onGtGs is set to FALSE but ignored
883      - refine warning related to stability of tracer time-stepping
884        regarding internal wave dynamics.
885      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
886        on staggerTimeStep & implicitIntGravWave (will now get a warning
887        if potentially unstable).
888    o pkg/kl10:
889      - add new pkg "kl10" for mixing due to internal wave breaking, from
890        http://www.sciencedirect.com/science/article/pii/S1463500310000144
891        (contribution from Jody Klymak), tested in verification experiment
892        verification/internal_wave/input.kl10/
893    o isomip experiment:
894      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
895        (input.htd) and update the output.
896    o cd_code experiments:
897      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
898        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
899        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
900        update the corresponding output.
901    o pkg/seaice:
902      - reduce the number of include files and store directives in
903        S/R seaice_lsr_tridiagu/v
904      - change the order of loops in one case in S/R seaice_lsr_tridiagv
905        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
906        get rid off one store directive (a TAF bug?)
907      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
908        S/R seaice_lsr_tridiagv to change the loop range for consistency
909      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
910      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
911        S/R seaice_lsr_tridiagu/v (requires update of
912        offline_exf_seaice/input.dyn_jfnk)
913    
914    checkpoint65a (2014/07/27)
915    o model/src:
916      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
917        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
918        (topo in p-coords, ice-shelf in z-coords); update output of experiments
919        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
920    o model/src:
921      - collect momentum forcing tendency into local 2-D array (passed as argument
922        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
923        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
924        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
925      - collect T & S forcing tendency into local 2-D array (passed as argument to
926        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
927        affects results at machine truncation level (e.g., ocean: if using
928        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
929        correction due to vertical advection).
930      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
931        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
932        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
933        obcs_ctrl (ad & fwd grd @ 12 & 7).
934    o pkg/ptracers & diagnostics:
935      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
936        title (to avoid some unexpected truncation); sort out ptracers diags units.
937      - collect ptracer forcing tendency into local 2-D array (passed as argument
938        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
939    
940    checkpoint65 (2014/07/18)
941    o pkg/fizhi:
942      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
943        affects results at machine truncation level. Update output of experiments
944        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
945    o pkg/seaice: more clean up
946      - rename TAF common block tapes to be more consistent and remove
947        unnecessary duplicates
948      - add store directives to remove more recomputations, but use smaller
949        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
950        The idea behind this flag is to reduce the memory footprint when the
951        adjoint of the LSR is not required. As of now, defining the flag
952        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
953        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
954        For experiment offline_exf_seaice, this means on a linux box with gfortran
955        nearly a factor of 10 (but keep in mind there is mostly seaice code in
956        this experiment):
957        > size mitgcmuv_ad
958        text    data        bss     dec        hex
959        5100659 1216  220458952  225560827  d71c8fb
960        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
961        but only a moderate increase of 36% for global_ocean.cs32x15:
962        text    data        bss     dec        hex
963        6695027 1648 1014578664 1021275339 3cdf6ccb
964        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
965      - note: there are still recomputations in global_ocean.cs32x15 and
966        offline_exf_seaice and the gradient agreement changes (gets a
967        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
968      - in general, the AD gradients still are wrong
969    o OpenAD
970      - clean up code_oad/ directories somewhat by moving files
971        dontCompile, dontTransform, keepOriginal to OAD_support/
972    o model/src:
973      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
974        (not currently tested): add dissipation terms before NLFS rescaling of
975        tendencies (previously done after).
976    o pkg/diagnostics:
977      - write stats-diags in ascii file with more digits (same as in monitor).
978    o pkg/down_slope:
979      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
980        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
981    o model/src:
982      - new file "apply_forcing.F" containing all the code previously in
983        external_forcing.F, but with new argument list: pass, as new argument,
984        the current level tendency array to update (instead of a direct update
985        of the common bloc array). Change the corresponding calls.
986      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
987        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
988    o pkg/seaice/seaice_lsr, a little bit of clean up
989      - rearrange some code blocks, so that now all calculations for
990        setting up the right-hand-sides done within one single block
991        (I find that easier to read and understand)
992      - rearrange freedrift-code to reduce the number of ifdefs
993      - adjust some indentations and comments
994    
995    checkpoint64z (2014/07/10)
996    o model/src and several pkgs:
997      - change argument list of all S/R called from external_forcing.F and
998        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
999        to pass, as argument, the current level tendency array to update
1000        (instead of a direct update of the common bloc array).
1001      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1002      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1003    o pkg/seaice/seaice_lsr.F
1004      - always initialize local arrays in seaice_lsr_tridiagu/v
1005      - add more local tapes to seaice_lsr_tridiagu/v
1006      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1007        keep it in bi/bj loop; this seems to be essential
1008      - gradients are still wrong but only by 4-7 orders of magnitude
1009        instead of 15 orders of magnitude, lab_sea improves a little
1010    o pkg/seaice
1011      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1012        generates unnecessary code in seaice_lsr_ad
1013      - add more store directives in seaice_lsr to avoid unnecessary code
1014        in seaice_lsr_ad
1015      - exclude some residual computations in seaice_lsr when
1016        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1017        in seaice_lsr_ad
1018      - add more storing, a new tape (model/src/the_main_loop.F) and
1019        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1020        and klockey should be checked by a specialist)
1021      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1022        and update lab_sea after previous changes in pkg/seaice below
1023    o pkg/autodiff:
1024      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1025        viscFacInAd : run time parameters allowing for adjoint switches
1026        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1027    o pkg/ecco:
1028      - introduce cost_gencost_boxmean.F that computes a box mean
1029        temperature (for use in adjoint sensitivity studies).
1030    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1031    o pkg/mom_common/mom_calc_visc.F:
1032      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1033    o pkg/seaice/seaice_summary.F:
1034      - statement for SEAICEadjMODE now in autodiff_readparms.F
1035    o pkg/seaice:
1036      - remove some store directives and add new ones in an effort to get
1037        finally rid off the recomputation warnings. This is successful
1038        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1039        defined (i.e. no extensive recomputation warnings left), but there
1040        are still too many recomputations on the solver iteration level
1041      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1042      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1043        SEAICE_SIZE.h
1044      - add a store directive in S/R seaice_calc_viscosities
1045    o pkg/seaice (ITD code):
1046      - fix definition of Hlimit for multi-threaded case
1047      - use double precision arithmetic to compute Hlimit: this affects results;
1048        update output of experiment seaice_itd.
1049    o replace content of verification/seaice_itd
1050      - instead of a 1D column use the configuration of offline_exf_seaice
1051        to test the ice thickness distribution code with ridging
1052      - this is a first shot at this experiment
1053      - change of some defaults of ridging parameters SEAICEhStar (from
1054        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1055        and lot of new comments.
1056    
1057    checkpoint64y (2014/06/20)
1058    o pkg/seaice/seaice_reg_ridge.F:
1059      - modify the regularization of very small volumes of ice; only check
1060        total volume HEFF, and do not apply correction to individual ice
1061        classes because that leads to funny patterns in the heat and fw-fluxes
1062        into the ocean. Adjust seaice_itd/results/output.txt
1063      - replace nITD by SEAICE_multDim in loop-ranges
1064    o pkg/exf:
1065      - add code to process the case field period = -12. with UV interpolation.
1066      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1067        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1068  o verification/global_with_exf:  o verification/global_with_exf:
1069    - swith all fields period to -12. (was previously untested) in input/data.exf    - switch all fields period to -12. (was previously untested) in input/data.exf
1070      (but keep secondary test ".yearly" unchanged); update the reference output.      (but keep secondary test ".yearly" unchanged); update the reference output.
1071  o pkg/cal:  o pkg/cal:
1072    - new calendar type "noLeapYear" for 365 days calendar without any leap year.    - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1073  o pkg/exf:  o pkg/exf:
1074    - new integer parameter "exf_debugLev" (default set to main model debugLevel)    - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1075      to replace logical switch "exf_verbose"      to replace logical switch "exf_verbose"
1076    - report in STDOUT when loading a new reccord (if exf_debugLev >= 3)    - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1077  o pkg/sbo:  o pkg/sbo:
1078    - update from Katherine Quinn: evaluate mass directly from density and SSH    - update from Katherine Quinn: evaluate mass directly from density and SSH
1079      (budget using Finite Volume method) instead of from bottom pressure.      (budget using Finite Volume method) instead of from bottom pressure.
# Line 28  o model/src & most packages: Line 1089  o model/src & most packages:
1089      + call LAND_READPARMS from packages_readparms.F      + call LAND_READPARMS from packages_readparms.F
1090  o pkg/seaice:  o pkg/seaice:
1091    - remove code that resets useThSice in S/R seaice_readparms and    - remove code that resets useThSice in S/R seaice_readparms and
1092      replace by a warning in S/R seaice_check      replace it by a warning in S/R seaice_check
1093    - remove parameter MULTDIM, replace with nITD and runtime    - remove parameter MULTDIM, replace with nITD and runtime
1094      parameter SEAICE_multDim (still hard-wired to nITD if      parameter SEAICE_multDim (still hard-wired to nITD if
1095      SEAICE_ITD is defined)      SEAICE_ITD is defined)
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