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revision 1.2033 by mlosch, Tue Jul 29 16:29:56 2014 UTC revision 1.2205 by jmc, Fri Nov 20 22:51:39 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:  o pkg/atm_compon_interf:
8      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
9        coupler: use last time-step value instead of average over cplSendFrq_iter
10        time-step, similar to what is done for seaIceMass.
11        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
12    o eesupp & genmake2:
13      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
14        <= remove until a fix is found for some ifort version on ia32 machine.
15    o pkg/seaice/seaice_evp:
16      - refine residual computation
17    
18    checkpoint65q (2015/11/18)
19    o pkg/seaice/seaice_evp:
20      - fix residual computations so that they no longer affect the actual
21        simulation code
22      - fix seaice_readparams to be able to actually set new parameters
23        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
24    o model/src:
25      - fix wrong truncation (single prec) from "FLOAT" function in expressions
26        like: deltaT*FLOAT(myIter) when myIter is large:
27         a) replaced by DFLOAT (if not seen by TAF);
28         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
29    o pkg/aim_v23:
30      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
31        when pickupSuff is set ; do write rolling pickups + at the end of the run.
32    o pkg/atm_ocn_coupler + ocn_compon_interf:
33      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
34        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
35        add corresponding call in DO_OCEANIC_PHYS.
36    o coupler pkgs:
37      Start a new way to set-up optionally-exchanged variables (previously, only
38       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
39       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
40       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
41       compononent param default can be set accordingly).
42      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
43       but rather applies to a group a fields (going both ways like for DIC)
44       and corresponds to an option of coupling config.
45      coupler (pkg/atm_ocn_coupler):
46      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
47        and read namelist directly (without eessup S/R calls) instead of
48        in the very un-flexible old way, 1 param per line, in fixed order;
49      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
50        cleanly in CPL_CHECK_CPLCONFIG
51      - add new coupling-exchange selectors (some not yet active) including
52        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
53                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
54      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
55        component ; called directly from coupler.F, after comp. registrations;
56      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
57         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
58          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
59      components (pkg/atm_ & ocn_compon_interf):
60      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
61        CPP header file in all pkg source files.
62      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
63        ATM/OCN_CHECK_CPLCONFIG;
64      - add error-counter to track errors (e.g., in "data.cpl") and to stop
65        cleanly in ATM/OCN_CHECK_CPLCONFIG;
66      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
67        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
68        before PACKAGES_READPARMS;
69      verification/cpl_aim+ocn/:
70      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
71        "data.cpl" for coupler (in input_cpl).
72    o eesupp/inc:
73      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
74        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
75        to always cumulate tile local-sum in the same order (still uses
76        MPI_Allreduce like standard code).
77      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
78        that are now identical to standard version (in eesupp/inc).
79    o pkg/shelfice:
80      - add SHELFICETransCoeffTFile for initializing spatially varying
81        heat and salt transfer coefficients
82    o pkg/atm_compon_interf & ocn_compon_interf:
83      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
84        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
85      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
86    o pkg/atm_ocn_coupler:
87      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
88    o pkg/rbcs:
89      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
90        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
91      - add a short report (to STDOUT) about RBCS-mask settings.
92    
93    checkpoint65p (2015/10/23)
94    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
95        there is no adjoint test for EVP, we don't know what it does to the adjoint
96        solution, but at least there are no more recomputation warnings left
97    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
98        a chance of giving the same results as a fully converged VP (JFNK) solver
99    o tools/adjoint_options/adjoint_diva:
100      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
101    o pkg/streamice:
102      - spotted bug in streamice_driving_stress using dyG where should have been dxG
103    o pkg/exf:
104      - remove STOP statement that prevented to use wind or (wind-)stress
105        interpolation for constant-in-time forcing fields (wind/stress period = 0).
106    o pkg/seaice:
107      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
108        5 additionals 2D fields and 6 new store directives
109      - change logic in seaice_readparms.F: EVP code can now be turned on in
110        various ways, setting SEAICE_deltaTev is no longer required,
111        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
112        or SEAICEaEVPcoeff
113    o pkg/shelfice/shelfice_thermodynamics.F
114      - redefining uLoc/vLoc to u/v, instead of 2u/v
115    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
116      - this is an intermediate state of a truely converging EVP that has
117        the potential of outperforming implicit VP methods, I do not recommend
118        using it yet.
119      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
120        and all parameters are hardwired
121      - for convergence it still requires very smooth regularisations, that means,
122        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
123        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
124        specific averaging appears to be required, still subject to tuning
125      - still needs cleaning and I need to turn parameter into runtime parameters
126      - add code to compute and print residuals of iteration, compile with
127        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
128    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
129      that entered with r1.54 on Sep04, 2015, -> update results
130    
131    checkpoint65o (2015/09/14)
132    o pkg/mom_vecinv & mom_common:
133      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
134        called from there.
135      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
136        allows to use Vector-Invariant form in deep atmos and anelastic formulation
137    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
138      and Koenig-Beatty+Holland (2012)
139      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
140      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
141      - requires an extra input argument for S/R seaice_calc_viscosities
142      - tensileStrength's depth dependence is different from Itkin et al. (2015)
143        (to be changed and played with, for now exponential)
144    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
145      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
146        by AREA according to Connelly et al. (2004), JPO.
147      - For EVP and the LSR solver, the implicit part of the drag term is
148        the only non-zero term in the denominator when there is no ice (which
149        prevented running the model with zero ice-ocean drag). If
150        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
151        (or zero main diagonals BU/BV) which need to be caught. A practical
152        consequence is that for open water, the momentum equation reduce
153        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
154        they happen to be zero, often leading to a non-zero solution over
155        open water.
156    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
157        efficient EVP method.
158      - introduce area-weighted averages for e12 (analogously to
159        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
160        remain, but also changing the order of terms in the previous average
161        changed the results as much) -> update experiment
162      - add SEAICE_DELTA_SMOOTHREG code
163      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
164        TEM-code
165      - adjust loop bounds so that only required fields are computed
166      - add new averaging code for zetaZ/deltaZ (again similar to
167        seaice_calc_viscosities.F), inactive by default for now (will change
168        results again), but will replace old code eventually
169    o eesupp/src:
170      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
171        to always cumulate tile local-sum in the same order
172        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
173        Still uses MPI_Allreduce (like standard code) but on array of tiles
174        and should be faster than GLOBAL_SUM_SEND_RECV code.
175      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
176        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
177      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
178         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
179         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
180         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
181         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
182    
183    checkpoint65n (2015/07/29)
184    o pkg/thsice:
185      - add a warning when used with pkg/aim but without updating SST
186        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
187    o pkg/offline:
188      - change where Offline-Fields are loaded, from load_fields_driver.F to
189        directly within FORWARD_STEP, just after updating iter number and time;
190      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
191        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
192       These changes allow:
193        a) to recover exactly on-line results using deltaToffline=deltaTClock,
194        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
195        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
196        time-step, both with GM & KPP files and with recomputing these fields;
197        b) no needs to switch on staggerTimeStep anymore;
198        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
199      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
200    o pkg/offline:
201      - change (rarely used) offset-iteration parameter to an offset time (in s):
202        can easily recover previous offset-iter effect by setting offset-time
203        (offlineTimeOffset) to offset-iter x deltaToffline;
204      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
205        in KPP as part of surface buoyancy forcing) in offline run.
206      - fix ptracers KPP non-local term in the case where KPP is re-computed.
207    o OpenAD
208      - Adding preliminary ggl90 test to OpenAD verification.
209        Config. with ggl90 currently diverges after 64 time steps
210        so will need more work to become more stable
211      - Adding preliminary kpp test to OpenAD verification.
212        required small tweakes in kpp_routines.F
213      - Merge and update from Krishna Narayanan's contrib area:
214        * Add one variable for preliminary OpenAD DIVA
215        * Add replacement time-stepping for OpenAD DIVA
216        * genmake2 flag -diva (but only for OpenAD; preliminary)
217        * required modifs for OAD_support
218        successful preliminary test for tutorial_global_oce_biogeo/
219    o pkg/seaice:
220      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
221      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
222        delta with a smooth function in s/r seaice_calc_viscosity
223        (no effect on EVP)
224      - rename local suffix "sqr" into "sq" for more consistent variable names
225    o pkg/seaice:
226        add new parameter SEAICE_deltaMin that is used ***only***
227        for regularizing Delta (and nothing else, like the parameter
228        which is also used for all sorts of things SEAICE_EPS).
229        Defaults to SEAICE_EPS for backward compatibility only.
230    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
231        the wrong key by inialising it before use -> fixes a recomputation
232        problem but does not fix the gradient
233    o pkg/layers:
234      - move resetting of flux arrays to outside the iLa loop
235        (this caused layers_diapycnal to not work with more than one layer coord.)
236      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
237    o pkg/layers:
238      - remove from common block 3D layers fields (used to diagnose transport
239        in tracer coords) and declare them as local arrays in layers_calc.F
240    o pkg/seaice:
241      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
242        in lab_sea forward experiment (changes results -> updated)
243      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
244    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
245       computations; for SEAICE_VECTORIZE_LSR
246      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
247        sweep to the outside,
248      - remove store directives and add "CADJ loop sequential" directives
249        in analogy to model/src/solve_tridiagonal.F
250      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
251        boundaries to yield more readable code. This has also the charming side
252        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
253        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
254        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
255        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
256        an additional option)
257       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
258       but the adjoint gradients (which are affected by this change) still explode.
259    o coupler (atm & ocn _compon_interf):
260      - avoid using Exch2 IO mapping if not suitable.
261    
262    checkpoint65m (2015/06/15)
263    o pkg/layers:
264      - clean-up old parameters setting (from Sep 2012):
265        + remove old parameters setting from common block (declared locally);
266        + stop if any old parameter is mixed with new parameters;
267        + check for valid or consistent parameter setting (e.g., layers_name)
268      - check that layers_bounds for Pot.Density are in the right range;
269        this is supposed to catch un-updated setting after recently shifting
270        potential density field "prho" by -1000 (now in "sigma" scale).
271    o pkg/layers:
272      - Added missing call to layers_fill for keeping track of tottend in
273        pkg/diagnostics/diagnostics_fill_state.F
274    o pkg/layers:
275      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
276        of diapycnal fluxes
277    o pkg/layers:
278      - reverted changes to interpolation to previous treatment; there
279        was never actually a problem
280    o pkg/layers:
281      - fix interpolation of layers tracers in the presence of partial cells
282      - add lots of new functionality to compute water mass transformation
283        (enabled by CPP flag LAYERS_THERMODYNAMICS)
284      - add new calls from main code (diags_oceanic_surf_flux.F,
285        thermodynamics.F, impldiff.F) and gad to save the necessary fields
286        for layers_thermodynamics calculations
287    o pkg/ptracers:
288      - add capability of stepping a passive tracer forward without advection
289        by setting PTRACERS_advScheme to 0.
290    o pkg/diagnostics:
291      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
292    o pkg/layers:
293      - shift potential density field "prho" by -1000 for density layer averaging so
294        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
295        Note that density bin boundaries (layers_bounds in data.layers) have
296        to be set accordingly (i.e., shifted, in sigma scale).
297    o pkg/layers:
298      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
299      - fix calculation of layer non-weighted velocity and layer probability
300      - add diagnostics for pot.density used for layer averaging
301    o pkg/seaice:
302      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
303        positiveness, modify a few comments and improve variable names,
304      - the changed computation of deltaC affects most seaice-related
305        experiments at the truncation level.
306        seaice_itd.thermo is affected by far the most, with
307        only 7 digits of agreement remaining; update experiments.
308    
309    checkpoint65l (2015/05/04)
310    o pkg/shelfice:
311      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
312        factor drKp1 to zero where it is negative (ie. do not use
313        SHELFICEBoundaryLayer if hFacC>1)
314      - the same for factor drLoc in shelfice_forcing.F
315    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
316        with modules in ptracers, when using testreport option "-small_f"
317    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
318      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
319    o verification/testreport
320      - add new option -small_f
321        with this option testreport first makes the target small_f (*.f files)
322        before running make (all). This is useful for explicit inlining when
323        all sources need to be full available.
324    o pkg/exf/exf_interp.F:
325        remove previous changes related to reverse (decreasing) input grids latitude
326    
327    checkpoint65k (2015/04/01)
328    o pkg/ecco:
329        fix missing cosphi initialization; use eccoiter in place of optimcycle;
330        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
331        instead of active read/write
332    o pkg/ctrl:
333        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
334        instead of active read/write.
335    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
336        return if .NOT.useAUTODIFF
337    o pkg/seaice: add CPP brackets (cost function related).
338    o model/src:
339        add useAUTODIFF run time switch.
340    o pkg/exf/exf_interp.F:
341        add code to allow input grids with latitude starting in the north (i.e. when
342        j=1 corresponds to northern edge of field); modify global_with_exf to test
343        this feature.
344    o verification/testreport:
345      - replace "grep -A3" with POSIX conformal sed command, because there are
346        implementations of grep that cannot do contextual searches
347      - replace "cat -n" by "nl" (two occurrences), because not all implementations
348        of "cat" have the option "-n"
349    o model/src:
350        add new file gsw_teos10.F that contains 3 functions, more or less a copy
351        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
352        convert from conservative to potential temperature. For now they are not
353        called anywhere.
354    o pkg/ggl90: make "useIDEMIX" useful
355      - re-organize code in s/r ggl90_calc a little to move computations that
356        are different for idemix into separate loops (changes verification
357        experiment idemix at truncation level, 12 digits remain -> updated)
358      - requires 2 new 2D fields KappaM, verticalShear
359      - make hFacI and recip_hFacI local 3D variables that are passed to
360        s/r ggl90_idemix
361      - fix and improve some comments
362    
363    checkpoint65j (2015/02/25)
364    o pkg/openad
365      - synchronize seawater.F with version in model/src: replace routine
366        body of sw_temp by calling sw_ptmp and fix/add a few comments.
367    o pkg/mnc:
368      - change default value of pickup_read/write_mnc params to FALSE
369        (since few features are missing in reading MNC pickup files).
370    o model/src:
371      - change default (background) vertical diffusivity for salt to be the
372        temperature (background) vertical diffusivity.
373      - change background vertical diffusivity in vertical mixing pkgs ggl90,
374        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
375        This makes ptracers default diffusivity (that uses salt diffKr) more
376        consistent with vertical mixing schemes.
377    o verification/testreport:
378      - fix typo in "-pcls" option ;
379      - put temp files in /tmp (instead of in local dir)
380      - add option "-ncad" to use genmake2 new option "-nocat4ad"
381      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
382    o pkg/ggl90 (idemix code):
383      - apply few fixes ; add some missing "_d 0" ; update output of exp.
384        global_ocean.90x40x15.idemix
385    o OpenAD
386      - enable active file I/O and begin removal of work-around code
387        for OpenAD for handling control variables (memory vs. active files)
388      - new CPP options file OPENAD_OPTIONS.h
389      - revert to genarr2d gradient check for hs94.1x64x5
390      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
391      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
392    o tools/genmake2:
393      - add option for an alternative Makefile (from Martin) where multiple
394        source files are sent to TAF (instead of all in one file).
395    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
396      - code provided by Carsten Eden as an extension of ggl90
397      - so far the code is turned on within ggl90 by setting a CPP-flag at
398        compile time; a runtime flag implementation is not yet complete
399      - tested in new verification experiment global_ocean.90x40x15.idemix
400    o verification:
401      - reduce length of the AD test run by half for experiments
402        global_ocean.cs32x15 (std + thsice) and isomip
403      - enable active file I/O for OpenAD, adjust verifications accordingly
404      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
405    o verification/testreport:
406      - fix two non-POSIX sed statements so that there are no error messages
407        on Mac OS X
408      - replace hostname -s with hostname | sed 's/\..*$//'
409    o model/src/seawater.F:
410      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
411        (following the matlab code), which would have avoided the bug caught
412        by Matt (see below) in the first place
413    o pkg/shelfice:
414      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
415        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
416      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
417        ice-shelf case (i.e., within surface level).
418      - add config summary in shelfice_check.F
419      - remove global variable recip_SHELFICElatentHeat and replace by a local
420        variable recip_latentHeat
421      - introduce diagnostics for friction velocity uStar (in case of
422        SHELFICEuseGammaFrict)
423      - change verification experiment isomip.htd:
424        + start from pickup (as input_ad at nIter0=8640)
425        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
426        + test SHELFICEuseGammaFrict = .TRUE.
427        + test SHELFICEadvDiffHeatFlux = .TRUE.
428    o model/src:
429      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
430        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
431        update output of experiments global_with_exf.yearly and isomip (all 6).
432    o pkg/shelfice:
433      - change setting of kTopC to also be zero where there is no ice-shelf.
434      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
435        ice-shelf is.
436      - first attempt to get RealFreshWaterFlux effects: for now, only without
437        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
438    o pkg/seaice: add the option to prescribe a fixed thickness PDF
439      for thermodynamic calculations
440      - because of divisions of the type 7/7 not exactly equal to 1, this change
441        affects results of some verification experiments by up to 4 digits:
442        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
443        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
444        adjoint: lab_sea, lab_sea.noseaicedyn
445        -> updated
446    
447    checkpoint65i (2015/01/23)
448    o model/src:
449      - change units of frictionHeating field from W to W/m^2
450      - fix bug in frictional heating from stratospheric drag in
451        S/R ATM_PHYS_TENDENCY_APPLY_V
452      - with synchronous time-stepping: move resetting to zero of frictionHeating
453        field from load_fields_driver.F to thermodynamics.F ;
454      - add diagnostics for frictional heating.
455    o model/src & gmredi K3D:
456      - add frictionHeating field to pickup-files (for synchronous time-stepping)
457      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
458      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
459        and name in pickup file).
460      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
461    o model/src:
462      - move (from ini_forcing.F) initialisation of all arrays in header file
463        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
464        (since Nov 2012) with option selectAddFluid=1.
465    o pkg/shelfice:
466      - change units (+ document) of newly added field "shelfIceMassDynTendency"
467      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
468    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
469    o pkg/seaice: two new runtime parameters:
470      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
471        long overdue
472      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
473        parameterization of tensil stress for fast ice (does not do anything yet)
474    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
475        for LSR: move checking overlaps out of JFNK-if-block
476    o pkg/atm_phys:
477      - move copy of grid and dynamical fields out of atm_phys_driver.F into
478        new S/R ATM_PHYS_DYN2PHYS.
479      - fix level height for Linear Free-Surf case (to be consistent with
480        fixed-in-time pressure levels).
481    o pkg/mom_common (bottomdrag):
482      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
483        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
484        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
485    o pkg/shelfice (u/v_drag):
486      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
487      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
488        (now similar to shelfice_u_drag.F)
489      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
490        from mom_vecinv.F (similar to mom_fluxform calls).
491    o pkg/mom_common (bottomdrag):
492      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
493      - add options for alternative discretisation of velocity norm in quadratic
494        bottom drag: averaging of grid-cell-center KE to U.point and V.point
495        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
496        improves when averaging only the other component (e.g. vVel for U bottom
497        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
498      - add options (bottomVisc_pCell) to account for partial-cell in bottom
499        friction (no-slip BC) thus getting the true distance from the bottom;
500        off by default since this also reduces model stability (explicit bottom
501        friction). Changes produce different machine truncation with linear-drag
502        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
503        front_relax (bvp & mxl, 10 & 11 digits).
504    o model/src & mom pkgs:
505      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
506        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
507      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
508        just copy level Nr value to level Nr+1.
509    o doc:
510      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
511    o pkg/streamice:
512      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
513        SHELFICE.h: move array shelficemass to init_varia, initialise
514        from array shelficemassinit, which is set in init_fixed and
515        has option to be set from file; introduce array
516        shelficeMassDynTend array, set thru file in init_fixed
517      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
518        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
519        pkg/streamice
520      - shelfice_thermodynamics.F: call shelfice_step_icemass if
521        SHELFICEMassStepping = .true.
522      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
523    
524    checkpoint65h (2014/12/17)
525    o verification/global_ocean.90x40x15, global_ocean_ebm:
526      - update to generic controls.
527    o pkg/ctrl:
528      - ctrl_map_ini_genarr.F: test for igen>0
529      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
530      - move gentim2d part of ctrl_map_ini_genarr.F to
531        new separate routine : ctrl_map_ini_gentim2d.F
532      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
533        add time variable weights and cyclic controls (time mean,
534        seasonal cycle, etc) capabilities to gentim2d
535    o pkg/ecco:
536      - move reading of error, conversion to weights from
537        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
538    o global_oce_llc90, cs32:
539      - activte sbo.
540      - CTRL_SIZE.h : add maxCtrlProc.
541      - activate the new genctrl capabilities.
542      - update following reorganization of global_oce_input_fields.tar.gz  
543    o pkg/ctrl/ctrl_ad_diff.list:
544      - add missing ctrl_init_rec.f
545    o tools/OAD_support/keepOriginal:
546      - add ctrl_init_rec.F
547    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
548      - avoid recomputations of xx_gentim2d_dummy.
549    o momentum diagnostics:
550      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
551        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
552    o pkg/seaice/seaice_lsr.F:
553      - fix computation of BU/BV, make sure they are non-zero, only necessary
554        for cubed sphere exchanges and SEAICE_OLx/y>0.
555        This makes calling s/r fill_cs_corner_rl obsolete (removed).
556    o verification/global_ocean.cs32x15/input.seaice
557      - add test for strong implicit coupling and restricted addtive Schwarz
558        methods for LSR
559      - update results/output.seaice.txt
560    o verification/tutorial_global_oce_biogeo:
561      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
562        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
563        update output_adm,_oadm,_tlm.txt
564    o pkg/dic:
565      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
566      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
567        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
568    o verification/tutorial_global_oce_biogeo:
569      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
570        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
571        update output_adm,_oadm,_tlm.txt
572    o eesupp/src:
573      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
574        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
575    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
576      LSR (following Hutchings et al. 2004)
577      - introduce zetaZ as a global variable (requires adjustments in
578        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
579        in seaice_calc_viscosities.F
580      - new flag SEAICEuseStrImpCpl (default off)
581      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
582        momentum equations
583      - JFNK-solver (preconditioner) adjusted to allow using this method
584        (where it does not have any positive effect)
585    o pkg/seaice
586      - add overlap for restrictive additive Schwartz method also to LSR, but
587        turn it off by default (because it only seems to work for non-cubed
588        sphere/llc topologies)
589    o pkg/autodiff
590      - add extra exchanges in addummy_in_steppging also for mnc output
591    o pkg/seaice:
592      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
593        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
594    o pkg/obcs:
595      - add option to specify domain-connected piece Id along OB though files
596        (for now, only used to diagnose PhiVel; default =1 -> global correction)
597      - modify obcs_diag_balance.F to process each connected-part separately;
598        exclude OB where Id = 0 but keep the full divergence there (-> constant
599        Psi along this portion of OB and all inflow derived from grad(Phi))
600      - add example of OB-conect files in verification/so_box_biogeo/input.
601    o pkg/diagnostics:
602      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
603      a) use non zero matrix element across OB and solve for Phi 1 grid point
604         outside OB (i.e, where tracer OBCS are applied).
605      b) global imbalance of inFlow/outFlow across OB: instead of modifying
606         velocity across OB, spread it uniformly along the OB in the RHS.
607    
608    checkpoint65g (2014/11/19)
609    o pkg/diagnostcis:
610      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
611    o pkg/my82,pp81,kl10:
612      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
613        field diffKr as background diffusivity to set minimum diffusivity value.
614    o pkg/seaice:
615      - add new parameter SEAICEuseEVPrev (for revisited EVP by
616        Bouillon et al 2013)
617      - add SEAICE_evpAlpha/Beta to namelist
618      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
619        involve trivial re-ordering of divisions/multiplications that should not
620        have any effects, but ... they do change the results of lab_sea.hb87 so
621        that only 2 digits of agreement remain, in line with the general
622        instability/fragility of the evp-code. For now, I do not care and just
623        update the verification experiment
624    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
625      - remove xx_genarr2d_numsmooth etc
626      - use xx_genarr2d_preproc etc instead
627      - carry out smooth_correl2D at initialization stage rather than during
628        time stepping.
629      - get smoothOpNb from xx_gentim2d_preproc
630    o global_oce_cs32 :
631      - add test of generic ecco capabilities.
632    o pkg/exf/exf_getsurfacefluxes.F :
633      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
634    o pkg/ctrl,ecco :
635      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
636        is defined.
637    o pkg/seaice: add diagnostics for Delta (deformation parameter)
638    o model/src:
639      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
640        diffusivity (background) is specified but ignored.
641    o verification:
642      - in testreport, convert hostname to lower case for default output dir name
643    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
644    o pkg/dic: add modifications from Hajoon:
645      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
646      - light attenuation: add self-shading effect by climatological Chlorophyll
647        (read from file).
648    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
649        compiles when SEAICE_ALLOW_DYNAMICS is undefined
650    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
651        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
652        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
653        approach where CPP_OPTIONS.h includes an omnipotent
654        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
655    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
656        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
657    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
658        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
659        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
660    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
661      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
662      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
663      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
664      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
665    o pkg/ctrl,ecco,exf :
666      - remove variables associated with NON-generic costs,
667        unless ECCO_CTRL_DEPRECATED is defined.
668      - remove NON-generic NON-obcs controls,
669        unless ECCO_CTRL_DEPRECATED is defined.
670    o pkg/ctrl : added ctrl_local_params.h
671    o pkg/ecco : added ecco_local_params.h
672    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
673        experiments, which will progressively be removed once the
674        experiments are revised to use only generic controls/costs.
675    
676    checkpoint65f (2014/10/13)
677    o pkg/ctrl, ecco, seaice : minor changes in headers
678    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
679        cost function and control capabilities added since checkpoint65c.
680    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
681    o pkg/ecco: increase modularity and improve logic
682      - ecco_toolbox.F (new) : basic operations that are often used,
683        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
684        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
685      - cost_gencal.F (new) : determine filnames and records.
686      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
687      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
688        and exploit the above functions leading to more compact code.
689      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
690      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
691        using_ers, using_gfo, using_mdt is now only defined within gencost)
692    o pkg/ecco: extend generic cost capabilities
693      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
694        capabilities via gencost_preproc (+ _c,_i,_r related params),
695        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
696        gencost_outputlevel arguments to cost_generic
697      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
698        and active_read, making room for gencost_preproc to take effect.
699        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
700      - pkg/ecco/cost_generic.F :
701        compute and store misfit maks*(model-data) in localdif that is
702        then used in cost and for output, output misfit if outlev.GT.0
703      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
704        rather gencost_barfile for deciding whether to write barfile
705      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
706      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
707        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
708      - pkg/ecco/ecco_summary.F : report gencost variables
709      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
710    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
711    o pkg/ecco: internal re-organization
712      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
713        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
714        mv relevant variables definition from ecco_cost.h to ecco.h,
715        make sure gencost routines only include ecco.h)
716      - throughout : add missing CCP switches, rm unused variables,
717        and rm un-necessary CPP switches
718      - throughout gencost routines : replace modelstartdate with
719        gencost_startdate when needed
720      - cost_bp_read.F : use arguments, instead of common blocs
721        so that it can be used also by (new) cost_gencost_bpv4.F
722      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
723      - ecco_phys.F : compute etanFull
724      - ecco_readparms.F : rename using_topex as using_tpj, add
725        bpv4-grace to gencost list, initialize added parameters
726      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
727    
728    checkpoint65e (2014/09/28)
729    o pkg/obcs:
730      - replaced the just-added CPP options with run-time variables
731        (see pkg/obcs/OBCS_PARAMS.h for details)
732    o pkg/obcs:
733      - add additional CPP options for sponge boundary layers
734        (see pkg/obcs/OBCS_OPTIONS.h for details)
735    o pkg/atm_phys:
736      - implement simple (obliquity only, assuming circular planet orbit)
737        seasonal cycle for incoming insolation ; used when run-time parameter
738        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
739    o pkg/exf, pkg/ecco, pkg/ctrl:
740      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
741      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
742      - implement gentim2d for xx_tauu, xx_tauv
743    o pkg/ctrl, pkg/ecco :
744      - fix and complement the generic controls implementation
745    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
746        pkg/shelfice/shelfice_thermodynamics.F,
747        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
748        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
749      - add weight in CTRL_GET_GEN calls
750    o pkg/ctrl :
751      - ctrl_get_gen.F : add weight as input parameter, and apply
752        it directly rather than using smooth_correl2Dw (to be retired).
753      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
754    o pkg/ctrl :
755      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
756        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
757      - re-activate ctrl_summary (call in ctrl_init.F)
758    o pkg/ctrl/ctrl_cost_gen.F :
759      - fix CCP brackets, remove un-necessary myiter, mytime
760    o pkg/ecco, pkg/ctrl :
761      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
762      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
763      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
764      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
765    
766    checkpoint65d (2014/09/15)
767    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
768      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
769        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
770    o pkg/ctrl/ctrl_map_ini_genarr.F :
771      - remove compilation failure
772      - replace hard coded example
773      - use ctrl_map_ini_gen2D, 3D
774    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
775      - on/off switch based upon xx_genarr2d_weight,3d
776    o src/packages_init_variables.F :
777      - regroup pkg/estimation calls
778      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
779        (moved to ctrl_init_variables)
780    o cost/cost_init_varia.F :
781      - remove ecco_cost_init_varia
782        (moved to ecco_init_varia)
783    o ctrl/ctrl_init_variables.F :
784      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
785      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
786    o ctrl/ctrl_map_ini.F :
787      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
788        (moved to ctrl_init_variables)
789    o ctrl/ctrl_map_ini_ecco.F :
790      - remove ECCO_PHYS (mv to ecco_init_varia)
791      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
792    o ecco/ecco_ad_diff.list :
793      - add ecco_init_varia.f
794    o ecco/ecco_init_varia.F
795      - new routine
796    o pkg/streamice:
797      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
798        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
799      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
800    o pkg/generic_advdiff:
801      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
802    o pkg/exf:
803      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
804         xxg_precip capability
805      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
806    o pkg/ctrl:
807      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
808    o model/src/load_fields_driver.F :
809      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
810        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
811    o OpenAD verification experiments:
812      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
813        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
814        for now, only in pkgs used in OpenAD verification experiments.
815      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
816        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
817        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
818        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
819    o OpenAD verification tests:
820      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
821      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
822        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
823      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
824        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
825    o model/src & generic_advdiff:
826      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
827        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
828        dynamics requires valid tracer forcing only over tile interior but, for
829        some diagnostics, may need to extend it over 1 point in tile halo region.
830      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
831        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
832        setting in temp/salt/ptracer_integrate.F
833    o pkg/dic:
834      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
835        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
836        in gchem_forcing_sep.F
837    o pkg/autodiff & obcs:
838      - add storage of current OB values for U & V (was already done for T & S).
839    
840    checkpoint65c (2014/08/30)
841    o pkg/dic:
842      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
843        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
844        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
845    o verification:
846      - new experiment testing OBCS and DIC pkgs, using params & output from
847        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
848        passage: take OBCS from the last year of a 2 yrs simulation and initial
849        conditions from t=1.yr while keeping the same forcing.
850    o model/src:
851      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
852        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
853    o pkg/diagnostics (Stats-Diags):
854      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
855        a) refine region where stats are computed, excluding where arrhFac=0 ;
856        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
857        c) extend regional stats over the region edges (for U or V pt location).
858    o pkg/gchem:
859      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
860        pkg/dic is currently changing/updating ptracers values beyond the OB).
861    o verification (hs94):
862      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
863        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
864        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
865        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
866    o pkg/ptracers:
867      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
868        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
869      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
870        with AB-2 code (so that it get tested).
871    o model/src:
872      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
873        with AB-2 code (previously only available with AB-3 code).
874        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
875        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
876        there, by calling CYCLE_AB_TRACER).
877    o pkg/generic_advdiff:
878      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
879        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
880        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
881        S/R temp/salt/ptracers_integrate.F
882    o model/src & pkg/ptracers:
883      - remove common block variables gT,gS (in DYNVARS.h), except when
884         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
885      - remove common block variable gPtr.
886    o model/src & pkgs:
887      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
888         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
889         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
890         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
891      + change accordingly all calling S/R.
892      - use local temperature/salinity/ptracer tendency array (without bi,bj)
893        in S/R temp/salt/ptracers_integrate.F
894    o pkg/seaice:
895      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
896        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
897      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
898        in seaice_lsr
899      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
900        in s/r seaice_lsr_calc_coeffs
901    o pkg/mdsio:
902      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
903        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
904        too long (e.g., > MAX_LEN_FNAM/2 )
905    
906    checkpoint65b (2014/08/12)
907    o pkg/matrix:
908      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
909    o model/src:
910      - fix initialisation of geothermalFile; compile geothermal-flux code in
911        natl_box verification experiment.
912    o model/src & pkg/down_slope:
913      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
914      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
915        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
916        results at machine truncation level: update output of experiments
917        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
918    o pkg/diagnostics (Stats-Diags):
919      - do not cumulate the full volume when DIAGNOSTICS_FILL is
920        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
921        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
922        times (but Min,Max and StD are still wrong).
923    o model/src:
924      - add geothermal flux forcing: read in ini_forcing.F as time-constant
925        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
926    o model/src:
927      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
928        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
929        arrays are already updated while adjustments (filters, conv.adjustment) are
930        still applied later, in S/R TRACERS_CORRECTION_STEP.
931    o model/src:
932      - store in common bloc array "rhoInSitu" the virtual potential temperature
933        anomaly that is used to compute geopotential: this make the atmos code
934        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
935    o pkg/seaice/seaice_lsr.F
936      - rename integer variable ilcall to ipass (that's what it is called
937        in the residual diagnostics
938      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
939        default) for improved non-linear convergence of the first few steps
940      - adjust a few comments and add new ones to explain some of the store
941        directives
942    o pkg/generic_advdiff (& ptracers):
943      - re-work the code to check for valid advection scheme and for minimum
944        size of overlap (now stored in local common bloc in gad_advscheme.F)
945    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
946      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
947      - add an auxilliary variable "bet" and fix store directives and keys in
948        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
949        less exact gradients in my tests); but there are still
950        recomputation warning (although gradients are sort of OK), when
951        SEAICE_LSR_VECTORIZE is not defined, so this flag and
952        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
953      - update verification experiments lab_sea.
954      - change some comments in S/R seaice_calc_viscosities
955    o model/src:
956      - if staggerTimeStep=T, always apply exchange to velocity field in
957        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
958        (independent of using multi-dim advection or not); no effect on FWD run
959        but affects AD results (at machine truncation level): update output of
960        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
961        and isomip (oad: 12.d).
962    o pkg/generic_advdiff:
963      - stop if doAB_onGtGs is set to FALSE but ignored
964      - refine warning related to stability of tracer time-stepping
965        regarding internal wave dynamics.
966      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
967        on staggerTimeStep & implicitIntGravWave (will now get a warning
968        if potentially unstable).
969    o pkg/kl10:
970      - add new pkg "kl10" for mixing due to internal wave breaking, from
971        http://www.sciencedirect.com/science/article/pii/S1463500310000144
972        (contribution from Jody Klymak), tested in verification experiment
973        verification/internal_wave/input.kl10/
974    o isomip experiment:
975      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
976        (input.htd) and update the output.
977    o cd_code experiments:
978      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
979        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
980        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
981        update the corresponding output.
982    o pkg/seaice:
983    - reduce the number of include files and store directives in    - reduce the number of include files and store directives in
984      S/R seaice_lsr_tridiagu/v      S/R seaice_lsr_tridiagu/v
985    - change the order of loops in one case in S/R seaice_lsr_tridiagv    - change the order of loops in one case in S/R seaice_lsr_tridiagv
986      (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to      (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
987      get rid off one store directive (a TAF bug?)      get rid off one store directive (a TAF bug?)
988    - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in    - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
989      S/R seaice_lsr_tridiagv to change the loop range for consistency      S/R seaice_lsr_tridiagv to change the loop range for consistency
990    - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v    - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
991    - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in    - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
992      S/R seaice_lsr_tridiagu/v (requires update of      S/R seaice_lsr_tridiagu/v (requires update of
993      offline_exf_seaice/input.dyn_jfnk)      offline_exf_seaice/input.dyn_jfnk)
994    
995  checkpoint65a (2014/07/27)  checkpoint65a (2014/07/27)
996  o model/src:  o model/src:
# Line 31  o model/src: Line 1006  o model/src:
1006    - collect T & S forcing tendency into local 2-D array (passed as argument to    - collect T & S forcing tendency into local 2-D array (passed as argument to
1007      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1008      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
1009      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1010      moist correction due to vertical advection).      correction due to vertical advection).
1011    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1012      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1013      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
# Line 61  o pkg/seaice: more clean up Line 1036  o pkg/seaice: more clean up
1036      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
1037      this experiment):      this experiment):
1038      > size mitgcmuv_ad      > size mitgcmuv_ad
1039      text    data        bss     dec        hex        text    data        bss     dec        hex
1040      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1041      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1042      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1043      text    data        bss     dec        hex      text    data        bss     dec        hex
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