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revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2219 by jmc, Sat Jan 2 02:58:37 2016 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/dic:
8      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
9    o pkg/thsice:
10      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
11        and writing of thsice pickup files.
12    o pkg/atm_compon_interf:
13      - move all field individual export-call out of cpl_export_import_data.F
14        into new S/R ATM_EXPORT_FIELDS
15    o pkg/atm_compon_interf:
16      - store state variables (for now, only thSIce fields) just before beeing
17        exported (in cpl_export_import_data.F, like on ocean side) instead of from
18        atm_store_my_data.F like all exported fluxes.
19      - new version of pickup_cpl: write field names into meta file and read meta
20        file to find field postion in pickup. Also only write/read fields meeded for
21        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
22    o pkg/dic:
23      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
24    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
25        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
26        value can be from domain [0,1] to average between the two methods
27    o pkg/atm_phys:
28      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
29        hold fixed in time).
30    
31    checkpoint65r (2015/12/21)
32    o pkg/seaice:
33        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
34        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
35    o pkg/seaice:
36      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
37        when SEAICEscaleSurfStress=.TRUE.,
38      - apply areaW and areaS in S/R seaice_calc_lhs
39    o pkg/atm_phys:
40      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
41        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
42        for individual contribution (convection, LSC cond, radiation)
43      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
44        information); activated with: solar_exponent=0. and wv_exponent=-1.
45    o pkg/ggl90:
46      - within IDEMIX add upper limit for horizontal group velocity to
47        avoid instability problems in the explicit horizontal diffusion term for
48        long time steps or high resolution
49    o pkg/diagnostics:
50      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
51        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
52    o testreport:
53      - remove "-v" (verbose option) in default mpirun command.
54    o pkg/seaice/seaice_growth:
55      - catch potential division by zero in ITD code, does not change
56        verification results
57    o pkg/ecco:
58      - retire old codes to the Attic. The calls to retired functions are
59        left in a commented form in case they ever need to be re-activated.
60      - ecco_check.F: issue warning if any old CPP option is
61        defined that corresponds to retired codes -- then stop.
62    o pkg/atm_compon_interf:
63      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
64        coupler: use last time-step value instead of average over cplSendFrq_iter
65        time-step, similar to what is done for seaIceMass.
66        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
67    o eesupp & genmake2:
68      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
69        <= remove until a fix is found for some ifort version on ia32 machine.
70    o pkg/seaice/seaice_evp:
71      - refine residual computation
72    
73    checkpoint65q (2015/11/18)
74    o pkg/seaice/seaice_evp:
75      - fix residual computations so that they no longer affect the actual
76        simulation code
77      - fix seaice_readparams to be able to actually set new parameters
78        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
79    o model/src:
80      - fix wrong truncation (single prec) from "FLOAT" function in expressions
81        like: deltaT*FLOAT(myIter) when myIter is large:
82         a) replaced by DFLOAT (if not seen by TAF);
83         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
84    o pkg/aim_v23:
85      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
86        when pickupSuff is set ; do write rolling pickups + at the end of the run.
87    o pkg/atm_ocn_coupler + ocn_compon_interf:
88      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
89        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
90        add corresponding call in DO_OCEANIC_PHYS.
91    o coupler pkgs:
92      Start a new way to set-up optionally-exchanged variables (previously, only
93       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
94       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
95       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
96       compononent param default can be set accordingly).
97      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
98       but rather applies to a group a fields (going both ways like for DIC)
99       and corresponds to an option of coupling config.
100      coupler (pkg/atm_ocn_coupler):
101      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
102        and read namelist directly (without eessup S/R calls) instead of
103        in the very un-flexible old way, 1 param per line, in fixed order;
104      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
105        cleanly in CPL_CHECK_CPLCONFIG
106      - add new coupling-exchange selectors (some not yet active) including
107        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
108                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
109      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
110        component ; called directly from coupler.F, after comp. registrations;
111      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
112         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
113          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
114      components (pkg/atm_ & ocn_compon_interf):
115      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
116        CPP header file in all pkg source files.
117      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
118        ATM/OCN_CHECK_CPLCONFIG;
119      - add error-counter to track errors (e.g., in "data.cpl") and to stop
120        cleanly in ATM/OCN_CHECK_CPLCONFIG;
121      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
122        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
123        before PACKAGES_READPARMS;
124      verification/cpl_aim+ocn/:
125      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
126        "data.cpl" for coupler (in input_cpl).
127    o eesupp/inc:
128      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
129        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
130        to always cumulate tile local-sum in the same order (still uses
131        MPI_Allreduce like standard code).
132      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
133        that are now identical to standard version (in eesupp/inc).
134    o pkg/shelfice:
135      - add SHELFICETransCoeffTFile for initializing spatially varying
136        heat and salt transfer coefficients
137    o pkg/atm_compon_interf & ocn_compon_interf:
138      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
139        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
140      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
141    o pkg/atm_ocn_coupler:
142      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
143    o pkg/rbcs:
144      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
145        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
146      - add a short report (to STDOUT) about RBCS-mask settings.
147    
148    checkpoint65p (2015/10/23)
149    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
150        there is no adjoint test for EVP, we don't know what it does to the adjoint
151        solution, but at least there are no more recomputation warnings left
152    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
153        a chance of giving the same results as a fully converged VP (JFNK) solver
154    o tools/adjoint_options/adjoint_diva:
155      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
156    o pkg/streamice:
157      - spotted bug in streamice_driving_stress using dyG where should have been dxG
158    o pkg/exf:
159      - remove STOP statement that prevented to use wind or (wind-)stress
160        interpolation for constant-in-time forcing fields (wind/stress period = 0).
161    o pkg/seaice:
162      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
163        5 additionals 2D fields and 6 new store directives
164      - change logic in seaice_readparms.F: EVP code can now be turned on in
165        various ways, setting SEAICE_deltaTev is no longer required,
166        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
167        or SEAICEaEVPcoeff
168    o pkg/shelfice/shelfice_thermodynamics.F
169      - redefining uLoc/vLoc to u/v, instead of 2u/v
170    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
171      - this is an intermediate state of a truely converging EVP that has
172        the potential of outperforming implicit VP methods, I do not recommend
173        using it yet.
174      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
175        and all parameters are hardwired
176      - for convergence it still requires very smooth regularisations, that means,
177        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
178        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
179        specific averaging appears to be required, still subject to tuning
180      - still needs cleaning and I need to turn parameter into runtime parameters
181      - add code to compute and print residuals of iteration, compile with
182        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
183    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
184      that entered with r1.54 on Sep04, 2015, -> update results
185    
186    checkpoint65o (2015/09/14)
187    o pkg/mom_vecinv & mom_common:
188      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
189        called from there.
190      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
191        allows to use Vector-Invariant form in deep atmos and anelastic formulation
192    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
193      and Koenig-Beatty+Holland (2012)
194      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
195      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
196      - requires an extra input argument for S/R seaice_calc_viscosities
197      - tensileStrength's depth dependence is different from Itkin et al. (2015)
198        (to be changed and played with, for now exponential)
199    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
200      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
201        by AREA according to Connelly et al. (2004), JPO.
202      - For EVP and the LSR solver, the implicit part of the drag term is
203        the only non-zero term in the denominator when there is no ice (which
204        prevented running the model with zero ice-ocean drag). If
205        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
206        (or zero main diagonals BU/BV) which need to be caught. A practical
207        consequence is that for open water, the momentum equation reduce
208        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
209        they happen to be zero, often leading to a non-zero solution over
210        open water.
211    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
212        efficient EVP method.
213      - introduce area-weighted averages for e12 (analogously to
214        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
215        remain, but also changing the order of terms in the previous average
216        changed the results as much) -> update experiment
217      - add SEAICE_DELTA_SMOOTHREG code
218      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
219        TEM-code
220      - adjust loop bounds so that only required fields are computed
221      - add new averaging code for zetaZ/deltaZ (again similar to
222        seaice_calc_viscosities.F), inactive by default for now (will change
223        results again), but will replace old code eventually
224    o eesupp/src:
225      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
226        to always cumulate tile local-sum in the same order
227        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
228        Still uses MPI_Allreduce (like standard code) but on array of tiles
229        and should be faster than GLOBAL_SUM_SEND_RECV code.
230      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
231        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
232      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
233         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
234         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
235         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
236         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
237    
238    checkpoint65n (2015/07/29)
239    o pkg/thsice:
240      - add a warning when used with pkg/aim but without updating SST
241        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
242    o pkg/offline:
243      - change where Offline-Fields are loaded, from load_fields_driver.F to
244        directly within FORWARD_STEP, just after updating iter number and time;
245      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
246        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
247       These changes allow:
248        a) to recover exactly on-line results using deltaToffline=deltaTClock,
249        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
250        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
251        time-step, both with GM & KPP files and with recomputing these fields;
252        b) no needs to switch on staggerTimeStep anymore;
253        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
254      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
255    o pkg/offline:
256      - change (rarely used) offset-iteration parameter to an offset time (in s):
257        can easily recover previous offset-iter effect by setting offset-time
258        (offlineTimeOffset) to offset-iter x deltaToffline;
259      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
260        in KPP as part of surface buoyancy forcing) in offline run.
261      - fix ptracers KPP non-local term in the case where KPP is re-computed.
262    o OpenAD
263      - Adding preliminary ggl90 test to OpenAD verification.
264        Config. with ggl90 currently diverges after 64 time steps
265        so will need more work to become more stable
266      - Adding preliminary kpp test to OpenAD verification.
267        required small tweakes in kpp_routines.F
268      - Merge and update from Krishna Narayanan's contrib area:
269        * Add one variable for preliminary OpenAD DIVA
270        * Add replacement time-stepping for OpenAD DIVA
271        * genmake2 flag -diva (but only for OpenAD; preliminary)
272        * required modifs for OAD_support
273        successful preliminary test for tutorial_global_oce_biogeo/
274    o pkg/seaice:
275      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
276      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
277        delta with a smooth function in s/r seaice_calc_viscosity
278        (no effect on EVP)
279      - rename local suffix "sqr" into "sq" for more consistent variable names
280    o pkg/seaice:
281        add new parameter SEAICE_deltaMin that is used ***only***
282        for regularizing Delta (and nothing else, like the parameter
283        which is also used for all sorts of things SEAICE_EPS).
284        Defaults to SEAICE_EPS for backward compatibility only.
285    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
286        the wrong key by inialising it before use -> fixes a recomputation
287        problem but does not fix the gradient
288    o pkg/layers:
289      - move resetting of flux arrays to outside the iLa loop
290        (this caused layers_diapycnal to not work with more than one layer coord.)
291      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
292    o pkg/layers:
293      - remove from common block 3D layers fields (used to diagnose transport
294        in tracer coords) and declare them as local arrays in layers_calc.F
295    o pkg/seaice:
296      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
297        in lab_sea forward experiment (changes results -> updated)
298      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
299    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
300       computations; for SEAICE_VECTORIZE_LSR
301      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
302        sweep to the outside,
303      - remove store directives and add "CADJ loop sequential" directives
304        in analogy to model/src/solve_tridiagonal.F
305      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
306        boundaries to yield more readable code. This has also the charming side
307        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
308        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
309        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
310        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
311        an additional option)
312       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
313       but the adjoint gradients (which are affected by this change) still explode.
314    o coupler (atm & ocn _compon_interf):
315      - avoid using Exch2 IO mapping if not suitable.
316    
317    checkpoint65m (2015/06/15)
318    o pkg/layers:
319      - clean-up old parameters setting (from Sep 2012):
320        + remove old parameters setting from common block (declared locally);
321        + stop if any old parameter is mixed with new parameters;
322        + check for valid or consistent parameter setting (e.g., layers_name)
323      - check that layers_bounds for Pot.Density are in the right range;
324        this is supposed to catch un-updated setting after recently shifting
325        potential density field "prho" by -1000 (now in "sigma" scale).
326    o pkg/layers:
327      - Added missing call to layers_fill for keeping track of tottend in
328        pkg/diagnostics/diagnostics_fill_state.F
329    o pkg/layers:
330      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
331        of diapycnal fluxes
332    o pkg/layers:
333      - reverted changes to interpolation to previous treatment; there
334        was never actually a problem
335    o pkg/layers:
336      - fix interpolation of layers tracers in the presence of partial cells
337      - add lots of new functionality to compute water mass transformation
338        (enabled by CPP flag LAYERS_THERMODYNAMICS)
339      - add new calls from main code (diags_oceanic_surf_flux.F,
340        thermodynamics.F, impldiff.F) and gad to save the necessary fields
341        for layers_thermodynamics calculations
342    o pkg/ptracers:
343      - add capability of stepping a passive tracer forward without advection
344        by setting PTRACERS_advScheme to 0.
345    o pkg/diagnostics:
346      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
347    o pkg/layers:
348      - shift potential density field "prho" by -1000 for density layer averaging so
349        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
350        Note that density bin boundaries (layers_bounds in data.layers) have
351        to be set accordingly (i.e., shifted, in sigma scale).
352    o pkg/layers:
353      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
354      - fix calculation of layer non-weighted velocity and layer probability
355      - add diagnostics for pot.density used for layer averaging
356    o pkg/seaice:
357      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
358        positiveness, modify a few comments and improve variable names,
359      - the changed computation of deltaC affects most seaice-related
360        experiments at the truncation level.
361        seaice_itd.thermo is affected by far the most, with
362        only 7 digits of agreement remaining; update experiments.
363    
364    checkpoint65l (2015/05/04)
365    o pkg/shelfice:
366      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
367        factor drKp1 to zero where it is negative (ie. do not use
368        SHELFICEBoundaryLayer if hFacC>1)
369      - the same for factor drLoc in shelfice_forcing.F
370    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
371        with modules in ptracers, when using testreport option "-small_f"
372    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
373      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
374    o verification/testreport
375      - add new option -small_f
376        with this option testreport first makes the target small_f (*.f files)
377        before running make (all). This is useful for explicit inlining when
378        all sources need to be full available.
379    o pkg/exf/exf_interp.F:
380        remove previous changes related to reverse (decreasing) input grids latitude
381    
382    checkpoint65k (2015/04/01)
383    o pkg/ecco:
384        fix missing cosphi initialization; use eccoiter in place of optimcycle;
385        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
386        instead of active read/write
387    o pkg/ctrl:
388        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
389        instead of active read/write.
390    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
391        return if .NOT.useAUTODIFF
392    o pkg/seaice: add CPP brackets (cost function related).
393    o model/src:
394        add useAUTODIFF run time switch.
395    o pkg/exf/exf_interp.F:
396        add code to allow input grids with latitude starting in the north (i.e. when
397        j=1 corresponds to northern edge of field); modify global_with_exf to test
398        this feature.
399    o verification/testreport:
400      - replace "grep -A3" with POSIX conformal sed command, because there are
401        implementations of grep that cannot do contextual searches
402      - replace "cat -n" by "nl" (two occurrences), because not all implementations
403        of "cat" have the option "-n"
404    o model/src:
405        add new file gsw_teos10.F that contains 3 functions, more or less a copy
406        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
407        convert from conservative to potential temperature. For now they are not
408        called anywhere.
409    o pkg/ggl90: make "useIDEMIX" useful
410      - re-organize code in s/r ggl90_calc a little to move computations that
411        are different for idemix into separate loops (changes verification
412        experiment idemix at truncation level, 12 digits remain -> updated)
413      - requires 2 new 2D fields KappaM, verticalShear
414      - make hFacI and recip_hFacI local 3D variables that are passed to
415        s/r ggl90_idemix
416      - fix and improve some comments
417    
418    checkpoint65j (2015/02/25)
419    o pkg/openad
420      - synchronize seawater.F with version in model/src: replace routine
421        body of sw_temp by calling sw_ptmp and fix/add a few comments.
422    o pkg/mnc:
423      - change default value of pickup_read/write_mnc params to FALSE
424        (since few features are missing in reading MNC pickup files).
425    o model/src:
426      - change default (background) vertical diffusivity for salt to be the
427        temperature (background) vertical diffusivity.
428      - change background vertical diffusivity in vertical mixing pkgs ggl90,
429        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
430        This makes ptracers default diffusivity (that uses salt diffKr) more
431        consistent with vertical mixing schemes.
432    o verification/testreport:
433      - fix typo in "-pcls" option ;
434      - put temp files in /tmp (instead of in local dir)
435      - add option "-ncad" to use genmake2 new option "-nocat4ad"
436      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
437    o pkg/ggl90 (idemix code):
438      - apply few fixes ; add some missing "_d 0" ; update output of exp.
439        global_ocean.90x40x15.idemix
440    o OpenAD
441      - enable active file I/O and begin removal of work-around code
442        for OpenAD for handling control variables (memory vs. active files)
443      - new CPP options file OPENAD_OPTIONS.h
444      - revert to genarr2d gradient check for hs94.1x64x5
445      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
446      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
447    o tools/genmake2:
448      - add option for an alternative Makefile (from Martin) where multiple
449        source files are sent to TAF (instead of all in one file).
450    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
451      - code provided by Carsten Eden as an extension of ggl90
452      - so far the code is turned on within ggl90 by setting a CPP-flag at
453        compile time; a runtime flag implementation is not yet complete
454      - tested in new verification experiment global_ocean.90x40x15.idemix
455    o verification:
456      - reduce length of the AD test run by half for experiments
457        global_ocean.cs32x15 (std + thsice) and isomip
458      - enable active file I/O for OpenAD, adjust verifications accordingly
459      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
460    o verification/testreport:
461      - fix two non-POSIX sed statements so that there are no error messages
462        on Mac OS X
463      - replace hostname -s with hostname | sed 's/\..*$//'
464    o model/src/seawater.F:
465      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
466        (following the matlab code), which would have avoided the bug caught
467        by Matt (see below) in the first place
468    o pkg/shelfice:
469      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
470        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
471      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
472        ice-shelf case (i.e., within surface level).
473      - add config summary in shelfice_check.F
474      - remove global variable recip_SHELFICElatentHeat and replace by a local
475        variable recip_latentHeat
476      - introduce diagnostics for friction velocity uStar (in case of
477        SHELFICEuseGammaFrict)
478      - change verification experiment isomip.htd:
479        + start from pickup (as input_ad at nIter0=8640)
480        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
481        + test SHELFICEuseGammaFrict = .TRUE.
482        + test SHELFICEadvDiffHeatFlux = .TRUE.
483    o model/src:
484      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
485        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
486        update output of experiments global_with_exf.yearly and isomip (all 6).
487    o pkg/shelfice:
488      - change setting of kTopC to also be zero where there is no ice-shelf.
489      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
490        ice-shelf is.
491      - first attempt to get RealFreshWaterFlux effects: for now, only without
492        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
493    o pkg/seaice: add the option to prescribe a fixed thickness PDF
494      for thermodynamic calculations
495      - because of divisions of the type 7/7 not exactly equal to 1, this change
496        affects results of some verification experiments by up to 4 digits:
497        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
498        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
499        adjoint: lab_sea, lab_sea.noseaicedyn
500        -> updated
501    
502    checkpoint65i (2015/01/23)
503    o model/src:
504      - change units of frictionHeating field from W to W/m^2
505      - fix bug in frictional heating from stratospheric drag in
506        S/R ATM_PHYS_TENDENCY_APPLY_V
507      - with synchronous time-stepping: move resetting to zero of frictionHeating
508        field from load_fields_driver.F to thermodynamics.F ;
509      - add diagnostics for frictional heating.
510    o model/src & gmredi K3D:
511      - add frictionHeating field to pickup-files (for synchronous time-stepping)
512      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
513      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
514        and name in pickup file).
515      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
516    o model/src:
517      - move (from ini_forcing.F) initialisation of all arrays in header file
518        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
519        (since Nov 2012) with option selectAddFluid=1.
520    o pkg/shelfice:
521      - change units (+ document) of newly added field "shelfIceMassDynTendency"
522      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
523    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
524    o pkg/seaice: two new runtime parameters:
525      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
526        long overdue
527      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
528        parameterization of tensil stress for fast ice (does not do anything yet)
529    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
530        for LSR: move checking overlaps out of JFNK-if-block
531    o pkg/atm_phys:
532      - move copy of grid and dynamical fields out of atm_phys_driver.F into
533        new S/R ATM_PHYS_DYN2PHYS.
534      - fix level height for Linear Free-Surf case (to be consistent with
535        fixed-in-time pressure levels).
536    o pkg/mom_common (bottomdrag):
537      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
538        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
539        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
540    o pkg/shelfice (u/v_drag):
541      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
542      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
543        (now similar to shelfice_u_drag.F)
544      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
545        from mom_vecinv.F (similar to mom_fluxform calls).
546    o pkg/mom_common (bottomdrag):
547      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
548      - add options for alternative discretisation of velocity norm in quadratic
549        bottom drag: averaging of grid-cell-center KE to U.point and V.point
550        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
551        improves when averaging only the other component (e.g. vVel for U bottom
552        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
553      - add options (bottomVisc_pCell) to account for partial-cell in bottom
554        friction (no-slip BC) thus getting the true distance from the bottom;
555        off by default since this also reduces model stability (explicit bottom
556        friction). Changes produce different machine truncation with linear-drag
557        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
558        front_relax (bvp & mxl, 10 & 11 digits).
559    o model/src & mom pkgs:
560      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
561        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
562      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
563        just copy level Nr value to level Nr+1.
564    o doc:
565      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
566    o pkg/streamice:
567      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
568        SHELFICE.h: move array shelficemass to init_varia, initialise
569        from array shelficemassinit, which is set in init_fixed and
570        has option to be set from file; introduce array
571        shelficeMassDynTend array, set thru file in init_fixed
572      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
573        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
574        pkg/streamice
575      - shelfice_thermodynamics.F: call shelfice_step_icemass if
576        SHELFICEMassStepping = .true.
577      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
578    
579    checkpoint65h (2014/12/17)
580    o verification/global_ocean.90x40x15, global_ocean_ebm:
581      - update to generic controls.
582    o pkg/ctrl:
583      - ctrl_map_ini_genarr.F: test for igen>0
584      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
585      - move gentim2d part of ctrl_map_ini_genarr.F to
586        new separate routine : ctrl_map_ini_gentim2d.F
587      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
588        add time variable weights and cyclic controls (time mean,
589        seasonal cycle, etc) capabilities to gentim2d
590    o pkg/ecco:
591      - move reading of error, conversion to weights from
592        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
593    o global_oce_llc90, cs32:
594      - activte sbo.
595      - CTRL_SIZE.h : add maxCtrlProc.
596      - activate the new genctrl capabilities.
597      - update following reorganization of global_oce_input_fields.tar.gz  
598    o pkg/ctrl/ctrl_ad_diff.list:
599      - add missing ctrl_init_rec.f
600    o tools/OAD_support/keepOriginal:
601      - add ctrl_init_rec.F
602    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
603      - avoid recomputations of xx_gentim2d_dummy.
604    o momentum diagnostics:
605      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
606        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
607    o pkg/seaice/seaice_lsr.F:
608      - fix computation of BU/BV, make sure they are non-zero, only necessary
609        for cubed sphere exchanges and SEAICE_OLx/y>0.
610        This makes calling s/r fill_cs_corner_rl obsolete (removed).
611    o verification/global_ocean.cs32x15/input.seaice
612      - add test for strong implicit coupling and restricted addtive Schwarz
613        methods for LSR
614      - update results/output.seaice.txt
615    o verification/tutorial_global_oce_biogeo:
616      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
617        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
618        update output_adm,_oadm,_tlm.txt
619    o pkg/dic:
620      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
621      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
622        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
623    o verification/tutorial_global_oce_biogeo:
624      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
625        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
626        update output_adm,_oadm,_tlm.txt
627    o eesupp/src:
628      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
629        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
630    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
631      LSR (following Hutchings et al. 2004)
632      - introduce zetaZ as a global variable (requires adjustments in
633        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
634        in seaice_calc_viscosities.F
635      - new flag SEAICEuseStrImpCpl (default off)
636      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
637        momentum equations
638      - JFNK-solver (preconditioner) adjusted to allow using this method
639        (where it does not have any positive effect)
640    o pkg/seaice
641      - add overlap for restrictive additive Schwartz method also to LSR, but
642        turn it off by default (because it only seems to work for non-cubed
643        sphere/llc topologies)
644    o pkg/autodiff
645      - add extra exchanges in addummy_in_steppging also for mnc output
646    o pkg/seaice:
647      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
648        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
649    o pkg/obcs:
650      - add option to specify domain-connected piece Id along OB though files
651        (for now, only used to diagnose PhiVel; default =1 -> global correction)
652      - modify obcs_diag_balance.F to process each connected-part separately;
653        exclude OB where Id = 0 but keep the full divergence there (-> constant
654        Psi along this portion of OB and all inflow derived from grad(Phi))
655      - add example of OB-conect files in verification/so_box_biogeo/input.
656    o pkg/diagnostics:
657      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
658      a) use non zero matrix element across OB and solve for Phi 1 grid point
659         outside OB (i.e, where tracer OBCS are applied).
660      b) global imbalance of inFlow/outFlow across OB: instead of modifying
661         velocity across OB, spread it uniformly along the OB in the RHS.
662    
663    checkpoint65g (2014/11/19)
664    o pkg/diagnostcis:
665      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
666    o pkg/my82,pp81,kl10:
667      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
668        field diffKr as background diffusivity to set minimum diffusivity value.
669    o pkg/seaice:
670      - add new parameter SEAICEuseEVPrev (for revisited EVP by
671        Bouillon et al 2013)
672      - add SEAICE_evpAlpha/Beta to namelist
673      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
674        involve trivial re-ordering of divisions/multiplications that should not
675        have any effects, but ... they do change the results of lab_sea.hb87 so
676        that only 2 digits of agreement remain, in line with the general
677        instability/fragility of the evp-code. For now, I do not care and just
678        update the verification experiment
679    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
680      - remove xx_genarr2d_numsmooth etc
681      - use xx_genarr2d_preproc etc instead
682      - carry out smooth_correl2D at initialization stage rather than during
683        time stepping.
684      - get smoothOpNb from xx_gentim2d_preproc
685    o global_oce_cs32 :
686      - add test of generic ecco capabilities.
687    o pkg/exf/exf_getsurfacefluxes.F :
688      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
689    o pkg/ctrl,ecco :
690      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
691        is defined.
692    o pkg/seaice: add diagnostics for Delta (deformation parameter)
693    o model/src:
694      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
695        diffusivity (background) is specified but ignored.
696    o verification:
697      - in testreport, convert hostname to lower case for default output dir name
698    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
699    o pkg/dic: add modifications from Hajoon:
700      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
701      - light attenuation: add self-shading effect by climatological Chlorophyll
702        (read from file).
703    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
704        compiles when SEAICE_ALLOW_DYNAMICS is undefined
705    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
706        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
707        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
708        approach where CPP_OPTIONS.h includes an omnipotent
709        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
710    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
711        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
712    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
713        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
714        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
715    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
716      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
717      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
718      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
719      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
720    o pkg/ctrl,ecco,exf :
721      - remove variables associated with NON-generic costs,
722        unless ECCO_CTRL_DEPRECATED is defined.
723      - remove NON-generic NON-obcs controls,
724        unless ECCO_CTRL_DEPRECATED is defined.
725    o pkg/ctrl : added ctrl_local_params.h
726    o pkg/ecco : added ecco_local_params.h
727    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
728        experiments, which will progressively be removed once the
729        experiments are revised to use only generic controls/costs.
730    
731    checkpoint65f (2014/10/13)
732    o pkg/ctrl, ecco, seaice : minor changes in headers
733    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
734        cost function and control capabilities added since checkpoint65c.
735    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
736    o pkg/ecco: increase modularity and improve logic
737      - ecco_toolbox.F (new) : basic operations that are often used,
738        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
739        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
740      - cost_gencal.F (new) : determine filnames and records.
741      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
742      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
743        and exploit the above functions leading to more compact code.
744      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
745      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
746        using_ers, using_gfo, using_mdt is now only defined within gencost)
747    o pkg/ecco: extend generic cost capabilities
748      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
749        capabilities via gencost_preproc (+ _c,_i,_r related params),
750        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
751        gencost_outputlevel arguments to cost_generic
752      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
753        and active_read, making room for gencost_preproc to take effect.
754        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
755      - pkg/ecco/cost_generic.F :
756        compute and store misfit maks*(model-data) in localdif that is
757        then used in cost and for output, output misfit if outlev.GT.0
758      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
759        rather gencost_barfile for deciding whether to write barfile
760      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
761      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
762        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
763      - pkg/ecco/ecco_summary.F : report gencost variables
764      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
765    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
766    o pkg/ecco: internal re-organization
767      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
768        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
769        mv relevant variables definition from ecco_cost.h to ecco.h,
770        make sure gencost routines only include ecco.h)
771      - throughout : add missing CCP switches, rm unused variables,
772        and rm un-necessary CPP switches
773      - throughout gencost routines : replace modelstartdate with
774        gencost_startdate when needed
775      - cost_bp_read.F : use arguments, instead of common blocs
776        so that it can be used also by (new) cost_gencost_bpv4.F
777      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
778      - ecco_phys.F : compute etanFull
779      - ecco_readparms.F : rename using_topex as using_tpj, add
780        bpv4-grace to gencost list, initialize added parameters
781      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
782    
783    checkpoint65e (2014/09/28)
784    o pkg/obcs:
785      - replaced the just-added CPP options with run-time variables
786        (see pkg/obcs/OBCS_PARAMS.h for details)
787    o pkg/obcs:
788      - add additional CPP options for sponge boundary layers
789        (see pkg/obcs/OBCS_OPTIONS.h for details)
790    o pkg/atm_phys:
791      - implement simple (obliquity only, assuming circular planet orbit)
792        seasonal cycle for incoming insolation ; used when run-time parameter
793        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
794    o pkg/exf, pkg/ecco, pkg/ctrl:
795      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
796      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
797      - implement gentim2d for xx_tauu, xx_tauv
798    o pkg/ctrl, pkg/ecco :
799      - fix and complement the generic controls implementation
800    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
801        pkg/shelfice/shelfice_thermodynamics.F,
802        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
803        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
804      - add weight in CTRL_GET_GEN calls
805    o pkg/ctrl :
806      - ctrl_get_gen.F : add weight as input parameter, and apply
807        it directly rather than using smooth_correl2Dw (to be retired).
808      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
809    o pkg/ctrl :
810      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
811        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
812      - re-activate ctrl_summary (call in ctrl_init.F)
813    o pkg/ctrl/ctrl_cost_gen.F :
814      - fix CCP brackets, remove un-necessary myiter, mytime
815    o pkg/ecco, pkg/ctrl :
816      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
817      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
818      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
819      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
820    
821    checkpoint65d (2014/09/15)
822    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
823      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
824        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
825    o pkg/ctrl/ctrl_map_ini_genarr.F :
826      - remove compilation failure
827      - replace hard coded example
828      - use ctrl_map_ini_gen2D, 3D
829    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
830      - on/off switch based upon xx_genarr2d_weight,3d
831    o src/packages_init_variables.F :
832      - regroup pkg/estimation calls
833      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
834        (moved to ctrl_init_variables)
835    o cost/cost_init_varia.F :
836      - remove ecco_cost_init_varia
837        (moved to ecco_init_varia)
838    o ctrl/ctrl_init_variables.F :
839      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
840      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
841    o ctrl/ctrl_map_ini.F :
842      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
843        (moved to ctrl_init_variables)
844    o ctrl/ctrl_map_ini_ecco.F :
845      - remove ECCO_PHYS (mv to ecco_init_varia)
846      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
847    o ecco/ecco_ad_diff.list :
848      - add ecco_init_varia.f
849    o ecco/ecco_init_varia.F
850      - new routine
851    o pkg/streamice:
852      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
853        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
854      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
855    o pkg/generic_advdiff:
856      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
857    o pkg/exf:
858      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
859         xxg_precip capability
860      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
861    o pkg/ctrl:
862      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
863    o model/src/load_fields_driver.F :
864      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
865        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
866    o OpenAD verification experiments:
867      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
868        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
869        for now, only in pkgs used in OpenAD verification experiments.
870      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
871        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
872        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
873        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
874    o OpenAD verification tests:
875      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
876      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
877        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
878      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
879        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
880    o model/src & generic_advdiff:
881      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
882        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
883        dynamics requires valid tracer forcing only over tile interior but, for
884        some diagnostics, may need to extend it over 1 point in tile halo region.
885      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
886        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
887        setting in temp/salt/ptracer_integrate.F
888    o pkg/dic:
889      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
890        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
891        in gchem_forcing_sep.F
892    o pkg/autodiff & obcs:
893      - add storage of current OB values for U & V (was already done for T & S).
894    
895    checkpoint65c (2014/08/30)
896    o pkg/dic:
897      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
898        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
899        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
900    o verification:
901      - new experiment testing OBCS and DIC pkgs, using params & output from
902        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
903        passage: take OBCS from the last year of a 2 yrs simulation and initial
904        conditions from t=1.yr while keeping the same forcing.
905    o model/src:
906      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
907        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
908    o pkg/diagnostics (Stats-Diags):
909      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
910        a) refine region where stats are computed, excluding where arrhFac=0 ;
911        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
912        c) extend regional stats over the region edges (for U or V pt location).
913    o pkg/gchem:
914      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
915        pkg/dic is currently changing/updating ptracers values beyond the OB).
916    o verification (hs94):
917      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
918        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
919        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
920        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
921    o pkg/ptracers:
922      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
923        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
924      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
925        with AB-2 code (so that it get tested).
926    o model/src:
927      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
928        with AB-2 code (previously only available with AB-3 code).
929        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
930        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
931        there, by calling CYCLE_AB_TRACER).
932    o pkg/generic_advdiff:
933      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
934        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
935        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
936        S/R temp/salt/ptracers_integrate.F
937    o model/src & pkg/ptracers:
938      - remove common block variables gT,gS (in DYNVARS.h), except when
939         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
940      - remove common block variable gPtr.
941    o model/src & pkgs:
942      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
943         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
944         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
945         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
946      + change accordingly all calling S/R.
947      - use local temperature/salinity/ptracer tendency array (without bi,bj)
948        in S/R temp/salt/ptracers_integrate.F
949    o pkg/seaice:
950      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
951        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
952      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
953        in seaice_lsr
954      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
955        in s/r seaice_lsr_calc_coeffs
956    o pkg/mdsio:
957      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
958        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
959        too long (e.g., > MAX_LEN_FNAM/2 )
960    
961    checkpoint65b (2014/08/12)
962    o pkg/matrix:
963      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
964    o model/src:
965      - fix initialisation of geothermalFile; compile geothermal-flux code in
966        natl_box verification experiment.
967    o model/src & pkg/down_slope:
968      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
969      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
970        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
971        results at machine truncation level: update output of experiments
972        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
973    o pkg/diagnostics (Stats-Diags):
974      - do not cumulate the full volume when DIAGNOSTICS_FILL is
975        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
976        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
977        times (but Min,Max and StD are still wrong).
978    o model/src:
979      - add geothermal flux forcing: read in ini_forcing.F as time-constant
980        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
981    o model/src:
982      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
983        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
984        arrays are already updated while adjustments (filters, conv.adjustment) are
985        still applied later, in S/R TRACERS_CORRECTION_STEP.
986    o model/src:
987      - store in common bloc array "rhoInSitu" the virtual potential temperature
988        anomaly that is used to compute geopotential: this make the atmos code
989        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
990    o pkg/seaice/seaice_lsr.F
991      - rename integer variable ilcall to ipass (that's what it is called
992        in the residual diagnostics
993      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
994        default) for improved non-linear convergence of the first few steps
995      - adjust a few comments and add new ones to explain some of the store
996        directives
997    o pkg/generic_advdiff (& ptracers):
998      - re-work the code to check for valid advection scheme and for minimum
999        size of overlap (now stored in local common bloc in gad_advscheme.F)
1000    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1001      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1002      - add an auxilliary variable "bet" and fix store directives and keys in
1003        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1004        less exact gradients in my tests); but there are still
1005        recomputation warning (although gradients are sort of OK), when
1006        SEAICE_LSR_VECTORIZE is not defined, so this flag and
1007        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1008      - update verification experiments lab_sea.
1009      - change some comments in S/R seaice_calc_viscosities
1010    o model/src:
1011      - if staggerTimeStep=T, always apply exchange to velocity field in
1012        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1013        (independent of using multi-dim advection or not); no effect on FWD run
1014        but affects AD results (at machine truncation level): update output of
1015        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1016        and isomip (oad: 12.d).
1017    o pkg/generic_advdiff:
1018      - stop if doAB_onGtGs is set to FALSE but ignored
1019      - refine warning related to stability of tracer time-stepping
1020        regarding internal wave dynamics.
1021      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1022        on staggerTimeStep & implicitIntGravWave (will now get a warning
1023        if potentially unstable).
1024    o pkg/kl10:
1025      - add new pkg "kl10" for mixing due to internal wave breaking, from
1026        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1027        (contribution from Jody Klymak), tested in verification experiment
1028        verification/internal_wave/input.kl10/
1029    o isomip experiment:
1030      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1031        (input.htd) and update the output.
1032    o cd_code experiments:
1033      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1034        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1035        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1036        update the corresponding output.
1037    o pkg/seaice:
1038      - reduce the number of include files and store directives in
1039        S/R seaice_lsr_tridiagu/v
1040      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1041        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1042        get rid off one store directive (a TAF bug?)
1043      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1044        S/R seaice_lsr_tridiagv to change the loop range for consistency
1045      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1046      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1047        S/R seaice_lsr_tridiagu/v (requires update of
1048        offline_exf_seaice/input.dyn_jfnk)
1049    
1050    checkpoint65a (2014/07/27)
1051    o model/src:
1052      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1053        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1054        (topo in p-coords, ice-shelf in z-coords); update output of experiments
1055        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1056    o model/src:
1057      - collect momentum forcing tendency into local 2-D array (passed as argument
1058        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1059        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1060        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1061      - collect T & S forcing tendency into local 2-D array (passed as argument to
1062        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1063        affects results at machine truncation level (e.g., ocean: if using
1064        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1065        correction due to vertical advection).
1066      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1067        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1068        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1069        obcs_ctrl (ad & fwd grd @ 12 & 7).
1070    o pkg/ptracers & diagnostics:
1071      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1072        title (to avoid some unexpected truncation); sort out ptracers diags units.
1073      - collect ptracer forcing tendency into local 2-D array (passed as argument
1074        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1075    
1076    checkpoint65 (2014/07/18)
1077    o pkg/fizhi:
1078      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1079        affects results at machine truncation level. Update output of experiments
1080        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1081    o pkg/seaice: more clean up
1082      - rename TAF common block tapes to be more consistent and remove
1083        unnecessary duplicates
1084      - add store directives to remove more recomputations, but use smaller
1085        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1086        The idea behind this flag is to reduce the memory footprint when the
1087        adjoint of the LSR is not required. As of now, defining the flag
1088        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1089        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1090        For experiment offline_exf_seaice, this means on a linux box with gfortran
1091        nearly a factor of 10 (but keep in mind there is mostly seaice code in
1092        this experiment):
1093        > size mitgcmuv_ad
1094        text    data        bss     dec        hex
1095        5100659 1216  220458952  225560827  d71c8fb
1096        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1097        but only a moderate increase of 36% for global_ocean.cs32x15:
1098        text    data        bss     dec        hex
1099        6695027 1648 1014578664 1021275339 3cdf6ccb
1100        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1101      - note: there are still recomputations in global_ocean.cs32x15 and
1102        offline_exf_seaice and the gradient agreement changes (gets a
1103        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1104      - in general, the AD gradients still are wrong
1105    o OpenAD
1106      - clean up code_oad/ directories somewhat by moving files
1107        dontCompile, dontTransform, keepOriginal to OAD_support/
1108    o model/src:
1109      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1110        (not currently tested): add dissipation terms before NLFS rescaling of
1111        tendencies (previously done after).
1112    o pkg/diagnostics:
1113      - write stats-diags in ascii file with more digits (same as in monitor).
1114    o pkg/down_slope:
1115      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1116        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1117    o model/src:
1118      - new file "apply_forcing.F" containing all the code previously in
1119        external_forcing.F, but with new argument list: pass, as new argument,
1120        the current level tendency array to update (instead of a direct update
1121        of the common bloc array). Change the corresponding calls.
1122      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1123        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1124    o pkg/seaice/seaice_lsr, a little bit of clean up
1125      - rearrange some code blocks, so that now all calculations for
1126        setting up the right-hand-sides done within one single block
1127        (I find that easier to read and understand)
1128      - rearrange freedrift-code to reduce the number of ifdefs
1129      - adjust some indentations and comments
1130    
1131    checkpoint64z (2014/07/10)
1132    o model/src and several pkgs:
1133      - change argument list of all S/R called from external_forcing.F and
1134        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1135        to pass, as argument, the current level tendency array to update
1136        (instead of a direct update of the common bloc array).
1137      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1138      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1139    o pkg/seaice/seaice_lsr.F
1140      - always initialize local arrays in seaice_lsr_tridiagu/v
1141      - add more local tapes to seaice_lsr_tridiagu/v
1142      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1143        keep it in bi/bj loop; this seems to be essential
1144      - gradients are still wrong but only by 4-7 orders of magnitude
1145        instead of 15 orders of magnitude, lab_sea improves a little
1146    o pkg/seaice
1147      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1148        generates unnecessary code in seaice_lsr_ad
1149      - add more store directives in seaice_lsr to avoid unnecessary code
1150        in seaice_lsr_ad
1151      - exclude some residual computations in seaice_lsr when
1152        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1153        in seaice_lsr_ad
1154      - add more storing, a new tape (model/src/the_main_loop.F) and
1155        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1156        and klockey should be checked by a specialist)
1157      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1158        and update lab_sea after previous changes in pkg/seaice below
1159    o pkg/autodiff:
1160      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1161        viscFacInAd : run time parameters allowing for adjoint switches
1162        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1163    o pkg/ecco:
1164      - introduce cost_gencost_boxmean.F that computes a box mean
1165        temperature (for use in adjoint sensitivity studies).
1166    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1167    o pkg/mom_common/mom_calc_visc.F:
1168      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1169    o pkg/seaice/seaice_summary.F:
1170      - statement for SEAICEadjMODE now in autodiff_readparms.F
1171    o pkg/seaice:
1172      - remove some store directives and add new ones in an effort to get
1173        finally rid off the recomputation warnings. This is successful
1174        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1175        defined (i.e. no extensive recomputation warnings left), but there
1176        are still too many recomputations on the solver iteration level
1177      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1178      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1179        SEAICE_SIZE.h
1180      - add a store directive in S/R seaice_calc_viscosities
1181    o pkg/seaice (ITD code):
1182      - fix definition of Hlimit for multi-threaded case
1183      - use double precision arithmetic to compute Hlimit: this affects results;
1184        update output of experiment seaice_itd.
1185    o replace content of verification/seaice_itd
1186      - instead of a 1D column use the configuration of offline_exf_seaice
1187        to test the ice thickness distribution code with ridging
1188      - this is a first shot at this experiment
1189      - change of some defaults of ridging parameters SEAICEhStar (from
1190        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1191        and lot of new comments.
1192    
1193    checkpoint64y (2014/06/20)
1194    o pkg/seaice/seaice_reg_ridge.F:
1195      - modify the regularization of very small volumes of ice; only check
1196        total volume HEFF, and do not apply correction to individual ice
1197        classes because that leads to funny patterns in the heat and fw-fluxes
1198        into the ocean. Adjust seaice_itd/results/output.txt
1199      - replace nITD by SEAICE_multDim in loop-ranges
1200    o pkg/exf:
1201      - add code to process the case field period = -12. with UV interpolation.
1202      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1203        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1204    o verification/global_with_exf:
1205      - switch all fields period to -12. (was previously untested) in input/data.exf
1206        (but keep secondary test ".yearly" unchanged); update the reference output.
1207    o pkg/cal:
1208      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1209    o pkg/exf:
1210      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1211        to replace logical switch "exf_verbose"
1212      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1213    o pkg/sbo:
1214      - update from Katherine Quinn: evaluate mass directly from density and SSH
1215        (budget using Finite Volume method) instead of from bottom pressure.
1216      - allow testreport to collect few selected SBO output ; tested in exp.
1217        global_ocean.90x40x15 (after updating the results, to include SBO output).
1218      - fix some multi-threading issues (in output part).
1219    o model/src & most packages:
1220      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1221      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1222        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1223        "data.{pkg}" exist ; and leave the S/R (return) just after.
1224      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1225        + call LAND_READPARMS from packages_readparms.F
1226    o pkg/seaice:
1227      - remove code that resets useThSice in S/R seaice_readparms and
1228        replace it by a warning in S/R seaice_check
1229      - remove parameter MULTDIM, replace with nITD and runtime
1230        parameter SEAICE_multDim (still hard-wired to nITD if
1231        SEAICE_ITD is defined)
1232    
1233    checkpoint64x (2014/05/24)
1234    o verification/lab_sea:
1235      - update adjoint and TLM output following changes to pkg/salt_plume
1236      - un-do the update after putting back local recip_Cp in few places.
1237    o pkg/salt_plume: modifications by An Nguyen:
1238      - add capability to do brine rejection (salt-plume) as function of
1239        volume+tracers (instead of only salinity tracer).
1240      - conserve volume by exchanging volume from each kLev to above to
1241        accommodate in-coming brine volume
1242      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1243      - switch KPP surf buoyancy due to brine forcing to 3-d
1244        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1245      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1246      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1247        in East/West Arctic.
1248    o pkg/sbo:
1249      - incorporate modifications from Katherine Quinn to enable the use of sbo
1250        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1251        output for future testreport verification (unfinished).
1252    o pkg/atm_phys:
1253      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1254        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1255        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1256    o pkg/seaice
1257      seaice_calc_ice_strength.F: modify expression to avoid divisions
1258        (affects truncation)
1259      seaice_do_ridging.F: clean up the insectarium
1260      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1261      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1262      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1263      - add some debugging information and error messages (warnings)
1264    o model/src: modifications relatd to atmosphere p*:
1265      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1266      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1267        of vertical profile tRef in geopotential background and anomaly.
1268      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1269        and pkg/atm_phys.
1270      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1271        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1272    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1273    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1274        not used right now, but can be used in BGC packages to fix conservation.
1275    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1276        other packages too.
1277    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1278        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1279    o model/src:
1280      - since we have several heat capacity (even in model/src), define "recip_Cp"
1281        as local variable (no longer in common block) to avoid any confusion.
1282      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1283    o pkg/exf:
1284      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1285        air density as function of air Temp, Humidity and atm pressure.
1286    
1287    checkpoint64w (2014/05/02)
1288    o verification:
1289      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1290        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1291        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1292        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1293        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1294    o model/src: for atmosphere in p* coords:
1295      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1296      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1297        but not yet activated.
1298    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1299      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1300      - this changes the results (but not for any verification experiment, because
1301        none tests this), but avoids having an extra field in the restart files
1302    o pkg/seaice: remove global variable TICE (not needed)
1303      - replace by TICES or local variable where necessary (cost_seaice_test,
1304        seaice_diagnostics_state)
1305      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1306      - use specific read/write routines for reading and writing individual leves
1307        of a multilevel field
1308    o pkg/ctrl & model/inc:
1309      - move additional anomaly fields of control vars (related to options:
1310         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1311        from DYNVARS.h into new header file: CTRL_FIELDS.h
1312    o pkg/seaice: some small modifications to the ridging code
1313      - make fw2ObyRidge a global variable and add the freshwater flux to
1314        seaice_growth
1315      - pass actual thickness from seaice_prepare_ridging, so that it is
1316        computed only in one place and compute it in the same way as in
1317        seaice_growth
1318      - initialise more fields in seaice_do_ridging that where cause floating
1319        point exceptions over land
1320  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1321    - move most of "PART 1" of S/R seaice_growth into a new and separate    - move most of "PART 1" of S/R seaice_growth into a new and separate
1322      S/R seaice_reg_ridge that will both regularize the state variable after      S/R seaice_reg_ridge that will both regularize the state variable after
1323      advection call the actual ridging routine;      advection call the actual ridging routine;
1324    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1325      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1326    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1327    - clean up remaining part 1 of seaice_growth in an attempt to make it    - clean up remaining part 1 of seaice_growth in an attempt to make it
1328      more readable (this is probably subjective)      more readable (this is probably subjective)
1329    - call seaice_itd_redist once in the initialisation phase to have the initial    - call seaice_itd_redist once in the initialisation phase to have the initial
1330      conditions in the correct category      conditions in the correct category
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