/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1980 by mlosch, Wed Apr 23 12:42:19 2014 UTC revision 1.2223 by jmc, Wed Jan 13 14:53:48 2016 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65s (2016/01/13)
8    o eesupp & genmake2:
9       - first check for Function ETIME and, if it fails, then check for subroutine
10         ETIME and consistent output; use the appropriate version in timers.F
11    o model/src:
12      - to check restart test, add option to apply EXCH to U,V earlier, just before
13        integr_continuity; turned off by default.
14    o pkg/dic:
15      - remove CPP option USE_ATMOSCO2 (not needed)
16    o tools/tst_2+2:
17      - try to ignore difference between +0 and -0 in binary file, causing test
18        to fail for no good reason.
19    o eesupp & genmake2:
20      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
21        but also check (in genmake2) that test runs and returns meaningful results.
22    o coupler pkgs:
23      Finish implementation of optionally-exchanged variable switches (started on
24       Nov 12) with addition of few more exchanged fields, including 2-way exchange
25       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
26       advection in OCN component; this requires sequential coupling.
27      coupler (pkg/atm_ocn_coupler):
28      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
29        routines (useful for debug).
30      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
31         flux, DIC fields) if corresponding switch is ON.
32      - add option to export RunOff to OCN (to use for DIC river input)
33      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
34      components (pkg/atm_ & ocn_compon_interf):
35      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
36        optionally exchanged fields; add a check & stop in cpl_readparms.F.
37        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
38        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
39      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
40        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
41      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
42      - hold in common block coupler optionally-exchanged variable switch
43        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
44      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
45        this is intended to replace the OCN cplFldtave.* output files (not updated
46        to contain new additional exchanged fields).
47    o pkg/dic:
48      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
49    o pkg/thsice:
50      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
51        and writing of thsice pickup files.
52    o pkg/atm_compon_interf:
53      - move all field individual export-call out of cpl_export_import_data.F
54        into new S/R ATM_EXPORT_FIELDS
55    o pkg/atm_compon_interf:
56      - store state variables (for now, only thSIce fields) just before beeing
57        exported (in cpl_export_import_data.F, like on ocean side) instead of from
58        atm_store_my_data.F like all exported fluxes.
59      - new version of pickup_cpl: write field names into meta file and read meta
60        file to find field postion in pickup. Also only write/read fields meeded for
61        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
62    o pkg/dic:
63      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
64    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
65        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
66        value can be from domain [0,1] to average between the two methods
67    o pkg/atm_phys:
68      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
69        hold fixed in time).
70    
71    checkpoint65r (2015/12/21)
72    o pkg/seaice:
73        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
74        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
75    o pkg/seaice:
76      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
77        when SEAICEscaleSurfStress=.TRUE.,
78      - apply areaW and areaS in S/R seaice_calc_lhs
79    o pkg/atm_phys:
80      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
81        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
82        for individual contribution (convection, LSC cond, radiation)
83      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
84        information); activated with: solar_exponent=0. and wv_exponent=-1.
85    o pkg/ggl90:
86      - within IDEMIX add upper limit for horizontal group velocity to
87        avoid instability problems in the explicit horizontal diffusion term for
88        long time steps or high resolution
89    o pkg/diagnostics:
90      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
91        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
92    o testreport:
93      - remove "-v" (verbose option) in default mpirun command.
94    o pkg/seaice/seaice_growth:
95      - catch potential division by zero in ITD code, does not change
96        verification results
97    o pkg/ecco:
98      - retire old codes to the Attic. The calls to retired functions are
99        left in a commented form in case they ever need to be re-activated.
100      - ecco_check.F: issue warning if any old CPP option is
101        defined that corresponds to retired codes -- then stop.
102    o pkg/atm_compon_interf:
103      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
104        coupler: use last time-step value instead of average over cplSendFrq_iter
105        time-step, similar to what is done for seaIceMass.
106        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
107    o eesupp & genmake2:
108      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
109        <= remove until a fix is found for some ifort version on ia32 machine.
110    o pkg/seaice/seaice_evp:
111      - refine residual computation
112    
113    checkpoint65q (2015/11/18)
114    o pkg/seaice/seaice_evp:
115      - fix residual computations so that they no longer affect the actual
116        simulation code
117      - fix seaice_readparams to be able to actually set new parameters
118        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
119    o model/src:
120      - fix wrong truncation (single prec) from "FLOAT" function in expressions
121        like: deltaT*FLOAT(myIter) when myIter is large:
122         a) replaced by DFLOAT (if not seen by TAF);
123         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
124    o pkg/aim_v23:
125      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
126        when pickupSuff is set ; do write rolling pickups + at the end of the run.
127    o pkg/atm_ocn_coupler + ocn_compon_interf:
128      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
129        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
130        add corresponding call in DO_OCEANIC_PHYS.
131    o coupler pkgs:
132      Start a new way to set-up optionally-exchanged variables (previously, only
133       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
134       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
135       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
136       compononent param default can be set accordingly).
137      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
138       but rather applies to a group a fields (going both ways like for DIC)
139       and corresponds to an option of coupling config.
140      coupler (pkg/atm_ocn_coupler):
141      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
142        and read namelist directly (without eessup S/R calls) instead of
143        in the very un-flexible old way, 1 param per line, in fixed order;
144      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
145        cleanly in CPL_CHECK_CPLCONFIG
146      - add new coupling-exchange selectors (some not yet active) including
147        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
148                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
149      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
150        component ; called directly from coupler.F, after comp. registrations;
151      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
152         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
153          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
154      components (pkg/atm_ & ocn_compon_interf):
155      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
156        CPP header file in all pkg source files.
157      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
158        ATM/OCN_CHECK_CPLCONFIG;
159      - add error-counter to track errors (e.g., in "data.cpl") and to stop
160        cleanly in ATM/OCN_CHECK_CPLCONFIG;
161      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
162        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
163        before PACKAGES_READPARMS;
164      verification/cpl_aim+ocn/:
165      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
166        "data.cpl" for coupler (in input_cpl).
167    o eesupp/inc:
168      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
169        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
170        to always cumulate tile local-sum in the same order (still uses
171        MPI_Allreduce like standard code).
172      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
173        that are now identical to standard version (in eesupp/inc).
174    o pkg/shelfice:
175      - add SHELFICETransCoeffTFile for initializing spatially varying
176        heat and salt transfer coefficients
177    o pkg/atm_compon_interf & ocn_compon_interf:
178      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
179        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
180      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
181    o pkg/atm_ocn_coupler:
182      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
183    o pkg/rbcs:
184      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
185        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
186      - add a short report (to STDOUT) about RBCS-mask settings.
187    
188    checkpoint65p (2015/10/23)
189    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
190        there is no adjoint test for EVP, we don't know what it does to the adjoint
191        solution, but at least there are no more recomputation warnings left
192    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
193        a chance of giving the same results as a fully converged VP (JFNK) solver
194    o tools/adjoint_options/adjoint_diva:
195      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
196    o pkg/streamice:
197      - spotted bug in streamice_driving_stress using dyG where should have been dxG
198    o pkg/exf:
199      - remove STOP statement that prevented to use wind or (wind-)stress
200        interpolation for constant-in-time forcing fields (wind/stress period = 0).
201    o pkg/seaice:
202      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
203        5 additionals 2D fields and 6 new store directives
204      - change logic in seaice_readparms.F: EVP code can now be turned on in
205        various ways, setting SEAICE_deltaTev is no longer required,
206        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
207        or SEAICEaEVPcoeff
208    o pkg/shelfice/shelfice_thermodynamics.F
209      - redefining uLoc/vLoc to u/v, instead of 2u/v
210    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
211      - this is an intermediate state of a truely converging EVP that has
212        the potential of outperforming implicit VP methods, I do not recommend
213        using it yet.
214      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
215        and all parameters are hardwired
216      - for convergence it still requires very smooth regularisations, that means,
217        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
218        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
219        specific averaging appears to be required, still subject to tuning
220      - still needs cleaning and I need to turn parameter into runtime parameters
221      - add code to compute and print residuals of iteration, compile with
222        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
223    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
224      that entered with r1.54 on Sep04, 2015, -> update results
225    
226    checkpoint65o (2015/09/14)
227    o pkg/mom_vecinv & mom_common:
228      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
229        called from there.
230      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
231        allows to use Vector-Invariant form in deep atmos and anelastic formulation
232    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
233      and Koenig-Beatty+Holland (2012)
234      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
235      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
236      - requires an extra input argument for S/R seaice_calc_viscosities
237      - tensileStrength's depth dependence is different from Itkin et al. (2015)
238        (to be changed and played with, for now exponential)
239    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
240      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
241        by AREA according to Connelly et al. (2004), JPO.
242      - For EVP and the LSR solver, the implicit part of the drag term is
243        the only non-zero term in the denominator when there is no ice (which
244        prevented running the model with zero ice-ocean drag). If
245        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
246        (or zero main diagonals BU/BV) which need to be caught. A practical
247        consequence is that for open water, the momentum equation reduce
248        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
249        they happen to be zero, often leading to a non-zero solution over
250        open water.
251    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
252        efficient EVP method.
253      - introduce area-weighted averages for e12 (analogously to
254        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
255        remain, but also changing the order of terms in the previous average
256        changed the results as much) -> update experiment
257      - add SEAICE_DELTA_SMOOTHREG code
258      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
259        TEM-code
260      - adjust loop bounds so that only required fields are computed
261      - add new averaging code for zetaZ/deltaZ (again similar to
262        seaice_calc_viscosities.F), inactive by default for now (will change
263        results again), but will replace old code eventually
264    o eesupp/src:
265      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
266        to always cumulate tile local-sum in the same order
267        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
268        Still uses MPI_Allreduce (like standard code) but on array of tiles
269        and should be faster than GLOBAL_SUM_SEND_RECV code.
270      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
271        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
272      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
273         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
274         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
275         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
276         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
277    
278    checkpoint65n (2015/07/29)
279    o pkg/thsice:
280      - add a warning when used with pkg/aim but without updating SST
281        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
282    o pkg/offline:
283      - change where Offline-Fields are loaded, from load_fields_driver.F to
284        directly within FORWARD_STEP, just after updating iter number and time;
285      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
286        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
287       These changes allow:
288        a) to recover exactly on-line results using deltaToffline=deltaTClock,
289        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
290        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
291        time-step, both with GM & KPP files and with recomputing these fields;
292        b) no needs to switch on staggerTimeStep anymore;
293        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
294      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
295    o pkg/offline:
296      - change (rarely used) offset-iteration parameter to an offset time (in s):
297        can easily recover previous offset-iter effect by setting offset-time
298        (offlineTimeOffset) to offset-iter x deltaToffline;
299      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
300        in KPP as part of surface buoyancy forcing) in offline run.
301      - fix ptracers KPP non-local term in the case where KPP is re-computed.
302    o OpenAD
303      - Adding preliminary ggl90 test to OpenAD verification.
304        Config. with ggl90 currently diverges after 64 time steps
305        so will need more work to become more stable
306      - Adding preliminary kpp test to OpenAD verification.
307        required small tweakes in kpp_routines.F
308      - Merge and update from Krishna Narayanan's contrib area:
309        * Add one variable for preliminary OpenAD DIVA
310        * Add replacement time-stepping for OpenAD DIVA
311        * genmake2 flag -diva (but only for OpenAD; preliminary)
312        * required modifs for OAD_support
313        successful preliminary test for tutorial_global_oce_biogeo/
314    o pkg/seaice:
315      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
316      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
317        delta with a smooth function in s/r seaice_calc_viscosity
318        (no effect on EVP)
319      - rename local suffix "sqr" into "sq" for more consistent variable names
320    o pkg/seaice:
321        add new parameter SEAICE_deltaMin that is used ***only***
322        for regularizing Delta (and nothing else, like the parameter
323        which is also used for all sorts of things SEAICE_EPS).
324        Defaults to SEAICE_EPS for backward compatibility only.
325    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
326        the wrong key by inialising it before use -> fixes a recomputation
327        problem but does not fix the gradient
328    o pkg/layers:
329      - move resetting of flux arrays to outside the iLa loop
330        (this caused layers_diapycnal to not work with more than one layer coord.)
331      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
332    o pkg/layers:
333      - remove from common block 3D layers fields (used to diagnose transport
334        in tracer coords) and declare them as local arrays in layers_calc.F
335    o pkg/seaice:
336      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
337        in lab_sea forward experiment (changes results -> updated)
338      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
339    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
340       computations; for SEAICE_VECTORIZE_LSR
341      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
342        sweep to the outside,
343      - remove store directives and add "CADJ loop sequential" directives
344        in analogy to model/src/solve_tridiagonal.F
345      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
346        boundaries to yield more readable code. This has also the charming side
347        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
348        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
349        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
350        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
351        an additional option)
352       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
353       but the adjoint gradients (which are affected by this change) still explode.
354    o coupler (atm & ocn _compon_interf):
355      - avoid using Exch2 IO mapping if not suitable.
356    
357    checkpoint65m (2015/06/15)
358    o pkg/layers:
359      - clean-up old parameters setting (from Sep 2012):
360        + remove old parameters setting from common block (declared locally);
361        + stop if any old parameter is mixed with new parameters;
362        + check for valid or consistent parameter setting (e.g., layers_name)
363      - check that layers_bounds for Pot.Density are in the right range;
364        this is supposed to catch un-updated setting after recently shifting
365        potential density field "prho" by -1000 (now in "sigma" scale).
366    o pkg/layers:
367      - Added missing call to layers_fill for keeping track of tottend in
368        pkg/diagnostics/diagnostics_fill_state.F
369    o pkg/layers:
370      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
371        of diapycnal fluxes
372    o pkg/layers:
373      - reverted changes to interpolation to previous treatment; there
374        was never actually a problem
375    o pkg/layers:
376      - fix interpolation of layers tracers in the presence of partial cells
377      - add lots of new functionality to compute water mass transformation
378        (enabled by CPP flag LAYERS_THERMODYNAMICS)
379      - add new calls from main code (diags_oceanic_surf_flux.F,
380        thermodynamics.F, impldiff.F) and gad to save the necessary fields
381        for layers_thermodynamics calculations
382    o pkg/ptracers:
383      - add capability of stepping a passive tracer forward without advection
384        by setting PTRACERS_advScheme to 0.
385    o pkg/diagnostics:
386      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
387    o pkg/layers:
388      - shift potential density field "prho" by -1000 for density layer averaging so
389        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
390        Note that density bin boundaries (layers_bounds in data.layers) have
391        to be set accordingly (i.e., shifted, in sigma scale).
392    o pkg/layers:
393      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
394      - fix calculation of layer non-weighted velocity and layer probability
395      - add diagnostics for pot.density used for layer averaging
396    o pkg/seaice:
397      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
398        positiveness, modify a few comments and improve variable names,
399      - the changed computation of deltaC affects most seaice-related
400        experiments at the truncation level.
401        seaice_itd.thermo is affected by far the most, with
402        only 7 digits of agreement remaining; update experiments.
403    
404    checkpoint65l (2015/05/04)
405    o pkg/shelfice:
406      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
407        factor drKp1 to zero where it is negative (ie. do not use
408        SHELFICEBoundaryLayer if hFacC>1)
409      - the same for factor drLoc in shelfice_forcing.F
410    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
411        with modules in ptracers, when using testreport option "-small_f"
412    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
413      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
414    o verification/testreport
415      - add new option -small_f
416        with this option testreport first makes the target small_f (*.f files)
417        before running make (all). This is useful for explicit inlining when
418        all sources need to be full available.
419    o pkg/exf/exf_interp.F:
420        remove previous changes related to reverse (decreasing) input grids latitude
421    
422    checkpoint65k (2015/04/01)
423    o pkg/ecco:
424        fix missing cosphi initialization; use eccoiter in place of optimcycle;
425        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
426        instead of active read/write
427    o pkg/ctrl:
428        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
429        instead of active read/write.
430    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
431        return if .NOT.useAUTODIFF
432    o pkg/seaice: add CPP brackets (cost function related).
433    o model/src:
434        add useAUTODIFF run time switch.
435    o pkg/exf/exf_interp.F:
436        add code to allow input grids with latitude starting in the north (i.e. when
437        j=1 corresponds to northern edge of field); modify global_with_exf to test
438        this feature.
439    o verification/testreport:
440      - replace "grep -A3" with POSIX conformal sed command, because there are
441        implementations of grep that cannot do contextual searches
442      - replace "cat -n" by "nl" (two occurrences), because not all implementations
443        of "cat" have the option "-n"
444    o model/src:
445        add new file gsw_teos10.F that contains 3 functions, more or less a copy
446        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
447        convert from conservative to potential temperature. For now they are not
448        called anywhere.
449    o pkg/ggl90: make "useIDEMIX" useful
450      - re-organize code in s/r ggl90_calc a little to move computations that
451        are different for idemix into separate loops (changes verification
452        experiment idemix at truncation level, 12 digits remain -> updated)
453      - requires 2 new 2D fields KappaM, verticalShear
454      - make hFacI and recip_hFacI local 3D variables that are passed to
455        s/r ggl90_idemix
456      - fix and improve some comments
457    
458    checkpoint65j (2015/02/25)
459    o pkg/openad
460      - synchronize seawater.F with version in model/src: replace routine
461        body of sw_temp by calling sw_ptmp and fix/add a few comments.
462    o pkg/mnc:
463      - change default value of pickup_read/write_mnc params to FALSE
464        (since few features are missing in reading MNC pickup files).
465    o model/src:
466      - change default (background) vertical diffusivity for salt to be the
467        temperature (background) vertical diffusivity.
468      - change background vertical diffusivity in vertical mixing pkgs ggl90,
469        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
470        This makes ptracers default diffusivity (that uses salt diffKr) more
471        consistent with vertical mixing schemes.
472    o verification/testreport:
473      - fix typo in "-pcls" option ;
474      - put temp files in /tmp (instead of in local dir)
475      - add option "-ncad" to use genmake2 new option "-nocat4ad"
476      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
477    o pkg/ggl90 (idemix code):
478      - apply few fixes ; add some missing "_d 0" ; update output of exp.
479        global_ocean.90x40x15.idemix
480    o OpenAD
481      - enable active file I/O and begin removal of work-around code
482        for OpenAD for handling control variables (memory vs. active files)
483      - new CPP options file OPENAD_OPTIONS.h
484      - revert to genarr2d gradient check for hs94.1x64x5
485      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
486      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
487    o tools/genmake2:
488      - add option for an alternative Makefile (from Martin) where multiple
489        source files are sent to TAF (instead of all in one file).
490    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
491      - code provided by Carsten Eden as an extension of ggl90
492      - so far the code is turned on within ggl90 by setting a CPP-flag at
493        compile time; a runtime flag implementation is not yet complete
494      - tested in new verification experiment global_ocean.90x40x15.idemix
495    o verification:
496      - reduce length of the AD test run by half for experiments
497        global_ocean.cs32x15 (std + thsice) and isomip
498      - enable active file I/O for OpenAD, adjust verifications accordingly
499      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
500    o verification/testreport:
501      - fix two non-POSIX sed statements so that there are no error messages
502        on Mac OS X
503      - replace hostname -s with hostname | sed 's/\..*$//'
504    o model/src/seawater.F:
505      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
506        (following the matlab code), which would have avoided the bug caught
507        by Matt (see below) in the first place
508    o pkg/shelfice:
509      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
510        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
511      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
512        ice-shelf case (i.e., within surface level).
513      - add config summary in shelfice_check.F
514      - remove global variable recip_SHELFICElatentHeat and replace by a local
515        variable recip_latentHeat
516      - introduce diagnostics for friction velocity uStar (in case of
517        SHELFICEuseGammaFrict)
518      - change verification experiment isomip.htd:
519        + start from pickup (as input_ad at nIter0=8640)
520        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
521        + test SHELFICEuseGammaFrict = .TRUE.
522        + test SHELFICEadvDiffHeatFlux = .TRUE.
523    o model/src:
524      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
525        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
526        update output of experiments global_with_exf.yearly and isomip (all 6).
527    o pkg/shelfice:
528      - change setting of kTopC to also be zero where there is no ice-shelf.
529      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
530        ice-shelf is.
531      - first attempt to get RealFreshWaterFlux effects: for now, only without
532        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
533    o pkg/seaice: add the option to prescribe a fixed thickness PDF
534      for thermodynamic calculations
535      - because of divisions of the type 7/7 not exactly equal to 1, this change
536        affects results of some verification experiments by up to 4 digits:
537        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
538        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
539        adjoint: lab_sea, lab_sea.noseaicedyn
540        -> updated
541    
542    checkpoint65i (2015/01/23)
543    o model/src:
544      - change units of frictionHeating field from W to W/m^2
545      - fix bug in frictional heating from stratospheric drag in
546        S/R ATM_PHYS_TENDENCY_APPLY_V
547      - with synchronous time-stepping: move resetting to zero of frictionHeating
548        field from load_fields_driver.F to thermodynamics.F ;
549      - add diagnostics for frictional heating.
550    o model/src & gmredi K3D:
551      - add frictionHeating field to pickup-files (for synchronous time-stepping)
552      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
553      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
554        and name in pickup file).
555      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
556    o model/src:
557      - move (from ini_forcing.F) initialisation of all arrays in header file
558        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
559        (since Nov 2012) with option selectAddFluid=1.
560    o pkg/shelfice:
561      - change units (+ document) of newly added field "shelfIceMassDynTendency"
562      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
563    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
564    o pkg/seaice: two new runtime parameters:
565      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
566        long overdue
567      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
568        parameterization of tensil stress for fast ice (does not do anything yet)
569    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
570        for LSR: move checking overlaps out of JFNK-if-block
571    o pkg/atm_phys:
572      - move copy of grid and dynamical fields out of atm_phys_driver.F into
573        new S/R ATM_PHYS_DYN2PHYS.
574      - fix level height for Linear Free-Surf case (to be consistent with
575        fixed-in-time pressure levels).
576    o pkg/mom_common (bottomdrag):
577      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
578        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
579        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
580    o pkg/shelfice (u/v_drag):
581      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
582      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
583        (now similar to shelfice_u_drag.F)
584      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
585        from mom_vecinv.F (similar to mom_fluxform calls).
586    o pkg/mom_common (bottomdrag):
587      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
588      - add options for alternative discretisation of velocity norm in quadratic
589        bottom drag: averaging of grid-cell-center KE to U.point and V.point
590        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
591        improves when averaging only the other component (e.g. vVel for U bottom
592        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
593      - add options (bottomVisc_pCell) to account for partial-cell in bottom
594        friction (no-slip BC) thus getting the true distance from the bottom;
595        off by default since this also reduces model stability (explicit bottom
596        friction). Changes produce different machine truncation with linear-drag
597        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
598        front_relax (bvp & mxl, 10 & 11 digits).
599    o model/src & mom pkgs:
600      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
601        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
602      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
603        just copy level Nr value to level Nr+1.
604    o doc:
605      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
606    o pkg/streamice:
607      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
608        SHELFICE.h: move array shelficemass to init_varia, initialise
609        from array shelficemassinit, which is set in init_fixed and
610        has option to be set from file; introduce array
611        shelficeMassDynTend array, set thru file in init_fixed
612      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
613        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
614        pkg/streamice
615      - shelfice_thermodynamics.F: call shelfice_step_icemass if
616        SHELFICEMassStepping = .true.
617      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
618    
619    checkpoint65h (2014/12/17)
620    o verification/global_ocean.90x40x15, global_ocean_ebm:
621      - update to generic controls.
622    o pkg/ctrl:
623      - ctrl_map_ini_genarr.F: test for igen>0
624      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
625      - move gentim2d part of ctrl_map_ini_genarr.F to
626        new separate routine : ctrl_map_ini_gentim2d.F
627      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
628        add time variable weights and cyclic controls (time mean,
629        seasonal cycle, etc) capabilities to gentim2d
630    o pkg/ecco:
631      - move reading of error, conversion to weights from
632        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
633    o global_oce_llc90, cs32:
634      - activte sbo.
635      - CTRL_SIZE.h : add maxCtrlProc.
636      - activate the new genctrl capabilities.
637      - update following reorganization of global_oce_input_fields.tar.gz  
638    o pkg/ctrl/ctrl_ad_diff.list:
639      - add missing ctrl_init_rec.f
640    o tools/OAD_support/keepOriginal:
641      - add ctrl_init_rec.F
642    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
643      - avoid recomputations of xx_gentim2d_dummy.
644    o momentum diagnostics:
645      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
646        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
647    o pkg/seaice/seaice_lsr.F:
648      - fix computation of BU/BV, make sure they are non-zero, only necessary
649        for cubed sphere exchanges and SEAICE_OLx/y>0.
650        This makes calling s/r fill_cs_corner_rl obsolete (removed).
651    o verification/global_ocean.cs32x15/input.seaice
652      - add test for strong implicit coupling and restricted addtive Schwarz
653        methods for LSR
654      - update results/output.seaice.txt
655    o verification/tutorial_global_oce_biogeo:
656      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
657        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
658        update output_adm,_oadm,_tlm.txt
659    o pkg/dic:
660      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
661      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
662        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
663    o verification/tutorial_global_oce_biogeo:
664      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
665        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
666        update output_adm,_oadm,_tlm.txt
667    o eesupp/src:
668      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
669        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
670    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
671      LSR (following Hutchings et al. 2004)
672      - introduce zetaZ as a global variable (requires adjustments in
673        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
674        in seaice_calc_viscosities.F
675      - new flag SEAICEuseStrImpCpl (default off)
676      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
677        momentum equations
678      - JFNK-solver (preconditioner) adjusted to allow using this method
679        (where it does not have any positive effect)
680    o pkg/seaice
681      - add overlap for restrictive additive Schwartz method also to LSR, but
682        turn it off by default (because it only seems to work for non-cubed
683        sphere/llc topologies)
684    o pkg/autodiff
685      - add extra exchanges in addummy_in_steppging also for mnc output
686    o pkg/seaice:
687      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
688        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
689    o pkg/obcs:
690      - add option to specify domain-connected piece Id along OB though files
691        (for now, only used to diagnose PhiVel; default =1 -> global correction)
692      - modify obcs_diag_balance.F to process each connected-part separately;
693        exclude OB where Id = 0 but keep the full divergence there (-> constant
694        Psi along this portion of OB and all inflow derived from grad(Phi))
695      - add example of OB-conect files in verification/so_box_biogeo/input.
696    o pkg/diagnostics:
697      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
698      a) use non zero matrix element across OB and solve for Phi 1 grid point
699         outside OB (i.e, where tracer OBCS are applied).
700      b) global imbalance of inFlow/outFlow across OB: instead of modifying
701         velocity across OB, spread it uniformly along the OB in the RHS.
702    
703    checkpoint65g (2014/11/19)
704    o pkg/diagnostcis:
705      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
706    o pkg/my82,pp81,kl10:
707      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
708        field diffKr as background diffusivity to set minimum diffusivity value.
709    o pkg/seaice:
710      - add new parameter SEAICEuseEVPrev (for revisited EVP by
711        Bouillon et al 2013)
712      - add SEAICE_evpAlpha/Beta to namelist
713      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
714        involve trivial re-ordering of divisions/multiplications that should not
715        have any effects, but ... they do change the results of lab_sea.hb87 so
716        that only 2 digits of agreement remain, in line with the general
717        instability/fragility of the evp-code. For now, I do not care and just
718        update the verification experiment
719    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
720      - remove xx_genarr2d_numsmooth etc
721      - use xx_genarr2d_preproc etc instead
722      - carry out smooth_correl2D at initialization stage rather than during
723        time stepping.
724      - get smoothOpNb from xx_gentim2d_preproc
725    o global_oce_cs32 :
726      - add test of generic ecco capabilities.
727    o pkg/exf/exf_getsurfacefluxes.F :
728      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
729    o pkg/ctrl,ecco :
730      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
731        is defined.
732    o pkg/seaice: add diagnostics for Delta (deformation parameter)
733    o model/src:
734      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
735        diffusivity (background) is specified but ignored.
736    o verification:
737      - in testreport, convert hostname to lower case for default output dir name
738    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
739    o pkg/dic: add modifications from Hajoon:
740      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
741      - light attenuation: add self-shading effect by climatological Chlorophyll
742        (read from file).
743    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
744        compiles when SEAICE_ALLOW_DYNAMICS is undefined
745    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
746        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
747        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
748        approach where CPP_OPTIONS.h includes an omnipotent
749        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
750    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
751        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
752    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
753        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
754        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
755    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
756      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
757      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
758      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
759      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
760    o pkg/ctrl,ecco,exf :
761      - remove variables associated with NON-generic costs,
762        unless ECCO_CTRL_DEPRECATED is defined.
763      - remove NON-generic NON-obcs controls,
764        unless ECCO_CTRL_DEPRECATED is defined.
765    o pkg/ctrl : added ctrl_local_params.h
766    o pkg/ecco : added ecco_local_params.h
767    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
768        experiments, which will progressively be removed once the
769        experiments are revised to use only generic controls/costs.
770    
771    checkpoint65f (2014/10/13)
772    o pkg/ctrl, ecco, seaice : minor changes in headers
773    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
774        cost function and control capabilities added since checkpoint65c.
775    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
776    o pkg/ecco: increase modularity and improve logic
777      - ecco_toolbox.F (new) : basic operations that are often used,
778        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
779        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
780      - cost_gencal.F (new) : determine filnames and records.
781      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
782      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
783        and exploit the above functions leading to more compact code.
784      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
785      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
786        using_ers, using_gfo, using_mdt is now only defined within gencost)
787    o pkg/ecco: extend generic cost capabilities
788      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
789        capabilities via gencost_preproc (+ _c,_i,_r related params),
790        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
791        gencost_outputlevel arguments to cost_generic
792      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
793        and active_read, making room for gencost_preproc to take effect.
794        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
795      - pkg/ecco/cost_generic.F :
796        compute and store misfit maks*(model-data) in localdif that is
797        then used in cost and for output, output misfit if outlev.GT.0
798      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
799        rather gencost_barfile for deciding whether to write barfile
800      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
801      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
802        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
803      - pkg/ecco/ecco_summary.F : report gencost variables
804      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
805    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
806    o pkg/ecco: internal re-organization
807      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
808        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
809        mv relevant variables definition from ecco_cost.h to ecco.h,
810        make sure gencost routines only include ecco.h)
811      - throughout : add missing CCP switches, rm unused variables,
812        and rm un-necessary CPP switches
813      - throughout gencost routines : replace modelstartdate with
814        gencost_startdate when needed
815      - cost_bp_read.F : use arguments, instead of common blocs
816        so that it can be used also by (new) cost_gencost_bpv4.F
817      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
818      - ecco_phys.F : compute etanFull
819      - ecco_readparms.F : rename using_topex as using_tpj, add
820        bpv4-grace to gencost list, initialize added parameters
821      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
822    
823    checkpoint65e (2014/09/28)
824    o pkg/obcs:
825      - replaced the just-added CPP options with run-time variables
826        (see pkg/obcs/OBCS_PARAMS.h for details)
827    o pkg/obcs:
828      - add additional CPP options for sponge boundary layers
829        (see pkg/obcs/OBCS_OPTIONS.h for details)
830    o pkg/atm_phys:
831      - implement simple (obliquity only, assuming circular planet orbit)
832        seasonal cycle for incoming insolation ; used when run-time parameter
833        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
834    o pkg/exf, pkg/ecco, pkg/ctrl:
835      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
836      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
837      - implement gentim2d for xx_tauu, xx_tauv
838    o pkg/ctrl, pkg/ecco :
839      - fix and complement the generic controls implementation
840    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
841        pkg/shelfice/shelfice_thermodynamics.F,
842        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
843        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
844      - add weight in CTRL_GET_GEN calls
845    o pkg/ctrl :
846      - ctrl_get_gen.F : add weight as input parameter, and apply
847        it directly rather than using smooth_correl2Dw (to be retired).
848      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
849    o pkg/ctrl :
850      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
851        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
852      - re-activate ctrl_summary (call in ctrl_init.F)
853    o pkg/ctrl/ctrl_cost_gen.F :
854      - fix CCP brackets, remove un-necessary myiter, mytime
855    o pkg/ecco, pkg/ctrl :
856      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
857      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
858      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
859      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
860    
861    checkpoint65d (2014/09/15)
862    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
863      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
864        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
865    o pkg/ctrl/ctrl_map_ini_genarr.F :
866      - remove compilation failure
867      - replace hard coded example
868      - use ctrl_map_ini_gen2D, 3D
869    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
870      - on/off switch based upon xx_genarr2d_weight,3d
871    o src/packages_init_variables.F :
872      - regroup pkg/estimation calls
873      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
874        (moved to ctrl_init_variables)
875    o cost/cost_init_varia.F :
876      - remove ecco_cost_init_varia
877        (moved to ecco_init_varia)
878    o ctrl/ctrl_init_variables.F :
879      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
880      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
881    o ctrl/ctrl_map_ini.F :
882      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
883        (moved to ctrl_init_variables)
884    o ctrl/ctrl_map_ini_ecco.F :
885      - remove ECCO_PHYS (mv to ecco_init_varia)
886      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
887    o ecco/ecco_ad_diff.list :
888      - add ecco_init_varia.f
889    o ecco/ecco_init_varia.F
890      - new routine
891    o pkg/streamice:
892      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
893        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
894      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
895    o pkg/generic_advdiff:
896      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
897    o pkg/exf:
898      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
899         xxg_precip capability
900      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
901    o pkg/ctrl:
902      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
903    o model/src/load_fields_driver.F :
904      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
905        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
906    o OpenAD verification experiments:
907      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
908        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
909        for now, only in pkgs used in OpenAD verification experiments.
910      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
911        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
912        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
913        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
914    o OpenAD verification tests:
915      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
916      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
917        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
918      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
919        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
920    o model/src & generic_advdiff:
921      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
922        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
923        dynamics requires valid tracer forcing only over tile interior but, for
924        some diagnostics, may need to extend it over 1 point in tile halo region.
925      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
926        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
927        setting in temp/salt/ptracer_integrate.F
928    o pkg/dic:
929      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
930        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
931        in gchem_forcing_sep.F
932    o pkg/autodiff & obcs:
933      - add storage of current OB values for U & V (was already done for T & S).
934    
935    checkpoint65c (2014/08/30)
936    o pkg/dic:
937      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
938        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
939        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
940    o verification:
941      - new experiment testing OBCS and DIC pkgs, using params & output from
942        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
943        passage: take OBCS from the last year of a 2 yrs simulation and initial
944        conditions from t=1.yr while keeping the same forcing.
945    o model/src:
946      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
947        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
948    o pkg/diagnostics (Stats-Diags):
949      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
950        a) refine region where stats are computed, excluding where arrhFac=0 ;
951        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
952        c) extend regional stats over the region edges (for U or V pt location).
953    o pkg/gchem:
954      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
955        pkg/dic is currently changing/updating ptracers values beyond the OB).
956    o verification (hs94):
957      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
958        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
959        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
960        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
961    o pkg/ptracers:
962      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
963        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
964      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
965        with AB-2 code (so that it get tested).
966    o model/src:
967      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
968        with AB-2 code (previously only available with AB-3 code).
969        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
970        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
971        there, by calling CYCLE_AB_TRACER).
972    o pkg/generic_advdiff:
973      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
974        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
975        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
976        S/R temp/salt/ptracers_integrate.F
977    o model/src & pkg/ptracers:
978      - remove common block variables gT,gS (in DYNVARS.h), except when
979         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
980      - remove common block variable gPtr.
981    o model/src & pkgs:
982      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
983         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
984         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
985         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
986      + change accordingly all calling S/R.
987      - use local temperature/salinity/ptracer tendency array (without bi,bj)
988        in S/R temp/salt/ptracers_integrate.F
989    o pkg/seaice:
990      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
991        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
992      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
993        in seaice_lsr
994      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
995        in s/r seaice_lsr_calc_coeffs
996    o pkg/mdsio:
997      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
998        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
999        too long (e.g., > MAX_LEN_FNAM/2 )
1000    
1001    checkpoint65b (2014/08/12)
1002    o pkg/matrix:
1003      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1004    o model/src:
1005      - fix initialisation of geothermalFile; compile geothermal-flux code in
1006        natl_box verification experiment.
1007    o model/src & pkg/down_slope:
1008      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1009      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1010        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1011        results at machine truncation level: update output of experiments
1012        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1013    o pkg/diagnostics (Stats-Diags):
1014      - do not cumulate the full volume when DIAGNOSTICS_FILL is
1015        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1016        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1017        times (but Min,Max and StD are still wrong).
1018    o model/src:
1019      - add geothermal flux forcing: read in ini_forcing.F as time-constant
1020        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1021    o model/src:
1022      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1023        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1024        arrays are already updated while adjustments (filters, conv.adjustment) are
1025        still applied later, in S/R TRACERS_CORRECTION_STEP.
1026    o model/src:
1027      - store in common bloc array "rhoInSitu" the virtual potential temperature
1028        anomaly that is used to compute geopotential: this make the atmos code
1029        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1030    o pkg/seaice/seaice_lsr.F
1031      - rename integer variable ilcall to ipass (that's what it is called
1032        in the residual diagnostics
1033      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1034        default) for improved non-linear convergence of the first few steps
1035      - adjust a few comments and add new ones to explain some of the store
1036        directives
1037    o pkg/generic_advdiff (& ptracers):
1038      - re-work the code to check for valid advection scheme and for minimum
1039        size of overlap (now stored in local common bloc in gad_advscheme.F)
1040    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1041      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1042      - add an auxilliary variable "bet" and fix store directives and keys in
1043        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1044        less exact gradients in my tests); but there are still
1045        recomputation warning (although gradients are sort of OK), when
1046        SEAICE_LSR_VECTORIZE is not defined, so this flag and
1047        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1048      - update verification experiments lab_sea.
1049      - change some comments in S/R seaice_calc_viscosities
1050    o model/src:
1051      - if staggerTimeStep=T, always apply exchange to velocity field in
1052        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1053        (independent of using multi-dim advection or not); no effect on FWD run
1054        but affects AD results (at machine truncation level): update output of
1055        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1056        and isomip (oad: 12.d).
1057    o pkg/generic_advdiff:
1058      - stop if doAB_onGtGs is set to FALSE but ignored
1059      - refine warning related to stability of tracer time-stepping
1060        regarding internal wave dynamics.
1061      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1062        on staggerTimeStep & implicitIntGravWave (will now get a warning
1063        if potentially unstable).
1064    o pkg/kl10:
1065      - add new pkg "kl10" for mixing due to internal wave breaking, from
1066        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1067        (contribution from Jody Klymak), tested in verification experiment
1068        verification/internal_wave/input.kl10/
1069    o isomip experiment:
1070      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1071        (input.htd) and update the output.
1072    o cd_code experiments:
1073      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1074        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1075        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1076        update the corresponding output.
1077    o pkg/seaice:
1078      - reduce the number of include files and store directives in
1079        S/R seaice_lsr_tridiagu/v
1080      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1081        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1082        get rid off one store directive (a TAF bug?)
1083      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1084        S/R seaice_lsr_tridiagv to change the loop range for consistency
1085      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1086      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1087        S/R seaice_lsr_tridiagu/v (requires update of
1088        offline_exf_seaice/input.dyn_jfnk)
1089    
1090    checkpoint65a (2014/07/27)
1091    o model/src:
1092      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1093        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1094        (topo in p-coords, ice-shelf in z-coords); update output of experiments
1095        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1096    o model/src:
1097      - collect momentum forcing tendency into local 2-D array (passed as argument
1098        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1099        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1100        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1101      - collect T & S forcing tendency into local 2-D array (passed as argument to
1102        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1103        affects results at machine truncation level (e.g., ocean: if using
1104        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1105        correction due to vertical advection).
1106      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1107        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1108        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1109        obcs_ctrl (ad & fwd grd @ 12 & 7).
1110    o pkg/ptracers & diagnostics:
1111      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1112        title (to avoid some unexpected truncation); sort out ptracers diags units.
1113      - collect ptracer forcing tendency into local 2-D array (passed as argument
1114        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1115    
1116    checkpoint65 (2014/07/18)
1117    o pkg/fizhi:
1118      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1119        affects results at machine truncation level. Update output of experiments
1120        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1121    o pkg/seaice: more clean up
1122      - rename TAF common block tapes to be more consistent and remove
1123        unnecessary duplicates
1124      - add store directives to remove more recomputations, but use smaller
1125        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1126        The idea behind this flag is to reduce the memory footprint when the
1127        adjoint of the LSR is not required. As of now, defining the flag
1128        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1129        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1130        For experiment offline_exf_seaice, this means on a linux box with gfortran
1131        nearly a factor of 10 (but keep in mind there is mostly seaice code in
1132        this experiment):
1133        > size mitgcmuv_ad
1134        text    data        bss     dec        hex
1135        5100659 1216  220458952  225560827  d71c8fb
1136        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1137        but only a moderate increase of 36% for global_ocean.cs32x15:
1138        text    data        bss     dec        hex
1139        6695027 1648 1014578664 1021275339 3cdf6ccb
1140        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1141      - note: there are still recomputations in global_ocean.cs32x15 and
1142        offline_exf_seaice and the gradient agreement changes (gets a
1143        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1144      - in general, the AD gradients still are wrong
1145    o OpenAD
1146      - clean up code_oad/ directories somewhat by moving files
1147        dontCompile, dontTransform, keepOriginal to OAD_support/
1148    o model/src:
1149      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1150        (not currently tested): add dissipation terms before NLFS rescaling of
1151        tendencies (previously done after).
1152    o pkg/diagnostics:
1153      - write stats-diags in ascii file with more digits (same as in monitor).
1154    o pkg/down_slope:
1155      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1156        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1157    o model/src:
1158      - new file "apply_forcing.F" containing all the code previously in
1159        external_forcing.F, but with new argument list: pass, as new argument,
1160        the current level tendency array to update (instead of a direct update
1161        of the common bloc array). Change the corresponding calls.
1162      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1163        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1164    o pkg/seaice/seaice_lsr, a little bit of clean up
1165      - rearrange some code blocks, so that now all calculations for
1166        setting up the right-hand-sides done within one single block
1167        (I find that easier to read and understand)
1168      - rearrange freedrift-code to reduce the number of ifdefs
1169      - adjust some indentations and comments
1170    
1171    checkpoint64z (2014/07/10)
1172    o model/src and several pkgs:
1173      - change argument list of all S/R called from external_forcing.F and
1174        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1175        to pass, as argument, the current level tendency array to update
1176        (instead of a direct update of the common bloc array).
1177      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1178      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1179    o pkg/seaice/seaice_lsr.F
1180      - always initialize local arrays in seaice_lsr_tridiagu/v
1181      - add more local tapes to seaice_lsr_tridiagu/v
1182      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1183        keep it in bi/bj loop; this seems to be essential
1184      - gradients are still wrong but only by 4-7 orders of magnitude
1185        instead of 15 orders of magnitude, lab_sea improves a little
1186    o pkg/seaice
1187      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1188        generates unnecessary code in seaice_lsr_ad
1189      - add more store directives in seaice_lsr to avoid unnecessary code
1190        in seaice_lsr_ad
1191      - exclude some residual computations in seaice_lsr when
1192        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1193        in seaice_lsr_ad
1194      - add more storing, a new tape (model/src/the_main_loop.F) and
1195        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1196        and klockey should be checked by a specialist)
1197      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1198        and update lab_sea after previous changes in pkg/seaice below
1199    o pkg/autodiff:
1200      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1201        viscFacInAd : run time parameters allowing for adjoint switches
1202        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1203    o pkg/ecco:
1204      - introduce cost_gencost_boxmean.F that computes a box mean
1205        temperature (for use in adjoint sensitivity studies).
1206    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1207    o pkg/mom_common/mom_calc_visc.F:
1208      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1209    o pkg/seaice/seaice_summary.F:
1210      - statement for SEAICEadjMODE now in autodiff_readparms.F
1211    o pkg/seaice:
1212      - remove some store directives and add new ones in an effort to get
1213        finally rid off the recomputation warnings. This is successful
1214        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1215        defined (i.e. no extensive recomputation warnings left), but there
1216        are still too many recomputations on the solver iteration level
1217      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1218      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1219        SEAICE_SIZE.h
1220      - add a store directive in S/R seaice_calc_viscosities
1221    o pkg/seaice (ITD code):
1222      - fix definition of Hlimit for multi-threaded case
1223      - use double precision arithmetic to compute Hlimit: this affects results;
1224        update output of experiment seaice_itd.
1225    o replace content of verification/seaice_itd
1226      - instead of a 1D column use the configuration of offline_exf_seaice
1227        to test the ice thickness distribution code with ridging
1228      - this is a first shot at this experiment
1229      - change of some defaults of ridging parameters SEAICEhStar (from
1230        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1231        and lot of new comments.
1232    
1233    checkpoint64y (2014/06/20)
1234    o pkg/seaice/seaice_reg_ridge.F:
1235      - modify the regularization of very small volumes of ice; only check
1236        total volume HEFF, and do not apply correction to individual ice
1237        classes because that leads to funny patterns in the heat and fw-fluxes
1238        into the ocean. Adjust seaice_itd/results/output.txt
1239      - replace nITD by SEAICE_multDim in loop-ranges
1240    o pkg/exf:
1241      - add code to process the case field period = -12. with UV interpolation.
1242      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
1243        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
1244    o verification/global_with_exf:
1245      - switch all fields period to -12. (was previously untested) in input/data.exf
1246        (but keep secondary test ".yearly" unchanged); update the reference output.
1247    o pkg/cal:
1248      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
1249    o pkg/exf:
1250      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
1251        to replace logical switch "exf_verbose"
1252      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
1253    o pkg/sbo:
1254      - update from Katherine Quinn: evaluate mass directly from density and SSH
1255        (budget using Finite Volume method) instead of from bottom pressure.
1256      - allow testreport to collect few selected SBO output ; tested in exp.
1257        global_ocean.90x40x15 (after updating the results, to include SBO output).
1258      - fix some multi-threading issues (in output part).
1259    o model/src & most packages:
1260      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
1261      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
1262        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
1263        "data.{pkg}" exist ; and leave the S/R (return) just after.
1264      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
1265        + call LAND_READPARMS from packages_readparms.F
1266    o pkg/seaice:
1267      - remove code that resets useThSice in S/R seaice_readparms and
1268        replace it by a warning in S/R seaice_check
1269      - remove parameter MULTDIM, replace with nITD and runtime
1270        parameter SEAICE_multDim (still hard-wired to nITD if
1271        SEAICE_ITD is defined)
1272    
1273    checkpoint64x (2014/05/24)
1274    o verification/lab_sea:
1275      - update adjoint and TLM output following changes to pkg/salt_plume
1276      - un-do the update after putting back local recip_Cp in few places.
1277    o pkg/salt_plume: modifications by An Nguyen:
1278      - add capability to do brine rejection (salt-plume) as function of
1279        volume+tracers (instead of only salinity tracer).
1280      - conserve volume by exchanging volume from each kLev to above to
1281        accommodate in-coming brine volume
1282      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
1283      - switch KPP surf buoyancy due to brine forcing to 3-d
1284        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
1285      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
1286      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
1287        in East/West Arctic.
1288    o pkg/sbo:
1289      - incorporate modifications from Katherine Quinn to enable the use of sbo
1290        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
1291        output for future testreport verification (unfinished).
1292    o pkg/atm_phys:
1293      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
1294        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
1295        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
1296    o pkg/seaice
1297      seaice_calc_ice_strength.F: modify expression to avoid divisions
1298        (affects truncation)
1299      seaice_do_ridging.F: clean up the insectarium
1300      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
1301      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
1302      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
1303      - add some debugging information and error messages (warnings)
1304    o model/src: modifications relatd to atmosphere p*:
1305      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
1306      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
1307        of vertical profile tRef in geopotential background and anomaly.
1308      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
1309        and pkg/atm_phys.
1310      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
1311        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
1312    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
1313    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
1314        not used right now, but can be used in BGC packages to fix conservation.
1315    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
1316        other packages too.
1317    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
1318        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
1319    o model/src:
1320      - since we have several heat capacity (even in model/src), define "recip_Cp"
1321        as local variable (no longer in common block) to avoid any confusion.
1322      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
1323    o pkg/exf:
1324      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
1325        air density as function of air Temp, Humidity and atm pressure.
1326    
1327    checkpoint64w (2014/05/02)
1328    o verification:
1329      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
1330        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
1331        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
1332        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
1333        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
1334    o model/src: for atmosphere in p* coords:
1335      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
1336      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
1337        but not yet activated.
1338    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
1339      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
1340      - this changes the results (but not for any verification experiment, because
1341        none tests this), but avoids having an extra field in the restart files
1342    o pkg/seaice: remove global variable TICE (not needed)
1343      - replace by TICES or local variable where necessary (cost_seaice_test,
1344        seaice_diagnostics_state)
1345      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
1346      - use specific read/write routines for reading and writing individual leves
1347        of a multilevel field
1348    o pkg/ctrl & model/inc:
1349      - move additional anomaly fields of control vars (related to options:
1350         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
1351        from DYNVARS.h into new header file: CTRL_FIELDS.h
1352    o pkg/seaice: some small modifications to the ridging code
1353      - make fw2ObyRidge a global variable and add the freshwater flux to
1354        seaice_growth
1355      - pass actual thickness from seaice_prepare_ridging, so that it is
1356        computed only in one place and compute it in the same way as in
1357        seaice_growth
1358      - initialise more fields in seaice_do_ridging that where cause floating
1359        point exceptions over land
1360  o pkg/seaice: preparations for ridging code and first real ridging code  o pkg/seaice: preparations for ridging code and first real ridging code
1361    - 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
1362      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
1363      advection call the actual ridging routine;      advection call the actual ridging routine;
1364    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,    - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
1365      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;      d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
1366    - remove ridging code from seaice_advdiff    - remove ridging code from seaice_advdiff
1367    - 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
1368      more readable (this is probably subjective)      more readable (this is probably subjective)
1369    - 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
1370      conditions in the correct category      conditions in the correct category
Legend:
Removed from v.1.1980  
changed lines
  Added in v.1.2223
  ViewVC Help
Powered by ViewVC 1.1.22