/[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 1.2008 by jmc, Fri Jun 20 13:13:37 2014 UTC revision 1.2222 by jmc, Wed Jan 13 00:47:25 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 eesupp & genmake2:
8       - first check for Function ETIME and, if it fails, then check for subroutine
9         ETIME and consistent output; use the appropriate version in timers.F
10    o model/src:
11      - to check restart test, add option to apply EXCH to U,V earlier, just before
12        integr_continuity; turned off by default.
13    o pkg/dic:
14      - remove CPP option USE_ATMOSCO2 (not needed)
15    o tools/tst_2+2:
16      - try to ignore difference between +0 and -0 in binary file, causing test
17        to fail for no good reason.
18    o eesupp & genmake2:
19      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
20        but also check (in genmake2) that test runs and returns meaningful results.
21    o coupler pkgs:
22      Finish implementation of optionally-exchanged variable switches (started on
23       Nov 12) with addition of few more exchanged fields, including 2-way exchange
24       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
25       advection in OCN component; this requires sequential coupling.
26      coupler (pkg/atm_ocn_coupler):
27      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
28        routines (useful for debug).
29      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
30         flux, DIC fields) if corresponding switch is ON.
31      - add option to export RunOff to OCN (to use for DIC river input)
32      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
33      components (pkg/atm_ & ocn_compon_interf):
34      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
35        optionally exchanged fields; add a check & stop in cpl_readparms.F.
36        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
37        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
38      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
39        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
40      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
41      - hold in common block coupler optionally-exchanged variable switch
42        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
43      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
44        this is intended to replace the OCN cplFldtave.* output files (not updated
45        to contain new additional exchanged fields).
46    o pkg/dic:
47      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
48    o pkg/thsice:
49      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
50        and writing of thsice pickup files.
51    o pkg/atm_compon_interf:
52      - move all field individual export-call out of cpl_export_import_data.F
53        into new S/R ATM_EXPORT_FIELDS
54    o pkg/atm_compon_interf:
55      - store state variables (for now, only thSIce fields) just before beeing
56        exported (in cpl_export_import_data.F, like on ocean side) instead of from
57        atm_store_my_data.F like all exported fluxes.
58      - new version of pickup_cpl: write field names into meta file and read meta
59        file to find field postion in pickup. Also only write/read fields meeded for
60        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
61    o pkg/dic:
62      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
63    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
64        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
65        value can be from domain [0,1] to average between the two methods
66    o pkg/atm_phys:
67      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
68        hold fixed in time).
69    
70    checkpoint65r (2015/12/21)
71    o pkg/seaice:
72        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
73        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
74    o pkg/seaice:
75      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
76        when SEAICEscaleSurfStress=.TRUE.,
77      - apply areaW and areaS in S/R seaice_calc_lhs
78    o pkg/atm_phys:
79      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
80        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
81        for individual contribution (convection, LSC cond, radiation)
82      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
83        information); activated with: solar_exponent=0. and wv_exponent=-1.
84    o pkg/ggl90:
85      - within IDEMIX add upper limit for horizontal group velocity to
86        avoid instability problems in the explicit horizontal diffusion term for
87        long time steps or high resolution
88    o pkg/diagnostics:
89      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
90        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
91    o testreport:
92      - remove "-v" (verbose option) in default mpirun command.
93    o pkg/seaice/seaice_growth:
94      - catch potential division by zero in ITD code, does not change
95        verification results
96    o pkg/ecco:
97      - retire old codes to the Attic. The calls to retired functions are
98        left in a commented form in case they ever need to be re-activated.
99      - ecco_check.F: issue warning if any old CPP option is
100        defined that corresponds to retired codes -- then stop.
101    o pkg/atm_compon_interf:
102      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
103        coupler: use last time-step value instead of average over cplSendFrq_iter
104        time-step, similar to what is done for seaIceMass.
105        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
106    o eesupp & genmake2:
107      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
108        <= remove until a fix is found for some ifort version on ia32 machine.
109    o pkg/seaice/seaice_evp:
110      - refine residual computation
111    
112    checkpoint65q (2015/11/18)
113    o pkg/seaice/seaice_evp:
114      - fix residual computations so that they no longer affect the actual
115        simulation code
116      - fix seaice_readparams to be able to actually set new parameters
117        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
118    o model/src:
119      - fix wrong truncation (single prec) from "FLOAT" function in expressions
120        like: deltaT*FLOAT(myIter) when myIter is large:
121         a) replaced by DFLOAT (if not seen by TAF);
122         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
123    o pkg/aim_v23:
124      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
125        when pickupSuff is set ; do write rolling pickups + at the end of the run.
126    o pkg/atm_ocn_coupler + ocn_compon_interf:
127      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
128        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
129        add corresponding call in DO_OCEANIC_PHYS.
130    o coupler pkgs:
131      Start a new way to set-up optionally-exchanged variables (previously, only
132       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
133       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
134       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
135       compononent param default can be set accordingly).
136      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
137       but rather applies to a group a fields (going both ways like for DIC)
138       and corresponds to an option of coupling config.
139      coupler (pkg/atm_ocn_coupler):
140      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
141        and read namelist directly (without eessup S/R calls) instead of
142        in the very un-flexible old way, 1 param per line, in fixed order;
143      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
144        cleanly in CPL_CHECK_CPLCONFIG
145      - add new coupling-exchange selectors (some not yet active) including
146        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
147                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
148      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
149        component ; called directly from coupler.F, after comp. registrations;
150      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
151         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
152          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
153      components (pkg/atm_ & ocn_compon_interf):
154      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
155        CPP header file in all pkg source files.
156      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
157        ATM/OCN_CHECK_CPLCONFIG;
158      - add error-counter to track errors (e.g., in "data.cpl") and to stop
159        cleanly in ATM/OCN_CHECK_CPLCONFIG;
160      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
161        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
162        before PACKAGES_READPARMS;
163      verification/cpl_aim+ocn/:
164      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
165        "data.cpl" for coupler (in input_cpl).
166    o eesupp/inc:
167      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
168        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
169        to always cumulate tile local-sum in the same order (still uses
170        MPI_Allreduce like standard code).
171      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
172        that are now identical to standard version (in eesupp/inc).
173    o pkg/shelfice:
174      - add SHELFICETransCoeffTFile for initializing spatially varying
175        heat and salt transfer coefficients
176    o pkg/atm_compon_interf & ocn_compon_interf:
177      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
178        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
179      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
180    o pkg/atm_ocn_coupler:
181      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
182    o pkg/rbcs:
183      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
184        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
185      - add a short report (to STDOUT) about RBCS-mask settings.
186    
187    checkpoint65p (2015/10/23)
188    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
189        there is no adjoint test for EVP, we don't know what it does to the adjoint
190        solution, but at least there are no more recomputation warnings left
191    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
192        a chance of giving the same results as a fully converged VP (JFNK) solver
193    o tools/adjoint_options/adjoint_diva:
194      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
195    o pkg/streamice:
196      - spotted bug in streamice_driving_stress using dyG where should have been dxG
197    o pkg/exf:
198      - remove STOP statement that prevented to use wind or (wind-)stress
199        interpolation for constant-in-time forcing fields (wind/stress period = 0).
200    o pkg/seaice:
201      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
202        5 additionals 2D fields and 6 new store directives
203      - change logic in seaice_readparms.F: EVP code can now be turned on in
204        various ways, setting SEAICE_deltaTev is no longer required,
205        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
206        or SEAICEaEVPcoeff
207    o pkg/shelfice/shelfice_thermodynamics.F
208      - redefining uLoc/vLoc to u/v, instead of 2u/v
209    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
210      - this is an intermediate state of a truely converging EVP that has
211        the potential of outperforming implicit VP methods, I do not recommend
212        using it yet.
213      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
214        and all parameters are hardwired
215      - for convergence it still requires very smooth regularisations, that means,
216        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
217        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
218        specific averaging appears to be required, still subject to tuning
219      - still needs cleaning and I need to turn parameter into runtime parameters
220      - add code to compute and print residuals of iteration, compile with
221        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
222    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
223      that entered with r1.54 on Sep04, 2015, -> update results
224    
225    checkpoint65o (2015/09/14)
226    o pkg/mom_vecinv & mom_common:
227      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
228        called from there.
229      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
230        allows to use Vector-Invariant form in deep atmos and anelastic formulation
231    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
232      and Koenig-Beatty+Holland (2012)
233      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
234      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
235      - requires an extra input argument for S/R seaice_calc_viscosities
236      - tensileStrength's depth dependence is different from Itkin et al. (2015)
237        (to be changed and played with, for now exponential)
238    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
239      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
240        by AREA according to Connelly et al. (2004), JPO.
241      - For EVP and the LSR solver, the implicit part of the drag term is
242        the only non-zero term in the denominator when there is no ice (which
243        prevented running the model with zero ice-ocean drag). If
244        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
245        (or zero main diagonals BU/BV) which need to be caught. A practical
246        consequence is that for open water, the momentum equation reduce
247        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
248        they happen to be zero, often leading to a non-zero solution over
249        open water.
250    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
251        efficient EVP method.
252      - introduce area-weighted averages for e12 (analogously to
253        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
254        remain, but also changing the order of terms in the previous average
255        changed the results as much) -> update experiment
256      - add SEAICE_DELTA_SMOOTHREG code
257      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
258        TEM-code
259      - adjust loop bounds so that only required fields are computed
260      - add new averaging code for zetaZ/deltaZ (again similar to
261        seaice_calc_viscosities.F), inactive by default for now (will change
262        results again), but will replace old code eventually
263    o eesupp/src:
264      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
265        to always cumulate tile local-sum in the same order
266        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
267        Still uses MPI_Allreduce (like standard code) but on array of tiles
268        and should be faster than GLOBAL_SUM_SEND_RECV code.
269      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
270        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
271      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
272         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
273         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
274         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
275         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
276    
277    checkpoint65n (2015/07/29)
278    o pkg/thsice:
279      - add a warning when used with pkg/aim but without updating SST
280        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
281    o pkg/offline:
282      - change where Offline-Fields are loaded, from load_fields_driver.F to
283        directly within FORWARD_STEP, just after updating iter number and time;
284      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
285        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
286       These changes allow:
287        a) to recover exactly on-line results using deltaToffline=deltaTClock,
288        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
289        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
290        time-step, both with GM & KPP files and with recomputing these fields;
291        b) no needs to switch on staggerTimeStep anymore;
292        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
293      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
294    o pkg/offline:
295      - change (rarely used) offset-iteration parameter to an offset time (in s):
296        can easily recover previous offset-iter effect by setting offset-time
297        (offlineTimeOffset) to offset-iter x deltaToffline;
298      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
299        in KPP as part of surface buoyancy forcing) in offline run.
300      - fix ptracers KPP non-local term in the case where KPP is re-computed.
301    o OpenAD
302      - Adding preliminary ggl90 test to OpenAD verification.
303        Config. with ggl90 currently diverges after 64 time steps
304        so will need more work to become more stable
305      - Adding preliminary kpp test to OpenAD verification.
306        required small tweakes in kpp_routines.F
307      - Merge and update from Krishna Narayanan's contrib area:
308        * Add one variable for preliminary OpenAD DIVA
309        * Add replacement time-stepping for OpenAD DIVA
310        * genmake2 flag -diva (but only for OpenAD; preliminary)
311        * required modifs for OAD_support
312        successful preliminary test for tutorial_global_oce_biogeo/
313    o pkg/seaice:
314      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
315      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
316        delta with a smooth function in s/r seaice_calc_viscosity
317        (no effect on EVP)
318      - rename local suffix "sqr" into "sq" for more consistent variable names
319    o pkg/seaice:
320        add new parameter SEAICE_deltaMin that is used ***only***
321        for regularizing Delta (and nothing else, like the parameter
322        which is also used for all sorts of things SEAICE_EPS).
323        Defaults to SEAICE_EPS for backward compatibility only.
324    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
325        the wrong key by inialising it before use -> fixes a recomputation
326        problem but does not fix the gradient
327    o pkg/layers:
328      - move resetting of flux arrays to outside the iLa loop
329        (this caused layers_diapycnal to not work with more than one layer coord.)
330      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
331    o pkg/layers:
332      - remove from common block 3D layers fields (used to diagnose transport
333        in tracer coords) and declare them as local arrays in layers_calc.F
334    o pkg/seaice:
335      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
336        in lab_sea forward experiment (changes results -> updated)
337      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
338    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
339       computations; for SEAICE_VECTORIZE_LSR
340      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
341        sweep to the outside,
342      - remove store directives and add "CADJ loop sequential" directives
343        in analogy to model/src/solve_tridiagonal.F
344      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
345        boundaries to yield more readable code. This has also the charming side
346        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
347        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
348        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
349        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
350        an additional option)
351       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
352       but the adjoint gradients (which are affected by this change) still explode.
353    o coupler (atm & ocn _compon_interf):
354      - avoid using Exch2 IO mapping if not suitable.
355    
356    checkpoint65m (2015/06/15)
357    o pkg/layers:
358      - clean-up old parameters setting (from Sep 2012):
359        + remove old parameters setting from common block (declared locally);
360        + stop if any old parameter is mixed with new parameters;
361        + check for valid or consistent parameter setting (e.g., layers_name)
362      - check that layers_bounds for Pot.Density are in the right range;
363        this is supposed to catch un-updated setting after recently shifting
364        potential density field "prho" by -1000 (now in "sigma" scale).
365    o pkg/layers:
366      - Added missing call to layers_fill for keeping track of tottend in
367        pkg/diagnostics/diagnostics_fill_state.F
368    o pkg/layers:
369      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
370        of diapycnal fluxes
371    o pkg/layers:
372      - reverted changes to interpolation to previous treatment; there
373        was never actually a problem
374    o pkg/layers:
375      - fix interpolation of layers tracers in the presence of partial cells
376      - add lots of new functionality to compute water mass transformation
377        (enabled by CPP flag LAYERS_THERMODYNAMICS)
378      - add new calls from main code (diags_oceanic_surf_flux.F,
379        thermodynamics.F, impldiff.F) and gad to save the necessary fields
380        for layers_thermodynamics calculations
381    o pkg/ptracers:
382      - add capability of stepping a passive tracer forward without advection
383        by setting PTRACERS_advScheme to 0.
384    o pkg/diagnostics:
385      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
386    o pkg/layers:
387      - shift potential density field "prho" by -1000 for density layer averaging so
388        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
389        Note that density bin boundaries (layers_bounds in data.layers) have
390        to be set accordingly (i.e., shifted, in sigma scale).
391    o pkg/layers:
392      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
393      - fix calculation of layer non-weighted velocity and layer probability
394      - add diagnostics for pot.density used for layer averaging
395    o pkg/seaice:
396      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
397        positiveness, modify a few comments and improve variable names,
398      - the changed computation of deltaC affects most seaice-related
399        experiments at the truncation level.
400        seaice_itd.thermo is affected by far the most, with
401        only 7 digits of agreement remaining; update experiments.
402    
403    checkpoint65l (2015/05/04)
404    o pkg/shelfice:
405      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
406        factor drKp1 to zero where it is negative (ie. do not use
407        SHELFICEBoundaryLayer if hFacC>1)
408      - the same for factor drLoc in shelfice_forcing.F
409    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
410        with modules in ptracers, when using testreport option "-small_f"
411    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
412      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
413    o verification/testreport
414      - add new option -small_f
415        with this option testreport first makes the target small_f (*.f files)
416        before running make (all). This is useful for explicit inlining when
417        all sources need to be full available.
418    o pkg/exf/exf_interp.F:
419        remove previous changes related to reverse (decreasing) input grids latitude
420    
421    checkpoint65k (2015/04/01)
422    o pkg/ecco:
423        fix missing cosphi initialization; use eccoiter in place of optimcycle;
424        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
425        instead of active read/write
426    o pkg/ctrl:
427        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
428        instead of active read/write.
429    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
430        return if .NOT.useAUTODIFF
431    o pkg/seaice: add CPP brackets (cost function related).
432    o model/src:
433        add useAUTODIFF run time switch.
434    o pkg/exf/exf_interp.F:
435        add code to allow input grids with latitude starting in the north (i.e. when
436        j=1 corresponds to northern edge of field); modify global_with_exf to test
437        this feature.
438    o verification/testreport:
439      - replace "grep -A3" with POSIX conformal sed command, because there are
440        implementations of grep that cannot do contextual searches
441      - replace "cat -n" by "nl" (two occurrences), because not all implementations
442        of "cat" have the option "-n"
443    o model/src:
444        add new file gsw_teos10.F that contains 3 functions, more or less a copy
445        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
446        convert from conservative to potential temperature. For now they are not
447        called anywhere.
448    o pkg/ggl90: make "useIDEMIX" useful
449      - re-organize code in s/r ggl90_calc a little to move computations that
450        are different for idemix into separate loops (changes verification
451        experiment idemix at truncation level, 12 digits remain -> updated)
452      - requires 2 new 2D fields KappaM, verticalShear
453      - make hFacI and recip_hFacI local 3D variables that are passed to
454        s/r ggl90_idemix
455      - fix and improve some comments
456    
457    checkpoint65j (2015/02/25)
458    o pkg/openad
459      - synchronize seawater.F with version in model/src: replace routine
460        body of sw_temp by calling sw_ptmp and fix/add a few comments.
461    o pkg/mnc:
462      - change default value of pickup_read/write_mnc params to FALSE
463        (since few features are missing in reading MNC pickup files).
464    o model/src:
465      - change default (background) vertical diffusivity for salt to be the
466        temperature (background) vertical diffusivity.
467      - change background vertical diffusivity in vertical mixing pkgs ggl90,
468        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
469        This makes ptracers default diffusivity (that uses salt diffKr) more
470        consistent with vertical mixing schemes.
471    o verification/testreport:
472      - fix typo in "-pcls" option ;
473      - put temp files in /tmp (instead of in local dir)
474      - add option "-ncad" to use genmake2 new option "-nocat4ad"
475      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
476    o pkg/ggl90 (idemix code):
477      - apply few fixes ; add some missing "_d 0" ; update output of exp.
478        global_ocean.90x40x15.idemix
479    o OpenAD
480      - enable active file I/O and begin removal of work-around code
481        for OpenAD for handling control variables (memory vs. active files)
482      - new CPP options file OPENAD_OPTIONS.h
483      - revert to genarr2d gradient check for hs94.1x64x5
484      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
485      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
486    o tools/genmake2:
487      - add option for an alternative Makefile (from Martin) where multiple
488        source files are sent to TAF (instead of all in one file).
489    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
490      - code provided by Carsten Eden as an extension of ggl90
491      - so far the code is turned on within ggl90 by setting a CPP-flag at
492        compile time; a runtime flag implementation is not yet complete
493      - tested in new verification experiment global_ocean.90x40x15.idemix
494    o verification:
495      - reduce length of the AD test run by half for experiments
496        global_ocean.cs32x15 (std + thsice) and isomip
497      - enable active file I/O for OpenAD, adjust verifications accordingly
498      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
499    o verification/testreport:
500      - fix two non-POSIX sed statements so that there are no error messages
501        on Mac OS X
502      - replace hostname -s with hostname | sed 's/\..*$//'
503    o model/src/seawater.F:
504      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
505        (following the matlab code), which would have avoided the bug caught
506        by Matt (see below) in the first place
507    o pkg/shelfice:
508      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
509        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
510      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
511        ice-shelf case (i.e., within surface level).
512      - add config summary in shelfice_check.F
513      - remove global variable recip_SHELFICElatentHeat and replace by a local
514        variable recip_latentHeat
515      - introduce diagnostics for friction velocity uStar (in case of
516        SHELFICEuseGammaFrict)
517      - change verification experiment isomip.htd:
518        + start from pickup (as input_ad at nIter0=8640)
519        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
520        + test SHELFICEuseGammaFrict = .TRUE.
521        + test SHELFICEadvDiffHeatFlux = .TRUE.
522    o model/src:
523      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
524        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
525        update output of experiments global_with_exf.yearly and isomip (all 6).
526    o pkg/shelfice:
527      - change setting of kTopC to also be zero where there is no ice-shelf.
528      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
529        ice-shelf is.
530      - first attempt to get RealFreshWaterFlux effects: for now, only without
531        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
532    o pkg/seaice: add the option to prescribe a fixed thickness PDF
533      for thermodynamic calculations
534      - because of divisions of the type 7/7 not exactly equal to 1, this change
535        affects results of some verification experiments by up to 4 digits:
536        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
537        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
538        adjoint: lab_sea, lab_sea.noseaicedyn
539        -> updated
540    
541    checkpoint65i (2015/01/23)
542    o model/src:
543      - change units of frictionHeating field from W to W/m^2
544      - fix bug in frictional heating from stratospheric drag in
545        S/R ATM_PHYS_TENDENCY_APPLY_V
546      - with synchronous time-stepping: move resetting to zero of frictionHeating
547        field from load_fields_driver.F to thermodynamics.F ;
548      - add diagnostics for frictional heating.
549    o model/src & gmredi K3D:
550      - add frictionHeating field to pickup-files (for synchronous time-stepping)
551      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
552      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
553        and name in pickup file).
554      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
555    o model/src:
556      - move (from ini_forcing.F) initialisation of all arrays in header file
557        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
558        (since Nov 2012) with option selectAddFluid=1.
559    o pkg/shelfice:
560      - change units (+ document) of newly added field "shelfIceMassDynTendency"
561      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
562    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
563    o pkg/seaice: two new runtime parameters:
564      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
565        long overdue
566      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
567        parameterization of tensil stress for fast ice (does not do anything yet)
568    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
569        for LSR: move checking overlaps out of JFNK-if-block
570    o pkg/atm_phys:
571      - move copy of grid and dynamical fields out of atm_phys_driver.F into
572        new S/R ATM_PHYS_DYN2PHYS.
573      - fix level height for Linear Free-Surf case (to be consistent with
574        fixed-in-time pressure levels).
575    o pkg/mom_common (bottomdrag):
576      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
577        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
578        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
579    o pkg/shelfice (u/v_drag):
580      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
581      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
582        (now similar to shelfice_u_drag.F)
583      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
584        from mom_vecinv.F (similar to mom_fluxform calls).
585    o pkg/mom_common (bottomdrag):
586      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
587      - add options for alternative discretisation of velocity norm in quadratic
588        bottom drag: averaging of grid-cell-center KE to U.point and V.point
589        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
590        improves when averaging only the other component (e.g. vVel for U bottom
591        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
592      - add options (bottomVisc_pCell) to account for partial-cell in bottom
593        friction (no-slip BC) thus getting the true distance from the bottom;
594        off by default since this also reduces model stability (explicit bottom
595        friction). Changes produce different machine truncation with linear-drag
596        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
597        front_relax (bvp & mxl, 10 & 11 digits).
598    o model/src & mom pkgs:
599      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
600        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
601      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
602        just copy level Nr value to level Nr+1.
603    o doc:
604      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
605    o pkg/streamice:
606      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
607        SHELFICE.h: move array shelficemass to init_varia, initialise
608        from array shelficemassinit, which is set in init_fixed and
609        has option to be set from file; introduce array
610        shelficeMassDynTend array, set thru file in init_fixed
611      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
612        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
613        pkg/streamice
614      - shelfice_thermodynamics.F: call shelfice_step_icemass if
615        SHELFICEMassStepping = .true.
616      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
617    
618    checkpoint65h (2014/12/17)
619    o verification/global_ocean.90x40x15, global_ocean_ebm:
620      - update to generic controls.
621    o pkg/ctrl:
622      - ctrl_map_ini_genarr.F: test for igen>0
623      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
624      - move gentim2d part of ctrl_map_ini_genarr.F to
625        new separate routine : ctrl_map_ini_gentim2d.F
626      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
627        add time variable weights and cyclic controls (time mean,
628        seasonal cycle, etc) capabilities to gentim2d
629    o pkg/ecco:
630      - move reading of error, conversion to weights from
631        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
632    o global_oce_llc90, cs32:
633      - activte sbo.
634      - CTRL_SIZE.h : add maxCtrlProc.
635      - activate the new genctrl capabilities.
636      - update following reorganization of global_oce_input_fields.tar.gz  
637    o pkg/ctrl/ctrl_ad_diff.list:
638      - add missing ctrl_init_rec.f
639    o tools/OAD_support/keepOriginal:
640      - add ctrl_init_rec.F
641    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
642      - avoid recomputations of xx_gentim2d_dummy.
643    o momentum diagnostics:
644      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
645        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
646    o pkg/seaice/seaice_lsr.F:
647      - fix computation of BU/BV, make sure they are non-zero, only necessary
648        for cubed sphere exchanges and SEAICE_OLx/y>0.
649        This makes calling s/r fill_cs_corner_rl obsolete (removed).
650    o verification/global_ocean.cs32x15/input.seaice
651      - add test for strong implicit coupling and restricted addtive Schwarz
652        methods for LSR
653      - update results/output.seaice.txt
654    o verification/tutorial_global_oce_biogeo:
655      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
656        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
657        update output_adm,_oadm,_tlm.txt
658    o pkg/dic:
659      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
660      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
661        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
662    o verification/tutorial_global_oce_biogeo:
663      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
664        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
665        update output_adm,_oadm,_tlm.txt
666    o eesupp/src:
667      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
668        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
669    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
670      LSR (following Hutchings et al. 2004)
671      - introduce zetaZ as a global variable (requires adjustments in
672        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
673        in seaice_calc_viscosities.F
674      - new flag SEAICEuseStrImpCpl (default off)
675      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
676        momentum equations
677      - JFNK-solver (preconditioner) adjusted to allow using this method
678        (where it does not have any positive effect)
679    o pkg/seaice
680      - add overlap for restrictive additive Schwartz method also to LSR, but
681        turn it off by default (because it only seems to work for non-cubed
682        sphere/llc topologies)
683    o pkg/autodiff
684      - add extra exchanges in addummy_in_steppging also for mnc output
685    o pkg/seaice:
686      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
687        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
688    o pkg/obcs:
689      - add option to specify domain-connected piece Id along OB though files
690        (for now, only used to diagnose PhiVel; default =1 -> global correction)
691      - modify obcs_diag_balance.F to process each connected-part separately;
692        exclude OB where Id = 0 but keep the full divergence there (-> constant
693        Psi along this portion of OB and all inflow derived from grad(Phi))
694      - add example of OB-conect files in verification/so_box_biogeo/input.
695    o pkg/diagnostics:
696      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
697      a) use non zero matrix element across OB and solve for Phi 1 grid point
698         outside OB (i.e, where tracer OBCS are applied).
699      b) global imbalance of inFlow/outFlow across OB: instead of modifying
700         velocity across OB, spread it uniformly along the OB in the RHS.
701    
702    checkpoint65g (2014/11/19)
703    o pkg/diagnostcis:
704      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
705    o pkg/my82,pp81,kl10:
706      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
707        field diffKr as background diffusivity to set minimum diffusivity value.
708    o pkg/seaice:
709      - add new parameter SEAICEuseEVPrev (for revisited EVP by
710        Bouillon et al 2013)
711      - add SEAICE_evpAlpha/Beta to namelist
712      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
713        involve trivial re-ordering of divisions/multiplications that should not
714        have any effects, but ... they do change the results of lab_sea.hb87 so
715        that only 2 digits of agreement remain, in line with the general
716        instability/fragility of the evp-code. For now, I do not care and just
717        update the verification experiment
718    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
719      - remove xx_genarr2d_numsmooth etc
720      - use xx_genarr2d_preproc etc instead
721      - carry out smooth_correl2D at initialization stage rather than during
722        time stepping.
723      - get smoothOpNb from xx_gentim2d_preproc
724    o global_oce_cs32 :
725      - add test of generic ecco capabilities.
726    o pkg/exf/exf_getsurfacefluxes.F :
727      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
728    o pkg/ctrl,ecco :
729      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
730        is defined.
731    o pkg/seaice: add diagnostics for Delta (deformation parameter)
732    o model/src:
733      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
734        diffusivity (background) is specified but ignored.
735    o verification:
736      - in testreport, convert hostname to lower case for default output dir name
737    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
738    o pkg/dic: add modifications from Hajoon:
739      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
740      - light attenuation: add self-shading effect by climatological Chlorophyll
741        (read from file).
742    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
743        compiles when SEAICE_ALLOW_DYNAMICS is undefined
744    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
745        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
746        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
747        approach where CPP_OPTIONS.h includes an omnipotent
748        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
749    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
750        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
751    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
752        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
753        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
754    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
755      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
756      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
757      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
758      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
759    o pkg/ctrl,ecco,exf :
760      - remove variables associated with NON-generic costs,
761        unless ECCO_CTRL_DEPRECATED is defined.
762      - remove NON-generic NON-obcs controls,
763        unless ECCO_CTRL_DEPRECATED is defined.
764    o pkg/ctrl : added ctrl_local_params.h
765    o pkg/ecco : added ecco_local_params.h
766    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
767        experiments, which will progressively be removed once the
768        experiments are revised to use only generic controls/costs.
769    
770    checkpoint65f (2014/10/13)
771    o pkg/ctrl, ecco, seaice : minor changes in headers
772    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
773        cost function and control capabilities added since checkpoint65c.
774    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
775    o pkg/ecco: increase modularity and improve logic
776      - ecco_toolbox.F (new) : basic operations that are often used,
777        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
778        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
779      - cost_gencal.F (new) : determine filnames and records.
780      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
781      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
782        and exploit the above functions leading to more compact code.
783      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
784      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
785        using_ers, using_gfo, using_mdt is now only defined within gencost)
786    o pkg/ecco: extend generic cost capabilities
787      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
788        capabilities via gencost_preproc (+ _c,_i,_r related params),
789        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
790        gencost_outputlevel arguments to cost_generic
791      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
792        and active_read, making room for gencost_preproc to take effect.
793        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
794      - pkg/ecco/cost_generic.F :
795        compute and store misfit maks*(model-data) in localdif that is
796        then used in cost and for output, output misfit if outlev.GT.0
797      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
798        rather gencost_barfile for deciding whether to write barfile
799      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
800      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
801        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
802      - pkg/ecco/ecco_summary.F : report gencost variables
803      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
804    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
805    o pkg/ecco: internal re-organization
806      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
807        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
808        mv relevant variables definition from ecco_cost.h to ecco.h,
809        make sure gencost routines only include ecco.h)
810      - throughout : add missing CCP switches, rm unused variables,
811        and rm un-necessary CPP switches
812      - throughout gencost routines : replace modelstartdate with
813        gencost_startdate when needed
814      - cost_bp_read.F : use arguments, instead of common blocs
815        so that it can be used also by (new) cost_gencost_bpv4.F
816      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
817      - ecco_phys.F : compute etanFull
818      - ecco_readparms.F : rename using_topex as using_tpj, add
819        bpv4-grace to gencost list, initialize added parameters
820      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
821    
822    checkpoint65e (2014/09/28)
823    o pkg/obcs:
824      - replaced the just-added CPP options with run-time variables
825        (see pkg/obcs/OBCS_PARAMS.h for details)
826    o pkg/obcs:
827      - add additional CPP options for sponge boundary layers
828        (see pkg/obcs/OBCS_OPTIONS.h for details)
829    o pkg/atm_phys:
830      - implement simple (obliquity only, assuming circular planet orbit)
831        seasonal cycle for incoming insolation ; used when run-time parameter
832        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
833    o pkg/exf, pkg/ecco, pkg/ctrl:
834      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
835      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
836      - implement gentim2d for xx_tauu, xx_tauv
837    o pkg/ctrl, pkg/ecco :
838      - fix and complement the generic controls implementation
839    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
840        pkg/shelfice/shelfice_thermodynamics.F,
841        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
842        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
843      - add weight in CTRL_GET_GEN calls
844    o pkg/ctrl :
845      - ctrl_get_gen.F : add weight as input parameter, and apply
846        it directly rather than using smooth_correl2Dw (to be retired).
847      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
848    o pkg/ctrl :
849      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
850        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
851      - re-activate ctrl_summary (call in ctrl_init.F)
852    o pkg/ctrl/ctrl_cost_gen.F :
853      - fix CCP brackets, remove un-necessary myiter, mytime
854    o pkg/ecco, pkg/ctrl :
855      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
856      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
857      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
858      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
859    
860    checkpoint65d (2014/09/15)
861    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
862      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
863        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
864    o pkg/ctrl/ctrl_map_ini_genarr.F :
865      - remove compilation failure
866      - replace hard coded example
867      - use ctrl_map_ini_gen2D, 3D
868    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
869      - on/off switch based upon xx_genarr2d_weight,3d
870    o src/packages_init_variables.F :
871      - regroup pkg/estimation calls
872      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
873        (moved to ctrl_init_variables)
874    o cost/cost_init_varia.F :
875      - remove ecco_cost_init_varia
876        (moved to ecco_init_varia)
877    o ctrl/ctrl_init_variables.F :
878      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
879      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
880    o ctrl/ctrl_map_ini.F :
881      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
882        (moved to ctrl_init_variables)
883    o ctrl/ctrl_map_ini_ecco.F :
884      - remove ECCO_PHYS (mv to ecco_init_varia)
885      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
886    o ecco/ecco_ad_diff.list :
887      - add ecco_init_varia.f
888    o ecco/ecco_init_varia.F
889      - new routine
890    o pkg/streamice:
891      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
892        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
893      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
894    o pkg/generic_advdiff:
895      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
896    o pkg/exf:
897      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
898         xxg_precip capability
899      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
900    o pkg/ctrl:
901      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
902    o model/src/load_fields_driver.F :
903      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
904        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
905    o OpenAD verification experiments:
906      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
907        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
908        for now, only in pkgs used in OpenAD verification experiments.
909      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
910        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
911        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
912        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
913    o OpenAD verification tests:
914      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
915      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
916        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
917      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
918        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
919    o model/src & generic_advdiff:
920      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
921        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
922        dynamics requires valid tracer forcing only over tile interior but, for
923        some diagnostics, may need to extend it over 1 point in tile halo region.
924      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
925        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
926        setting in temp/salt/ptracer_integrate.F
927    o pkg/dic:
928      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
929        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
930        in gchem_forcing_sep.F
931    o pkg/autodiff & obcs:
932      - add storage of current OB values for U & V (was already done for T & S).
933    
934    checkpoint65c (2014/08/30)
935    o pkg/dic:
936      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
937        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
938        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
939    o verification:
940      - new experiment testing OBCS and DIC pkgs, using params & output from
941        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
942        passage: take OBCS from the last year of a 2 yrs simulation and initial
943        conditions from t=1.yr while keeping the same forcing.
944    o model/src:
945      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
946        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
947    o pkg/diagnostics (Stats-Diags):
948      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
949        a) refine region where stats are computed, excluding where arrhFac=0 ;
950        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
951        c) extend regional stats over the region edges (for U or V pt location).
952    o pkg/gchem:
953      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
954        pkg/dic is currently changing/updating ptracers values beyond the OB).
955    o verification (hs94):
956      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
957        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
958        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
959        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
960    o pkg/ptracers:
961      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
962        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
963      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
964        with AB-2 code (so that it get tested).
965    o model/src:
966      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
967        with AB-2 code (previously only available with AB-3 code).
968        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
969        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
970        there, by calling CYCLE_AB_TRACER).
971    o pkg/generic_advdiff:
972      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
973        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
974        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
975        S/R temp/salt/ptracers_integrate.F
976    o model/src & pkg/ptracers:
977      - remove common block variables gT,gS (in DYNVARS.h), except when
978         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
979      - remove common block variable gPtr.
980    o model/src & pkgs:
981      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
982         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
983         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
984         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
985      + change accordingly all calling S/R.
986      - use local temperature/salinity/ptracer tendency array (without bi,bj)
987        in S/R temp/salt/ptracers_integrate.F
988    o pkg/seaice:
989      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
990        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
991      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
992        in seaice_lsr
993      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
994        in s/r seaice_lsr_calc_coeffs
995    o pkg/mdsio:
996      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
997        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
998        too long (e.g., > MAX_LEN_FNAM/2 )
999    
1000    checkpoint65b (2014/08/12)
1001    o pkg/matrix:
1002      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1003    o model/src:
1004      - fix initialisation of geothermalFile; compile geothermal-flux code in
1005        natl_box verification experiment.
1006    o model/src & pkg/down_slope:
1007      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1008      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1009        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1010        results at machine truncation level: update output of experiments
1011        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1012    o pkg/diagnostics (Stats-Diags):
1013      - do not cumulate the full volume when DIAGNOSTICS_FILL is
1014        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1015        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1016        times (but Min,Max and StD are still wrong).
1017    o model/src:
1018      - add geothermal flux forcing: read in ini_forcing.F as time-constant
1019        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1020    o model/src:
1021      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1022        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1023        arrays are already updated while adjustments (filters, conv.adjustment) are
1024        still applied later, in S/R TRACERS_CORRECTION_STEP.
1025    o model/src:
1026      - store in common bloc array "rhoInSitu" the virtual potential temperature
1027        anomaly that is used to compute geopotential: this make the atmos code
1028        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1029    o pkg/seaice/seaice_lsr.F
1030      - rename integer variable ilcall to ipass (that's what it is called
1031        in the residual diagnostics
1032      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1033        default) for improved non-linear convergence of the first few steps
1034      - adjust a few comments and add new ones to explain some of the store
1035        directives
1036    o pkg/generic_advdiff (& ptracers):
1037      - re-work the code to check for valid advection scheme and for minimum
1038        size of overlap (now stored in local common bloc in gad_advscheme.F)
1039    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1040      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1041      - add an auxilliary variable "bet" and fix store directives and keys in
1042        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1043        less exact gradients in my tests); but there are still
1044        recomputation warning (although gradients are sort of OK), when
1045        SEAICE_LSR_VECTORIZE is not defined, so this flag and
1046        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1047      - update verification experiments lab_sea.
1048      - change some comments in S/R seaice_calc_viscosities
1049    o model/src:
1050      - if staggerTimeStep=T, always apply exchange to velocity field in
1051        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1052        (independent of using multi-dim advection or not); no effect on FWD run
1053        but affects AD results (at machine truncation level): update output of
1054        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1055        and isomip (oad: 12.d).
1056    o pkg/generic_advdiff:
1057      - stop if doAB_onGtGs is set to FALSE but ignored
1058      - refine warning related to stability of tracer time-stepping
1059        regarding internal wave dynamics.
1060      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1061        on staggerTimeStep & implicitIntGravWave (will now get a warning
1062        if potentially unstable).
1063    o pkg/kl10:
1064      - add new pkg "kl10" for mixing due to internal wave breaking, from
1065        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1066        (contribution from Jody Klymak), tested in verification experiment
1067        verification/internal_wave/input.kl10/
1068    o isomip experiment:
1069      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1070        (input.htd) and update the output.
1071    o cd_code experiments:
1072      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1073        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1074        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1075        update the corresponding output.
1076    o pkg/seaice:
1077      - reduce the number of include files and store directives in
1078        S/R seaice_lsr_tridiagu/v
1079      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1080        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1081        get rid off one store directive (a TAF bug?)
1082      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1083        S/R seaice_lsr_tridiagv to change the loop range for consistency
1084      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1085      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1086        S/R seaice_lsr_tridiagu/v (requires update of
1087        offline_exf_seaice/input.dyn_jfnk)
1088    
1089    checkpoint65a (2014/07/27)
1090    o model/src:
1091      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
1092        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
1093        (topo in p-coords, ice-shelf in z-coords); update output of experiments
1094        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
1095    o model/src:
1096      - collect momentum forcing tendency into local 2-D array (passed as argument
1097        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
1098        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
1099        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
1100      - collect T & S forcing tendency into local 2-D array (passed as argument to
1101        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1102        affects results at machine truncation level (e.g., ocean: if using
1103        SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1104        correction due to vertical advection).
1105      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1106        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1107        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
1108        obcs_ctrl (ad & fwd grd @ 12 & 7).
1109    o pkg/ptracers & diagnostics:
1110      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
1111        title (to avoid some unexpected truncation); sort out ptracers diags units.
1112      - collect ptracer forcing tendency into local 2-D array (passed as argument
1113        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
1114    
1115    checkpoint65 (2014/07/18)
1116    o pkg/fizhi:
1117      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
1118        affects results at machine truncation level. Update output of experiments
1119        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
1120    o pkg/seaice: more clean up
1121      - rename TAF common block tapes to be more consistent and remove
1122        unnecessary duplicates
1123      - add store directives to remove more recomputations, but use smaller
1124        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
1125        The idea behind this flag is to reduce the memory footprint when the
1126        adjoint of the LSR is not required. As of now, defining the flag
1127        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
1128        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
1129        For experiment offline_exf_seaice, this means on a linux box with gfortran
1130        nearly a factor of 10 (but keep in mind there is mostly seaice code in
1131        this experiment):
1132        > size mitgcmuv_ad
1133        text    data        bss     dec        hex
1134        5100659 1216  220458952  225560827  d71c8fb
1135        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1136        but only a moderate increase of 36% for global_ocean.cs32x15:
1137        text    data        bss     dec        hex
1138        6695027 1648 1014578664 1021275339 3cdf6ccb
1139        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
1140      - note: there are still recomputations in global_ocean.cs32x15 and
1141        offline_exf_seaice and the gradient agreement changes (gets a
1142        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
1143      - in general, the AD gradients still are wrong
1144    o OpenAD
1145      - clean up code_oad/ directories somewhat by moving files
1146        dontCompile, dontTransform, keepOriginal to OAD_support/
1147    o model/src:
1148      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
1149        (not currently tested): add dissipation terms before NLFS rescaling of
1150        tendencies (previously done after).
1151    o pkg/diagnostics:
1152      - write stats-diags in ascii file with more digits (same as in monitor).
1153    o pkg/down_slope:
1154      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
1155        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
1156    o model/src:
1157      - new file "apply_forcing.F" containing all the code previously in
1158        external_forcing.F, but with new argument list: pass, as new argument,
1159        the current level tendency array to update (instead of a direct update
1160        of the common bloc array). Change the corresponding calls.
1161      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
1162        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
1163    o pkg/seaice/seaice_lsr, a little bit of clean up
1164      - rearrange some code blocks, so that now all calculations for
1165        setting up the right-hand-sides done within one single block
1166        (I find that easier to read and understand)
1167      - rearrange freedrift-code to reduce the number of ifdefs
1168      - adjust some indentations and comments
1169    
1170    checkpoint64z (2014/07/10)
1171    o model/src and several pkgs:
1172      - change argument list of all S/R called from external_forcing.F and
1173        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
1174        to pass, as argument, the current level tendency array to update
1175        (instead of a direct update of the common bloc array).
1176      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
1177      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
1178    o pkg/seaice/seaice_lsr.F
1179      - always initialize local arrays in seaice_lsr_tridiagu/v
1180      - add more local tapes to seaice_lsr_tridiagu/v
1181      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
1182        keep it in bi/bj loop; this seems to be essential
1183      - gradients are still wrong but only by 4-7 orders of magnitude
1184        instead of 15 orders of magnitude, lab_sea improves a little
1185    o pkg/seaice
1186      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
1187        generates unnecessary code in seaice_lsr_ad
1188      - add more store directives in seaice_lsr to avoid unnecessary code
1189        in seaice_lsr_ad
1190      - exclude some residual computations in seaice_lsr when
1191        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
1192        in seaice_lsr_ad
1193      - add more storing, a new tape (model/src/the_main_loop.F) and
1194        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
1195        and klockey should be checked by a specialist)
1196      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
1197        and update lab_sea after previous changes in pkg/seaice below
1198    o pkg/autodiff:
1199      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
1200        viscFacInAd : run time parameters allowing for adjoint switches
1201        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
1202    o pkg/ecco:
1203      - introduce cost_gencost_boxmean.F that computes a box mean
1204        temperature (for use in adjoint sensitivity studies).
1205    o model/src/set_defaults.F : initialize viscFacAdj to 1.
1206    o pkg/mom_common/mom_calc_visc.F:
1207      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
1208    o pkg/seaice/seaice_summary.F:
1209      - statement for SEAICEadjMODE now in autodiff_readparms.F
1210    o pkg/seaice:
1211      - remove some store directives and add new ones in an effort to get
1212        finally rid off the recomputation warnings. This is successful
1213        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
1214        defined (i.e. no extensive recomputation warnings left), but there
1215        are still too many recomputations on the solver iteration level
1216      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
1217      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
1218        SEAICE_SIZE.h
1219      - add a store directive in S/R seaice_calc_viscosities
1220    o pkg/seaice (ITD code):
1221      - fix definition of Hlimit for multi-threaded case
1222      - use double precision arithmetic to compute Hlimit: this affects results;
1223        update output of experiment seaice_itd.
1224    o replace content of verification/seaice_itd
1225      - instead of a 1D column use the configuration of offline_exf_seaice
1226        to test the ice thickness distribution code with ridging
1227      - this is a first shot at this experiment
1228      - change of some defaults of ridging parameters SEAICEhStar (from
1229        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
1230        and lot of new comments.
1231    
1232  checkpoint64y (2014/06/20)  checkpoint64y (2014/06/20)
1233  o pkg/seaice/seaice_reg_ridge.F:  o pkg/seaice/seaice_reg_ridge.F:
1234    - modify the regularization of very small volumes of ice; only check    - modify the regularization of very small volumes of ice; only check
Legend:
Removed from v.1.2008  
changed lines
  Added in v.1.2222
  ViewVC Help
Powered by ViewVC 1.1.22