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revision 1.2032 by jmc, Sun Jul 27 18:04:14 2014 UTC revision 1.2262 by mlosch, Mon Aug 22 14:38:37 2016 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/ptracers: add Bruno Deremble's code to complete the linear surface
8      correction for tracer conservation
9    
10    checkpoint65y (2016/07/29)
11    o pkg/debug (stats):
12      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
13        proc/thread mapping);
14      - fix Min & Max for case where 1 thread has only empty tiles;
15      - use RL variable to count number of wet grid points (with big domain,
16        can be too large to fit into integer*4).
17    o pkg/monitor:
18      - use RL variable to count number of wet grid points (but used only for del2)
19      - add new routine to compute Advective CFL within tracer time-stepping with
20        writing delayed until next monitor output.
21    o pkg/obcs:
22      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
23    o pkg/dic & seaice:
24      - fix compilation of ocean component for coupled atm+ocn model with
25        seaice dynamics & dic.
26    
27    checkpoint65x (2016/06/11)
28    o add a license text file in main MITgcm tree.
29    o added pkg/bling:
30      - intermediate complexity biogeochemical model
31      - see bling_description.txt for details
32      - verification experiment is global_oce_biogeo_bling (for now, in
33        Contrib/verification_other/); tested daily on baudelaire with gfortran.
34      - add entry point in pkg/gchem for new pkg "bling".
35    o pkg/seaice: fix tensile stength computation
36      - replace global field tensileStrength by tensileStrFac
37      - tensileStrFac can be computed once in S/R seaice_init_varia
38      - fortunately that does not affect any verification results
39    
40    checkpoint65w (2016/05/12)
41    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
42         with ECCO_CTRL_DEPRECATED defined
43    o verification/global_ocean.cs32x15:
44      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
45        with "selectNHfreeSurf=1".
46    o model/src (non-hydrostatic free-surface):
47      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
48        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
49      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
50        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
51        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
52        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
53      - Update output (changes at machine truncation level) of verification exp:
54        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
55        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
56    o pkg/seaice: ITD code
57      - fix picking up from a single category model by initialising
58        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
59      - split a long warning message in seaice_check_pickup.F into two lines,
60        because NEC SX-ACE cannot deal with the long line.
61    o model/src:
62      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
63    o pkg/seaice:
64      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
65    o pkg/seaice:
66      - add basal stress as parameterisation for grounding ice
67        following Lemieux et al. (2015)
68      - turn on by setting new parameter SEAICEbasalDragK2 to a value
69        larger than 0. Lemieux et al. (2015) recommend 15.
70      - The adjoint complains with extra recomputations so there is also a
71        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
72        order to postpone the problem
73      - compile the new code in lab_sea
74    o verification/halfpipe_streamice:
75      - update both TAF and OpenAD adm output (machine truncation differences)
76    
77    checkpoint65v (2016/04/08)
78    o verification/advect_xz:
79      - increase overlap size from 3 to 4 and add new secondary test for PQM
80        advection scheme (with mono & wino limiter).
81      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
82    o model/src:
83      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
84        added phi0Ref) to set vertical axis origin and phiRef origin;
85        keep Ro_SeaLevel for backward compatibility (with a warning).
86       According to coordinate and fluid type:
87        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
88        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
89        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
90        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
91      - remove Ro_SeaLevel from ATM experiment parameter files;
92      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
93        complement; update output.txt (changes at machine truncation level).
94    o pkg/seaice/seaice_evp.F
95      - simplify computation of deltaZ and zetaZ to simple averaging following
96        Bouillon et al. (2013). This removes a lot of code, but also changes
97        verification experiment lab_sea.hb87 -> updated
98    
99    checkpoint65u (2016/03/14)
100    o pkg/generic_advdiff:
101      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
102        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
103        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
104        testing and not for actual use.
105    o model/src:
106      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
107        origin r = rF(1);
108      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
109        in EOS for height coordinate: enable to include NH Pressure or to use
110        more accurate pressure vertical profile; options not linked to EOS type
111        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
112      - start to implement variable gravity (along vertical): for now, only with
113        z-coords (not even z*).
114      - add Ideal Gas equation of state for height coordinate.
115      - update OpenAD output (affected at machine truncation level) of exp:
116        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
117    o pkg/exf:
118      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
119        of exf interpolation (before any rescaling, rotation or interpolation
120        to velocity point) for each field that gets loaded from file. This option
121        identically mimics the input file organization (e.g. record numbers in year
122        by year input files) besides the change in horizontal grid.
123      - add rotateStressOnAgrid run-time switch so that wind stress fields
124        can be provided on the A-grid in zonal/meridional direction and
125        rotated on the fly. This only applies to the case when the exf
126        interpolation is off and rotateStressOnAgrid is false by default.
127    o model/src:
128      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
129        it's also used with pkg/atm_phys) and add few more parameters (but still
130        inactive, src code yet to come)
131    
132    checkpoint65t (2016/02/10)
133    o pkg/atm_phys:
134      - from Ruth Geen: add optical depth dependence on CO2 concentration.
135    o model/src:
136      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
137        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
138        Update output of exp. deep_anelastic (changes at truncation level).
139    o tools:
140      - add a hack in "remove_comments_sed" (used only with TAF) for recent
141        version of OpenMPI (shipped with FC.23): comment out the new header
142        file "mpif-sizeof.h" which causes problems to TAF.
143    o pkg/seaice:
144      - change the termination criterion so that maxits (SEAICElinearIterMax)
145        has an effect
146      - unify iteration parameters for implicit solvers (JFNK and Picard)
147        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
148        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
149        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
150        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
151        SEAICEnonLinTol     replaces JFNKgamma_nonlin
152      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
153      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
154        use with SEAICEuseKrylov
155    o pkg/seaice/seaice_lsr.F
156        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
157        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
158        an effect.
159    o pkg/seaice: add two new parameters
160      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
161        parameter is not in any namelist)
162      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
163        a preconditioner for the non-linear Newton iteration of the JFNK
164        solver
165    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
166      affects some experiments at truncation level:
167      - global_ocean.cs32x15.icedyn (11 digits),
168      - global_ocean.cs32x15.seaice (11 digits),
169      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
170      - also update global_ocean.cs32x15 adjoint and tangent-linear results
171    o pkg/salt_plume & pkg/thsice:
172      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
173        connect salt_plume flux to ATM-OCN coupling pkgs interface:
174       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
175         export to coupler interface) even without compiling pkg/salt_plume ;
176       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
177         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
178    o pkg/dic:
179      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
180        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
181        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
182      - move also update with values from ATM-OCN Coupler in the same new S/R
183        (previously done in ocn_apply_import.F).
184    o tools/adjoint_options:
185      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
186        has been changed on Jan 14, 2016.
187    o pkg/ggl90:
188      - add alternative discretisation of vertical shear (off by default), to
189        compute the mean (@ grid-cell center) of vertical shear compon instead of
190        vertical shear of mean flow (@ grid-cell center).
191      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
192        results on adjacent faces of cubed-sphere grids; this fix the restart.
193    o pkg/atm_compon_interf:
194      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
195        pass last value, stored directly before export to CPL ;
196        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
197      - remove atmSLPr from pickup files (no longer needed for restart)
198    
199    checkpoint65s (2016/01/13)
200    o eesupp & genmake2:
201       - first check for Function ETIME and, if it fails, then check for subroutine
202         ETIME and consistent output; use the appropriate version in timers.F
203    o model/src:
204      - to check restart test, add option to apply EXCH to U,V earlier, just before
205        integr_continuity; turned off by default.
206    o pkg/dic:
207      - remove CPP option USE_ATMOSCO2 (not needed)
208    o tools/tst_2+2:
209      - try to ignore difference between +0 and -0 in binary file, causing test
210        to fail for no good reason.
211    o eesupp & genmake2:
212      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
213        but also check (in genmake2) that test runs and returns meaningful results.
214    o coupler pkgs:
215      Finish implementation of optionally-exchanged variable switches (started on
216       Nov 12) with addition of few more exchanged fields, including 2-way exchange
217       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
218       advection in OCN component; this requires sequential coupling.
219      coupler (pkg/atm_ocn_coupler):
220      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
221        routines (useful for debug).
222      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
223         flux, DIC fields) if corresponding switch is ON.
224      - add option to export RunOff to OCN (to use for DIC river input)
225      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
226      components (pkg/atm_ & ocn_compon_interf):
227      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
228        optionally exchanged fields; add a check & stop in cpl_readparms.F.
229        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
230        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
231      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
232        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
233      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
234      - hold in common block coupler optionally-exchanged variable switch
235        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
236      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
237        this is intended to replace the OCN cplFldtave.* output files (not updated
238        to contain new additional exchanged fields).
239    o pkg/dic:
240      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
241    o pkg/thsice:
242      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
243        and writing of thsice pickup files.
244    o pkg/atm_compon_interf:
245      - move all field individual export-call out of cpl_export_import_data.F
246        into new S/R ATM_EXPORT_FIELDS
247    o pkg/atm_compon_interf:
248      - store state variables (for now, only thSIce fields) just before beeing
249        exported (in cpl_export_import_data.F, like on ocean side) instead of from
250        atm_store_my_data.F like all exported fluxes.
251      - new version of pickup_cpl: write field names into meta file and read meta
252        file to find field postion in pickup. Also only write/read fields meeded for
253        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
254    o pkg/dic:
255      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
256    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
257        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
258        value can be from domain [0,1] to average between the two methods
259    o pkg/atm_phys:
260      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
261        hold fixed in time).
262    
263    checkpoint65r (2015/12/21)
264    o pkg/seaice:
265        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
266        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
267    o pkg/seaice:
268      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
269        when SEAICEscaleSurfStress=.TRUE.,
270      - apply areaW and areaS in S/R seaice_calc_lhs
271    o pkg/atm_phys:
272      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
273        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
274        for individual contribution (convection, LSC cond, radiation)
275      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
276        information); activated with: solar_exponent=0. and wv_exponent=-1.
277    o pkg/ggl90:
278      - within IDEMIX add upper limit for horizontal group velocity to
279        avoid instability problems in the explicit horizontal diffusion term for
280        long time steps or high resolution
281    o pkg/diagnostics:
282      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
283        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
284    o testreport:
285      - remove "-v" (verbose option) in default mpirun command.
286    o pkg/seaice/seaice_growth:
287      - catch potential division by zero in ITD code, does not change
288        verification results
289    o pkg/ecco:
290      - retire old codes to the Attic. The calls to retired functions are
291        left in a commented form in case they ever need to be re-activated.
292      - ecco_check.F: issue warning if any old CPP option is
293        defined that corresponds to retired codes -- then stop.
294    o pkg/atm_compon_interf:
295      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
296        coupler: use last time-step value instead of average over cplSendFrq_iter
297        time-step, similar to what is done for seaIceMass.
298        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
299    o eesupp & genmake2:
300      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
301        <= remove until a fix is found for some ifort version on ia32 machine.
302    o pkg/seaice/seaice_evp:
303      - refine residual computation
304    
305    checkpoint65q (2015/11/18)
306    o pkg/seaice/seaice_evp:
307      - fix residual computations so that they no longer affect the actual
308        simulation code
309      - fix seaice_readparams to be able to actually set new parameters
310        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
311    o model/src:
312      - fix wrong truncation (single prec) from "FLOAT" function in expressions
313        like: deltaT*FLOAT(myIter) when myIter is large:
314         a) replaced by DFLOAT (if not seen by TAF);
315         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
316    o pkg/aim_v23:
317      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
318        when pickupSuff is set ; do write rolling pickups + at the end of the run.
319    o pkg/atm_ocn_coupler + ocn_compon_interf:
320      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
321        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
322        add corresponding call in DO_OCEANIC_PHYS.
323    o coupler pkgs:
324      Start a new way to set-up optionally-exchanged variables (previously, only
325       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
326       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
327       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
328       compononent param default can be set accordingly).
329      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
330       but rather applies to a group a fields (going both ways like for DIC)
331       and corresponds to an option of coupling config.
332      coupler (pkg/atm_ocn_coupler):
333      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
334        and read namelist directly (without eessup S/R calls) instead of
335        in the very un-flexible old way, 1 param per line, in fixed order;
336      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
337        cleanly in CPL_CHECK_CPLCONFIG
338      - add new coupling-exchange selectors (some not yet active) including
339        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
340                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
341      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
342        component ; called directly from coupler.F, after comp. registrations;
343      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
344         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
345          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
346      components (pkg/atm_ & ocn_compon_interf):
347      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
348        CPP header file in all pkg source files.
349      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
350        ATM/OCN_CHECK_CPLCONFIG;
351      - add error-counter to track errors (e.g., in "data.cpl") and to stop
352        cleanly in ATM/OCN_CHECK_CPLCONFIG;
353      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
354        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
355        before PACKAGES_READPARMS;
356      verification/cpl_aim+ocn/:
357      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
358        "data.cpl" for coupler (in input_cpl).
359    o eesupp/inc:
360      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
361        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
362        to always cumulate tile local-sum in the same order (still uses
363        MPI_Allreduce like standard code).
364      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
365        that are now identical to standard version (in eesupp/inc).
366    o pkg/shelfice:
367      - add SHELFICETransCoeffTFile for initializing spatially varying
368        heat and salt transfer coefficients
369    o pkg/atm_compon_interf & ocn_compon_interf:
370      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
371        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
372      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
373    o pkg/atm_ocn_coupler:
374      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
375    o pkg/rbcs:
376      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
377        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
378      - add a short report (to STDOUT) about RBCS-mask settings.
379    
380    checkpoint65p (2015/10/23)
381    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
382        there is no adjoint test for EVP, we don't know what it does to the adjoint
383        solution, but at least there are no more recomputation warnings left
384    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
385        a chance of giving the same results as a fully converged VP (JFNK) solver
386    o tools/adjoint_options/adjoint_diva:
387      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
388    o pkg/streamice:
389      - spotted bug in streamice_driving_stress using dyG where should have been dxG
390    o pkg/exf:
391      - remove STOP statement that prevented to use wind or (wind-)stress
392        interpolation for constant-in-time forcing fields (wind/stress period = 0).
393    o pkg/seaice:
394      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
395        5 additionals 2D fields and 6 new store directives
396      - change logic in seaice_readparms.F: EVP code can now be turned on in
397        various ways, setting SEAICE_deltaTev is no longer required,
398        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
399        or SEAICEaEVPcoeff
400    o pkg/shelfice/shelfice_thermodynamics.F
401      - redefining uLoc/vLoc to u/v, instead of 2u/v
402    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
403      - this is an intermediate state of a truely converging EVP that has
404        the potential of outperforming implicit VP methods, I do not recommend
405        using it yet.
406      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
407        and all parameters are hardwired
408      - for convergence it still requires very smooth regularisations, that means,
409        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
410        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
411        specific averaging appears to be required, still subject to tuning
412      - still needs cleaning and I need to turn parameter into runtime parameters
413      - add code to compute and print residuals of iteration, compile with
414        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
415    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
416      that entered with r1.54 on Sep04, 2015, -> update results
417    
418    checkpoint65o (2015/09/14)
419    o pkg/mom_vecinv & mom_common:
420      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
421        called from there.
422      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
423        allows to use Vector-Invariant form in deep atmos and anelastic formulation
424    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
425      and Koenig-Beatty+Holland (2012)
426      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
427      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
428      - requires an extra input argument for S/R seaice_calc_viscosities
429      - tensileStrength's depth dependence is different from Itkin et al. (2015)
430        (to be changed and played with, for now exponential)
431    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
432      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
433        by AREA according to Connelly et al. (2004), JPO.
434      - For EVP and the LSR solver, the implicit part of the drag term is
435        the only non-zero term in the denominator when there is no ice (which
436        prevented running the model with zero ice-ocean drag). If
437        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
438        (or zero main diagonals BU/BV) which need to be caught. A practical
439        consequence is that for open water, the momentum equation reduce
440        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
441        they happen to be zero, often leading to a non-zero solution over
442        open water.
443    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
444        efficient EVP method.
445      - introduce area-weighted averages for e12 (analogously to
446        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
447        remain, but also changing the order of terms in the previous average
448        changed the results as much) -> update experiment
449      - add SEAICE_DELTA_SMOOTHREG code
450      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
451        TEM-code
452      - adjust loop bounds so that only required fields are computed
453      - add new averaging code for zetaZ/deltaZ (again similar to
454        seaice_calc_viscosities.F), inactive by default for now (will change
455        results again), but will replace old code eventually
456    o eesupp/src:
457      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
458        to always cumulate tile local-sum in the same order
459        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
460        Still uses MPI_Allreduce (like standard code) but on array of tiles
461        and should be faster than GLOBAL_SUM_SEND_RECV code.
462      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
463        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
464      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
465         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
466         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
467         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
468         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
469    
470    checkpoint65n (2015/07/29)
471    o pkg/thsice:
472      - add a warning when used with pkg/aim but without updating SST
473        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
474    o pkg/offline:
475      - change where Offline-Fields are loaded, from load_fields_driver.F to
476        directly within FORWARD_STEP, just after updating iter number and time;
477      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
478        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
479       These changes allow:
480        a) to recover exactly on-line results using deltaToffline=deltaTClock,
481        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
482        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
483        time-step, both with GM & KPP files and with recomputing these fields;
484        b) no needs to switch on staggerTimeStep anymore;
485        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
486      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
487    o pkg/offline:
488      - change (rarely used) offset-iteration parameter to an offset time (in s):
489        can easily recover previous offset-iter effect by setting offset-time
490        (offlineTimeOffset) to offset-iter x deltaToffline;
491      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
492        in KPP as part of surface buoyancy forcing) in offline run.
493      - fix ptracers KPP non-local term in the case where KPP is re-computed.
494    o OpenAD
495      - Adding preliminary ggl90 test to OpenAD verification.
496        Config. with ggl90 currently diverges after 64 time steps
497        so will need more work to become more stable
498      - Adding preliminary kpp test to OpenAD verification.
499        required small tweakes in kpp_routines.F
500      - Merge and update from Krishna Narayanan's contrib area:
501        * Add one variable for preliminary OpenAD DIVA
502        * Add replacement time-stepping for OpenAD DIVA
503        * genmake2 flag -diva (but only for OpenAD; preliminary)
504        * required modifs for OAD_support
505        successful preliminary test for tutorial_global_oce_biogeo/
506    o pkg/seaice:
507      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
508      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
509        delta with a smooth function in s/r seaice_calc_viscosity
510        (no effect on EVP)
511      - rename local suffix "sqr" into "sq" for more consistent variable names
512    o pkg/seaice:
513        add new parameter SEAICE_deltaMin that is used ***only***
514        for regularizing Delta (and nothing else, like the parameter
515        which is also used for all sorts of things SEAICE_EPS).
516        Defaults to SEAICE_EPS for backward compatibility only.
517    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
518        the wrong key by inialising it before use -> fixes a recomputation
519        problem but does not fix the gradient
520    o pkg/layers:
521      - move resetting of flux arrays to outside the iLa loop
522        (this caused layers_diapycnal to not work with more than one layer coord.)
523      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
524    o pkg/layers:
525      - remove from common block 3D layers fields (used to diagnose transport
526        in tracer coords) and declare them as local arrays in layers_calc.F
527    o pkg/seaice:
528      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
529        in lab_sea forward experiment (changes results -> updated)
530      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
531    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
532       computations; for SEAICE_VECTORIZE_LSR
533      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
534        sweep to the outside,
535      - remove store directives and add "CADJ loop sequential" directives
536        in analogy to model/src/solve_tridiagonal.F
537      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
538        boundaries to yield more readable code. This has also the charming side
539        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
540        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
541        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
542        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
543        an additional option)
544       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
545       but the adjoint gradients (which are affected by this change) still explode.
546    o coupler (atm & ocn _compon_interf):
547      - avoid using Exch2 IO mapping if not suitable.
548    
549    checkpoint65m (2015/06/15)
550    o pkg/layers:
551      - clean-up old parameters setting (from Sep 2012):
552        + remove old parameters setting from common block (declared locally);
553        + stop if any old parameter is mixed with new parameters;
554        + check for valid or consistent parameter setting (e.g., layers_name)
555      - check that layers_bounds for Pot.Density are in the right range;
556        this is supposed to catch un-updated setting after recently shifting
557        potential density field "prho" by -1000 (now in "sigma" scale).
558    o pkg/layers:
559      - Added missing call to layers_fill for keeping track of tottend in
560        pkg/diagnostics/diagnostics_fill_state.F
561    o pkg/layers:
562      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
563        of diapycnal fluxes
564    o pkg/layers:
565      - reverted changes to interpolation to previous treatment; there
566        was never actually a problem
567    o pkg/layers:
568      - fix interpolation of layers tracers in the presence of partial cells
569      - add lots of new functionality to compute water mass transformation
570        (enabled by CPP flag LAYERS_THERMODYNAMICS)
571      - add new calls from main code (diags_oceanic_surf_flux.F,
572        thermodynamics.F, impldiff.F) and gad to save the necessary fields
573        for layers_thermodynamics calculations
574    o pkg/ptracers:
575      - add capability of stepping a passive tracer forward without advection
576        by setting PTRACERS_advScheme to 0.
577    o pkg/diagnostics:
578      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
579    o pkg/layers:
580      - shift potential density field "prho" by -1000 for density layer averaging so
581        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
582        Note that density bin boundaries (layers_bounds in data.layers) have
583        to be set accordingly (i.e., shifted, in sigma scale).
584    o pkg/layers:
585      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
586      - fix calculation of layer non-weighted velocity and layer probability
587      - add diagnostics for pot.density used for layer averaging
588    o pkg/seaice:
589      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
590        positiveness, modify a few comments and improve variable names,
591      - the changed computation of deltaC affects most seaice-related
592        experiments at the truncation level.
593        seaice_itd.thermo is affected by far the most, with
594        only 7 digits of agreement remaining; update experiments.
595    
596    checkpoint65l (2015/05/04)
597    o pkg/shelfice:
598      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
599        factor drKp1 to zero where it is negative (ie. do not use
600        SHELFICEBoundaryLayer if hFacC>1)
601      - the same for factor drLoc in shelfice_forcing.F
602    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
603        with modules in ptracers, when using testreport option "-small_f"
604    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
605      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
606    o verification/testreport
607      - add new option -small_f
608        with this option testreport first makes the target small_f (*.f files)
609        before running make (all). This is useful for explicit inlining when
610        all sources need to be full available.
611    o pkg/exf/exf_interp.F:
612        remove previous changes related to reverse (decreasing) input grids latitude
613    
614    checkpoint65k (2015/04/01)
615    o pkg/ecco:
616        fix missing cosphi initialization; use eccoiter in place of optimcycle;
617        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
618        instead of active read/write
619    o pkg/ctrl:
620        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
621        instead of active read/write.
622    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
623        return if .NOT.useAUTODIFF
624    o pkg/seaice: add CPP brackets (cost function related).
625    o model/src:
626        add useAUTODIFF run time switch.
627    o pkg/exf/exf_interp.F:
628        add code to allow input grids with latitude starting in the north (i.e. when
629        j=1 corresponds to northern edge of field); modify global_with_exf to test
630        this feature.
631    o verification/testreport:
632      - replace "grep -A3" with POSIX conformal sed command, because there are
633        implementations of grep that cannot do contextual searches
634      - replace "cat -n" by "nl" (two occurrences), because not all implementations
635        of "cat" have the option "-n"
636    o model/src:
637        add new file gsw_teos10.F that contains 3 functions, more or less a copy
638        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
639        convert from conservative to potential temperature. For now they are not
640        called anywhere.
641    o pkg/ggl90: make "useIDEMIX" useful
642      - re-organize code in s/r ggl90_calc a little to move computations that
643        are different for idemix into separate loops (changes verification
644        experiment idemix at truncation level, 12 digits remain -> updated)
645      - requires 2 new 2D fields KappaM, verticalShear
646      - make hFacI and recip_hFacI local 3D variables that are passed to
647        s/r ggl90_idemix
648      - fix and improve some comments
649    
650    checkpoint65j (2015/02/25)
651    o pkg/openad
652      - synchronize seawater.F with version in model/src: replace routine
653        body of sw_temp by calling sw_ptmp and fix/add a few comments.
654    o pkg/mnc:
655      - change default value of pickup_read/write_mnc params to FALSE
656        (since few features are missing in reading MNC pickup files).
657    o model/src:
658      - change default (background) vertical diffusivity for salt to be the
659        temperature (background) vertical diffusivity.
660      - change background vertical diffusivity in vertical mixing pkgs ggl90,
661        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
662        This makes ptracers default diffusivity (that uses salt diffKr) more
663        consistent with vertical mixing schemes.
664    o verification/testreport:
665      - fix typo in "-pcls" option ;
666      - put temp files in /tmp (instead of in local dir)
667      - add option "-ncad" to use genmake2 new option "-nocat4ad"
668      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
669    o pkg/ggl90 (idemix code):
670      - apply few fixes ; add some missing "_d 0" ; update output of exp.
671        global_ocean.90x40x15.idemix
672    o OpenAD
673      - enable active file I/O and begin removal of work-around code
674        for OpenAD for handling control variables (memory vs. active files)
675      - new CPP options file OPENAD_OPTIONS.h
676      - revert to genarr2d gradient check for hs94.1x64x5
677      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
678      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
679    o tools/genmake2:
680      - add option for an alternative Makefile (from Martin) where multiple
681        source files are sent to TAF (instead of all in one file).
682    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
683      - code provided by Carsten Eden as an extension of ggl90
684      - so far the code is turned on within ggl90 by setting a CPP-flag at
685        compile time; a runtime flag implementation is not yet complete
686      - tested in new verification experiment global_ocean.90x40x15.idemix
687    o verification:
688      - reduce length of the AD test run by half for experiments
689        global_ocean.cs32x15 (std + thsice) and isomip
690      - enable active file I/O for OpenAD, adjust verifications accordingly
691      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
692    o verification/testreport:
693      - fix two non-POSIX sed statements so that there are no error messages
694        on Mac OS X
695      - replace hostname -s with hostname | sed 's/\..*$//'
696    o model/src/seawater.F:
697      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
698        (following the matlab code), which would have avoided the bug caught
699        by Matt (see below) in the first place
700    o pkg/shelfice:
701      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
702        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
703      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
704        ice-shelf case (i.e., within surface level).
705      - add config summary in shelfice_check.F
706      - remove global variable recip_SHELFICElatentHeat and replace by a local
707        variable recip_latentHeat
708      - introduce diagnostics for friction velocity uStar (in case of
709        SHELFICEuseGammaFrict)
710      - change verification experiment isomip.htd:
711        + start from pickup (as input_ad at nIter0=8640)
712        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
713        + test SHELFICEuseGammaFrict = .TRUE.
714        + test SHELFICEadvDiffHeatFlux = .TRUE.
715    o model/src:
716      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
717        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
718        update output of experiments global_with_exf.yearly and isomip (all 6).
719    o pkg/shelfice:
720      - change setting of kTopC to also be zero where there is no ice-shelf.
721      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
722        ice-shelf is.
723      - first attempt to get RealFreshWaterFlux effects: for now, only without
724        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
725    o pkg/seaice: add the option to prescribe a fixed thickness PDF
726      for thermodynamic calculations
727      - because of divisions of the type 7/7 not exactly equal to 1, this change
728        affects results of some verification experiments by up to 4 digits:
729        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
730        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
731        adjoint: lab_sea, lab_sea.noseaicedyn
732        -> updated
733    
734    checkpoint65i (2015/01/23)
735    o model/src:
736      - change units of frictionHeating field from W to W/m^2
737      - fix bug in frictional heating from stratospheric drag in
738        S/R ATM_PHYS_TENDENCY_APPLY_V
739      - with synchronous time-stepping: move resetting to zero of frictionHeating
740        field from load_fields_driver.F to thermodynamics.F ;
741      - add diagnostics for frictional heating.
742    o model/src & gmredi K3D:
743      - add frictionHeating field to pickup-files (for synchronous time-stepping)
744      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
745      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
746        and name in pickup file).
747      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
748    o model/src:
749      - move (from ini_forcing.F) initialisation of all arrays in header file
750        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
751        (since Nov 2012) with option selectAddFluid=1.
752    o pkg/shelfice:
753      - change units (+ document) of newly added field "shelfIceMassDynTendency"
754      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
755    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
756    o pkg/seaice: two new runtime parameters:
757      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
758        long overdue
759      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
760        parameterization of tensil stress for fast ice (does not do anything yet)
761    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
762        for LSR: move checking overlaps out of JFNK-if-block
763    o pkg/atm_phys:
764      - move copy of grid and dynamical fields out of atm_phys_driver.F into
765        new S/R ATM_PHYS_DYN2PHYS.
766      - fix level height for Linear Free-Surf case (to be consistent with
767        fixed-in-time pressure levels).
768    o pkg/mom_common (bottomdrag):
769      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
770        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
771        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
772    o pkg/shelfice (u/v_drag):
773      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
774      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
775        (now similar to shelfice_u_drag.F)
776      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
777        from mom_vecinv.F (similar to mom_fluxform calls).
778    o pkg/mom_common (bottomdrag):
779      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
780      - add options for alternative discretisation of velocity norm in quadratic
781        bottom drag: averaging of grid-cell-center KE to U.point and V.point
782        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
783        improves when averaging only the other component (e.g. vVel for U bottom
784        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
785      - add options (bottomVisc_pCell) to account for partial-cell in bottom
786        friction (no-slip BC) thus getting the true distance from the bottom;
787        off by default since this also reduces model stability (explicit bottom
788        friction). Changes produce different machine truncation with linear-drag
789        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
790        front_relax (bvp & mxl, 10 & 11 digits).
791    o model/src & mom pkgs:
792      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
793        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
794      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
795        just copy level Nr value to level Nr+1.
796    o doc:
797      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
798    o pkg/shelfice:
799      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
800        SHELFICE.h: move array shelficemass to init_varia, initialise
801        from array shelficemassinit, which is set in init_fixed and
802        has option to be set from file; introduce array
803        shelficeMassDynTend array, set thru file in init_fixed
804      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
805        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
806        pkg/streamice
807      - shelfice_thermodynamics.F: call shelfice_step_icemass if
808        SHELFICEMassStepping = .true.
809      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
810    
811    checkpoint65h (2014/12/17)
812    o verification/global_ocean.90x40x15, global_ocean_ebm:
813      - update to generic controls.
814    o pkg/ctrl:
815      - ctrl_map_ini_genarr.F: test for igen>0
816      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
817      - move gentim2d part of ctrl_map_ini_genarr.F to
818        new separate routine : ctrl_map_ini_gentim2d.F
819      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
820        add time variable weights and cyclic controls (time mean,
821        seasonal cycle, etc) capabilities to gentim2d
822    o pkg/ecco:
823      - move reading of error, conversion to weights from
824        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
825    o global_oce_llc90, cs32:
826      - activte sbo.
827      - CTRL_SIZE.h : add maxCtrlProc.
828      - activate the new genctrl capabilities.
829      - update following reorganization of global_oce_input_fields.tar.gz  
830    o pkg/ctrl/ctrl_ad_diff.list:
831      - add missing ctrl_init_rec.f
832    o tools/OAD_support/keepOriginal:
833      - add ctrl_init_rec.F
834    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
835      - avoid recomputations of xx_gentim2d_dummy.
836    o momentum diagnostics:
837      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
838        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
839    o pkg/seaice/seaice_lsr.F:
840      - fix computation of BU/BV, make sure they are non-zero, only necessary
841        for cubed sphere exchanges and SEAICE_OLx/y>0.
842        This makes calling s/r fill_cs_corner_rl obsolete (removed).
843    o verification/global_ocean.cs32x15/input.seaice
844      - add test for strong implicit coupling and restricted addtive Schwarz
845        methods for LSR
846      - update results/output.seaice.txt
847    o verification/tutorial_global_oce_biogeo:
848      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
849        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
850        update output_adm,_oadm,_tlm.txt
851    o pkg/dic:
852      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
853      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
854        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
855    o verification/tutorial_global_oce_biogeo:
856      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
857        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
858        update output_adm,_oadm,_tlm.txt
859    o eesupp/src:
860      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
861        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
862    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
863      LSR (following Hutchings et al. 2004)
864      - introduce zetaZ as a global variable (requires adjustments in
865        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
866        in seaice_calc_viscosities.F
867      - new flag SEAICEuseStrImpCpl (default off)
868      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
869        momentum equations
870      - JFNK-solver (preconditioner) adjusted to allow using this method
871        (where it does not have any positive effect)
872    o pkg/seaice
873      - add overlap for restrictive additive Schwartz method also to LSR, but
874        turn it off by default (because it only seems to work for non-cubed
875        sphere/llc topologies)
876    o pkg/autodiff
877      - add extra exchanges in addummy_in_steppging also for mnc output
878    o pkg/seaice:
879      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
880        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
881    o pkg/obcs:
882      - add option to specify domain-connected piece Id along OB though files
883        (for now, only used to diagnose PhiVel; default =1 -> global correction)
884      - modify obcs_diag_balance.F to process each connected-part separately;
885        exclude OB where Id = 0 but keep the full divergence there (-> constant
886        Psi along this portion of OB and all inflow derived from grad(Phi))
887      - add example of OB-conect files in verification/so_box_biogeo/input.
888    o pkg/diagnostics:
889      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
890      a) use non zero matrix element across OB and solve for Phi 1 grid point
891         outside OB (i.e, where tracer OBCS are applied).
892      b) global imbalance of inFlow/outFlow across OB: instead of modifying
893         velocity across OB, spread it uniformly along the OB in the RHS.
894    
895    checkpoint65g (2014/11/19)
896    o pkg/diagnostcis:
897      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
898    o pkg/my82,pp81,kl10:
899      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
900        field diffKr as background diffusivity to set minimum diffusivity value.
901    o pkg/seaice:
902      - add new parameter SEAICEuseEVPrev (for revisited EVP by
903        Bouillon et al 2013)
904      - add SEAICE_evpAlpha/Beta to namelist
905      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
906        involve trivial re-ordering of divisions/multiplications that should not
907        have any effects, but ... they do change the results of lab_sea.hb87 so
908        that only 2 digits of agreement remain, in line with the general
909        instability/fragility of the evp-code. For now, I do not care and just
910        update the verification experiment
911    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
912      - remove xx_genarr2d_numsmooth etc
913      - use xx_genarr2d_preproc etc instead
914      - carry out smooth_correl2D at initialization stage rather than during
915        time stepping.
916      - get smoothOpNb from xx_gentim2d_preproc
917    o global_oce_cs32 :
918      - add test of generic ecco capabilities.
919    o pkg/exf/exf_getsurfacefluxes.F :
920      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
921    o pkg/ctrl,ecco :
922      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
923        is defined.
924    o pkg/seaice: add diagnostics for Delta (deformation parameter)
925    o model/src:
926      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
927        diffusivity (background) is specified but ignored.
928    o verification:
929      - in testreport, convert hostname to lower case for default output dir name
930    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
931    o pkg/dic: add modifications from Hajoon:
932      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
933      - light attenuation: add self-shading effect by climatological Chlorophyll
934        (read from file).
935    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
936        compiles when SEAICE_ALLOW_DYNAMICS is undefined
937    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
938        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
939        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
940        approach where CPP_OPTIONS.h includes an omnipotent
941        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
942    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
943        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
944    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
945        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
946        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
947    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
948      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
949      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
950      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
951      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
952    o pkg/ctrl,ecco,exf :
953      - remove variables associated with NON-generic costs,
954        unless ECCO_CTRL_DEPRECATED is defined.
955      - remove NON-generic NON-obcs controls,
956        unless ECCO_CTRL_DEPRECATED is defined.
957    o pkg/ctrl : added ctrl_local_params.h
958    o pkg/ecco : added ecco_local_params.h
959    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
960        experiments, which will progressively be removed once the
961        experiments are revised to use only generic controls/costs.
962    
963    checkpoint65f (2014/10/13)
964    o pkg/ctrl, ecco, seaice : minor changes in headers
965    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
966        cost function and control capabilities added since checkpoint65c.
967    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
968    o pkg/ecco: increase modularity and improve logic
969      - ecco_toolbox.F (new) : basic operations that are often used,
970        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
971        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
972      - cost_gencal.F (new) : determine filnames and records.
973      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
974      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
975        and exploit the above functions leading to more compact code.
976      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
977      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
978        using_ers, using_gfo, using_mdt is now only defined within gencost)
979    o pkg/ecco: extend generic cost capabilities
980      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
981        capabilities via gencost_preproc (+ _c,_i,_r related params),
982        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
983        gencost_outputlevel arguments to cost_generic
984      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
985        and active_read, making room for gencost_preproc to take effect.
986        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
987      - pkg/ecco/cost_generic.F :
988        compute and store misfit maks*(model-data) in localdif that is
989        then used in cost and for output, output misfit if outlev.GT.0
990      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
991        rather gencost_barfile for deciding whether to write barfile
992      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
993      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
994        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
995      - pkg/ecco/ecco_summary.F : report gencost variables
996      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
997    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
998    o pkg/ecco: internal re-organization
999      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
1000        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
1001        mv relevant variables definition from ecco_cost.h to ecco.h,
1002        make sure gencost routines only include ecco.h)
1003      - throughout : add missing CCP switches, rm unused variables,
1004        and rm un-necessary CPP switches
1005      - throughout gencost routines : replace modelstartdate with
1006        gencost_startdate when needed
1007      - cost_bp_read.F : use arguments, instead of common blocs
1008        so that it can be used also by (new) cost_gencost_bpv4.F
1009      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
1010      - ecco_phys.F : compute etanFull
1011      - ecco_readparms.F : rename using_topex as using_tpj, add
1012        bpv4-grace to gencost list, initialize added parameters
1013      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
1014    
1015    checkpoint65e (2014/09/28)
1016    o pkg/obcs:
1017      - replaced the just-added CPP options with run-time variables
1018        (see pkg/obcs/OBCS_PARAMS.h for details)
1019    o pkg/obcs:
1020      - add additional CPP options for sponge boundary layers
1021        (see pkg/obcs/OBCS_OPTIONS.h for details)
1022    o pkg/atm_phys:
1023      - implement simple (obliquity only, assuming circular planet orbit)
1024        seasonal cycle for incoming insolation ; used when run-time parameter
1025        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
1026    o pkg/exf, pkg/ecco, pkg/ctrl:
1027      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
1028      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
1029      - implement gentim2d for xx_tauu, xx_tauv
1030    o pkg/ctrl, pkg/ecco :
1031      - fix and complement the generic controls implementation
1032    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
1033        pkg/shelfice/shelfice_thermodynamics.F,
1034        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
1035        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
1036      - add weight in CTRL_GET_GEN calls
1037    o pkg/ctrl :
1038      - ctrl_get_gen.F : add weight as input parameter, and apply
1039        it directly rather than using smooth_correl2Dw (to be retired).
1040      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
1041    o pkg/ctrl :
1042      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
1043        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
1044      - re-activate ctrl_summary (call in ctrl_init.F)
1045    o pkg/ctrl/ctrl_cost_gen.F :
1046      - fix CCP brackets, remove un-necessary myiter, mytime
1047    o pkg/ecco, pkg/ctrl :
1048      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
1049      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
1050      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
1051      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
1052    
1053    checkpoint65d (2014/09/15)
1054    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
1055      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
1056        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
1057    o pkg/ctrl/ctrl_map_ini_genarr.F :
1058      - remove compilation failure
1059      - replace hard coded example
1060      - use ctrl_map_ini_gen2D, 3D
1061    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
1062      - on/off switch based upon xx_genarr2d_weight,3d
1063    o src/packages_init_variables.F :
1064      - regroup pkg/estimation calls
1065      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1066        (moved to ctrl_init_variables)
1067    o cost/cost_init_varia.F :
1068      - remove ecco_cost_init_varia
1069        (moved to ecco_init_varia)
1070    o ctrl/ctrl_init_variables.F :
1071      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
1072      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
1073    o ctrl/ctrl_map_ini.F :
1074      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
1075        (moved to ctrl_init_variables)
1076    o ctrl/ctrl_map_ini_ecco.F :
1077      - remove ECCO_PHYS (mv to ecco_init_varia)
1078      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
1079    o ecco/ecco_ad_diff.list :
1080      - add ecco_init_varia.f
1081    o ecco/ecco_init_varia.F
1082      - new routine
1083    o pkg/streamice:
1084      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
1085        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
1086      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
1087    o pkg/generic_advdiff:
1088      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
1089    o pkg/exf:
1090      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
1091         xxg_precip capability
1092      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
1093    o pkg/ctrl:
1094      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
1095    o model/src/load_fields_driver.F :
1096      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
1097        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
1098    o OpenAD verification experiments:
1099      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
1100        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
1101        for now, only in pkgs used in OpenAD verification experiments.
1102      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
1103        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
1104        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
1105        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
1106    o OpenAD verification tests:
1107      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
1108      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
1109        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
1110      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
1111        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
1112    o model/src & generic_advdiff:
1113      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
1114        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
1115        dynamics requires valid tracer forcing only over tile interior but, for
1116        some diagnostics, may need to extend it over 1 point in tile halo region.
1117      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
1118        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
1119        setting in temp/salt/ptracer_integrate.F
1120    o pkg/dic:
1121      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
1122        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
1123        in gchem_forcing_sep.F
1124    o pkg/autodiff & obcs:
1125      - add storage of current OB values for U & V (was already done for T & S).
1126    
1127    checkpoint65c (2014/08/30)
1128    o pkg/dic:
1129      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
1130        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
1131        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
1132    o verification:
1133      - new experiment testing OBCS and DIC pkgs, using params & output from
1134        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
1135        passage: take OBCS from the last year of a 2 yrs simulation and initial
1136        conditions from t=1.yr while keeping the same forcing.
1137    o model/src:
1138      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
1139        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
1140    o pkg/diagnostics (Stats-Diags):
1141      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
1142        a) refine region where stats are computed, excluding where arrhFac=0 ;
1143        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
1144        c) extend regional stats over the region edges (for U or V pt location).
1145    o pkg/gchem:
1146      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
1147        pkg/dic is currently changing/updating ptracers values beyond the OB).
1148    o verification (hs94):
1149      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
1150        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
1151        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
1152        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1153    o pkg/ptracers:
1154      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
1155        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
1156      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
1157        with AB-2 code (so that it get tested).
1158    o model/src:
1159      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
1160        with AB-2 code (previously only available with AB-3 code).
1161        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
1162        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
1163        there, by calling CYCLE_AB_TRACER).
1164    o pkg/generic_advdiff:
1165      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
1166        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
1167        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
1168        S/R temp/salt/ptracers_integrate.F
1169    o model/src & pkg/ptracers:
1170      - remove common block variables gT,gS (in DYNVARS.h), except when
1171         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
1172      - remove common block variable gPtr.
1173    o model/src & pkgs:
1174      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
1175         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
1176         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
1177         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
1178      + change accordingly all calling S/R.
1179      - use local temperature/salinity/ptracer tendency array (without bi,bj)
1180        in S/R temp/salt/ptracers_integrate.F
1181    o pkg/seaice:
1182      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
1183        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
1184      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
1185        in seaice_lsr
1186      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
1187        in s/r seaice_lsr_calc_coeffs
1188    o pkg/mdsio:
1189      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
1190        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
1191        too long (e.g., > MAX_LEN_FNAM/2 )
1192    
1193    checkpoint65b (2014/08/12)
1194    o pkg/matrix:
1195      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1196    o model/src:
1197      - fix initialisation of geothermalFile; compile geothermal-flux code in
1198        natl_box verification experiment.
1199    o model/src & pkg/down_slope:
1200      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1201      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1202        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1203        results at machine truncation level: update output of experiments
1204        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1205    o pkg/diagnostics (Stats-Diags):
1206      - do not cumulate the full volume when DIAGNOSTICS_FILL is
1207        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1208        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1209        times (but Min,Max and StD are still wrong).
1210    o model/src:
1211      - add geothermal flux forcing: read in ini_forcing.F as time-constant
1212        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1213    o model/src:
1214      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1215        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1216        arrays are already updated while adjustments (filters, conv.adjustment) are
1217        still applied later, in S/R TRACERS_CORRECTION_STEP.
1218    o model/src:
1219      - store in common bloc array "rhoInSitu" the virtual potential temperature
1220        anomaly that is used to compute geopotential: this make the atmos code
1221        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
1222    o pkg/seaice/seaice_lsr.F
1223      - rename integer variable ilcall to ipass (that's what it is called
1224        in the residual diagnostics
1225      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
1226        default) for improved non-linear convergence of the first few steps
1227      - adjust a few comments and add new ones to explain some of the store
1228        directives
1229    o pkg/generic_advdiff (& ptracers):
1230      - re-work the code to check for valid advection scheme and for minimum
1231        size of overlap (now stored in local common bloc in gad_advscheme.F)
1232    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
1233      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
1234      - add an auxilliary variable "bet" and fix store directives and keys in
1235        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
1236        less exact gradients in my tests); but there are still
1237        recomputation warning (although gradients are sort of OK), when
1238        SEAICE_LSR_VECTORIZE is not defined, so this flag and
1239        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
1240      - update verification experiments lab_sea.
1241      - change some comments in S/R seaice_calc_viscosities
1242    o model/src:
1243      - if staggerTimeStep=T, always apply exchange to velocity field in
1244        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
1245        (independent of using multi-dim advection or not); no effect on FWD run
1246        but affects AD results (at machine truncation level): update output of
1247        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
1248        and isomip (oad: 12.d).
1249    o pkg/generic_advdiff:
1250      - stop if doAB_onGtGs is set to FALSE but ignored
1251      - refine warning related to stability of tracer time-stepping
1252        regarding internal wave dynamics.
1253      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
1254        on staggerTimeStep & implicitIntGravWave (will now get a warning
1255        if potentially unstable).
1256    o pkg/kl10:
1257      - add new pkg "kl10" for mixing due to internal wave breaking, from
1258        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1259        (contribution from Jody Klymak), tested in verification experiment
1260        verification/internal_wave/input.kl10/
1261    o isomip experiment:
1262      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1263        (input.htd) and update the output.
1264    o cd_code experiments:
1265      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1266        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1267        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1268        update the corresponding output.
1269    o pkg/seaice:
1270      - reduce the number of include files and store directives in
1271        S/R seaice_lsr_tridiagu/v
1272      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1273        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1274        get rid off one store directive (a TAF bug?)
1275      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1276        S/R seaice_lsr_tridiagv to change the loop range for consistency
1277      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1278      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1279        S/R seaice_lsr_tridiagu/v (requires update of
1280        offline_exf_seaice/input.dyn_jfnk)
1281    
1282  checkpoint65a (2014/07/27)  checkpoint65a (2014/07/27)
1283  o model/src:  o model/src:
1284    - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than    - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
# Line 18  o model/src: Line 1293  o model/src:
1293    - collect T & S forcing tendency into local 2-D array (passed as argument to    - collect T & S forcing tendency into local 2-D array (passed as argument to
1294      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1295      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
1296      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1297      moist correction due to vertical advection).      correction due to vertical advection).
1298    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1299      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1300      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
# Line 48  o pkg/seaice: more clean up Line 1323  o pkg/seaice: more clean up
1323      nearly a factor of 10 (but keep in mind there is mostly seaice code in      nearly a factor of 10 (but keep in mind there is mostly seaice code in
1324      this experiment):      this experiment):
1325      > size mitgcmuv_ad      > size mitgcmuv_ad
1326      text    data        bss     dec        hex        text    data        bss     dec        hex
1327      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1328      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1329      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1330      text    data        bss     dec        hex      text    data        bss     dec        hex
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