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revision 1.2075 by gforget, Mon Sep 29 17:16:46 2014 UTC revision 1.2259 by jmc, Mon Jul 18 16:48:34 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/monitor:
8      - add new routine to compute Advective CFL within tracer time-stepping with
9        writing delayed until next monitor output.
10    o pkg/obcs:
11      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
12    o pkg/dic & seaice:
13      - fix compilation of ocean component for coupled atm+ocn model with
14        seaice dynamics & dic.
15    
16    checkpoint65x (2016/06/11)
17    o add a license text file in main MITgcm tree.
18    o added pkg/bling:
19      - intermediate complexity biogeochemical model
20      - see bling_description.txt for details
21      - verification experiment is global_oce_biogeo_bling (for now, in
22        Contrib/verification_other/); tested daily on baudelaire with gfortran.
23      - add entry point in pkg/gchem for new pkg "bling".
24    o pkg/seaice: fix tensile stength computation
25      - replace global field tensileStrength by tensileStrFac
26      - tensileStrFac can be computed once in S/R seaice_init_varia
27      - fortunately that does not affect any verification results
28    
29    checkpoint65w (2016/05/12)
30    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
31         with ECCO_CTRL_DEPRECATED defined
32    o verification/global_ocean.cs32x15:
33      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
34        with "selectNHfreeSurf=1".
35    o model/src (non-hydrostatic free-surface):
36      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
37        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
38      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
39        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
40        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
41        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
42      - Update output (changes at machine truncation level) of verification exp:
43        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
44        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
45    o pkg/seaice: ITD code
46      - fix picking up from a single category model by initialising
47        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
48      - split a long warning message in seaice_check_pickup.F into two lines,
49        because NEC SX-ACE cannot deal with the long line.
50    o model/src:
51      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
52    o pkg/seaice:
53      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
54    o pkg/seaice:
55      - add basal stress as parameterisation for grounding ice
56        following Lemieux et al. (2015)
57      - turn on by setting new parameter SEAICEbasalDragK2 to a value
58        larger than 0. Lemieux et al. (2015) recommend 15.
59      - The adjoint complains with extra recomputations so there is also a
60        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
61        order to postpone the problem
62      - compile the new code in lab_sea
63    o verification/halfpipe_streamice:
64      - update both TAF and OpenAD adm output (machine truncation differences)
65    
66    checkpoint65v (2016/04/08)
67    o verification/advect_xz:
68      - increase overlap size from 3 to 4 and add new secondary test for PQM
69        advection scheme (with mono & wino limiter).
70      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
71    o model/src:
72      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
73        added phi0Ref) to set vertical axis origin and phiRef origin;
74        keep Ro_SeaLevel for backward compatibility (with a warning).
75       According to coordinate and fluid type:
76        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
77        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
78        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
79        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
80      - remove Ro_SeaLevel from ATM experiment parameter files;
81      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
82        complement; update output.txt (changes at machine truncation level).
83    o pkg/seaice/seaice_evp.F
84      - simplify computation of deltaZ and zetaZ to simple averaging following
85        Bouillon et al. (2013). This removes a lot of code, but also changes
86        verification experiment lab_sea.hb87 -> updated
87    
88    checkpoint65u (2016/03/14)
89    o pkg/generic_advdiff:
90      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
91        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
92        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
93        testing and not for actual use.
94    o model/src:
95      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
96        origin r = rF(1);
97      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
98        in EOS for height coordinate: enable to include NH Pressure or to use
99        more accurate pressure vertical profile; options not linked to EOS type
100        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
101      - start to implement variable gravity (along vertical): for now, only with
102        z-coords (not even z*).
103      - add Ideal Gas equation of state for height coordinate.
104      - update OpenAD output (affected at machine truncation level) of exp:
105        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
106    o pkg/exf:
107      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
108        of exf interpolation (before any rescaling, rotation or interpolation
109        to velocity point) for each field that gets loaded from file. This option
110        identically mimics the input file organization (e.g. record numbers in year
111        by year input files) besides the change in horizontal grid.
112      - add rotateStressOnAgrid run-time switch so that wind stress fields
113        can be provided on the A-grid in zonal/meridional direction and
114        rotated on the fly. This only applies to the case when the exf
115        interpolation is off and rotateStressOnAgrid is false by default.
116    o model/src:
117      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
118        it's also used with pkg/atm_phys) and add few more parameters (but still
119        inactive, src code yet to come)
120    
121    checkpoint65t (2016/02/10)
122    o pkg/atm_phys:
123      - from Ruth Geen: add optical depth dependence on CO2 concentration.
124    o model/src:
125      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
126        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
127        Update output of exp. deep_anelastic (changes at truncation level).
128    o tools:
129      - add a hack in "remove_comments_sed" (used only with TAF) for recent
130        version of OpenMPI (shipped with FC.23): comment out the new header
131        file "mpif-sizeof.h" which causes problems to TAF.
132    o pkg/seaice:
133      - change the termination criterion so that maxits (SEAICElinearIterMax)
134        has an effect
135      - unify iteration parameters for implicit solvers (JFNK and Picard)
136        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
137        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
138        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
139        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
140        SEAICEnonLinTol     replaces JFNKgamma_nonlin
141      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
142      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
143        use with SEAICEuseKrylov
144    o pkg/seaice/seaice_lsr.F
145        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
146        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
147        an effect.
148    o pkg/seaice: add two new parameters
149      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
150        parameter is not in any namelist)
151      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
152        a preconditioner for the non-linear Newton iteration of the JFNK
153        solver
154    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
155      affects some experiments at truncation level:
156      - global_ocean.cs32x15.icedyn (11 digits),
157      - global_ocean.cs32x15.seaice (11 digits),
158      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
159      - also update global_ocean.cs32x15 adjoint and tangent-linear results
160    o pkg/salt_plume & pkg/thsice:
161      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
162        connect salt_plume flux to ATM-OCN coupling pkgs interface:
163       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
164         export to coupler interface) even without compiling pkg/salt_plume ;
165       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
166         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
167    o pkg/dic:
168      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
169        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
170        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
171      - move also update with values from ATM-OCN Coupler in the same new S/R
172        (previously done in ocn_apply_import.F).
173    o tools/adjoint_options:
174      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
175        has been changed on Jan 14, 2016.
176    o pkg/ggl90:
177      - add alternative discretisation of vertical shear (off by default), to
178        compute the mean (@ grid-cell center) of vertical shear compon instead of
179        vertical shear of mean flow (@ grid-cell center).
180      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
181        results on adjacent faces of cubed-sphere grids; this fix the restart.
182    o pkg/atm_compon_interf:
183      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
184        pass last value, stored directly before export to CPL ;
185        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
186      - remove atmSLPr from pickup files (no longer needed for restart)
187    
188    checkpoint65s (2016/01/13)
189    o eesupp & genmake2:
190       - first check for Function ETIME and, if it fails, then check for subroutine
191         ETIME and consistent output; use the appropriate version in timers.F
192    o model/src:
193      - to check restart test, add option to apply EXCH to U,V earlier, just before
194        integr_continuity; turned off by default.
195    o pkg/dic:
196      - remove CPP option USE_ATMOSCO2 (not needed)
197    o tools/tst_2+2:
198      - try to ignore difference between +0 and -0 in binary file, causing test
199        to fail for no good reason.
200    o eesupp & genmake2:
201      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
202        but also check (in genmake2) that test runs and returns meaningful results.
203    o coupler pkgs:
204      Finish implementation of optionally-exchanged variable switches (started on
205       Nov 12) with addition of few more exchanged fields, including 2-way exchange
206       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
207       advection in OCN component; this requires sequential coupling.
208      coupler (pkg/atm_ocn_coupler):
209      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
210        routines (useful for debug).
211      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
212         flux, DIC fields) if corresponding switch is ON.
213      - add option to export RunOff to OCN (to use for DIC river input)
214      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
215      components (pkg/atm_ & ocn_compon_interf):
216      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
217        optionally exchanged fields; add a check & stop in cpl_readparms.F.
218        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
219        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
220      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
221        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
222      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
223      - hold in common block coupler optionally-exchanged variable switch
224        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
225      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
226        this is intended to replace the OCN cplFldtave.* output files (not updated
227        to contain new additional exchanged fields).
228    o pkg/dic:
229      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
230    o pkg/thsice:
231      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
232        and writing of thsice pickup files.
233    o pkg/atm_compon_interf:
234      - move all field individual export-call out of cpl_export_import_data.F
235        into new S/R ATM_EXPORT_FIELDS
236    o pkg/atm_compon_interf:
237      - store state variables (for now, only thSIce fields) just before beeing
238        exported (in cpl_export_import_data.F, like on ocean side) instead of from
239        atm_store_my_data.F like all exported fluxes.
240      - new version of pickup_cpl: write field names into meta file and read meta
241        file to find field postion in pickup. Also only write/read fields meeded for
242        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
243    o pkg/dic:
244      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
245    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
246        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
247        value can be from domain [0,1] to average between the two methods
248    o pkg/atm_phys:
249      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
250        hold fixed in time).
251    
252    checkpoint65r (2015/12/21)
253    o pkg/seaice:
254        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
255        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
256    o pkg/seaice:
257      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
258        when SEAICEscaleSurfStress=.TRUE.,
259      - apply areaW and areaS in S/R seaice_calc_lhs
260    o pkg/atm_phys:
261      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
262        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
263        for individual contribution (convection, LSC cond, radiation)
264      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
265        information); activated with: solar_exponent=0. and wv_exponent=-1.
266    o pkg/ggl90:
267      - within IDEMIX add upper limit for horizontal group velocity to
268        avoid instability problems in the explicit horizontal diffusion term for
269        long time steps or high resolution
270    o pkg/diagnostics:
271      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
272        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
273    o testreport:
274      - remove "-v" (verbose option) in default mpirun command.
275    o pkg/seaice/seaice_growth:
276      - catch potential division by zero in ITD code, does not change
277        verification results
278    o pkg/ecco:
279      - retire old codes to the Attic. The calls to retired functions are
280        left in a commented form in case they ever need to be re-activated.
281      - ecco_check.F: issue warning if any old CPP option is
282        defined that corresponds to retired codes -- then stop.
283    o pkg/atm_compon_interf:
284      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
285        coupler: use last time-step value instead of average over cplSendFrq_iter
286        time-step, similar to what is done for seaIceMass.
287        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
288    o eesupp & genmake2:
289      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
290        <= remove until a fix is found for some ifort version on ia32 machine.
291    o pkg/seaice/seaice_evp:
292      - refine residual computation
293    
294    checkpoint65q (2015/11/18)
295    o pkg/seaice/seaice_evp:
296      - fix residual computations so that they no longer affect the actual
297        simulation code
298      - fix seaice_readparams to be able to actually set new parameters
299        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
300    o model/src:
301      - fix wrong truncation (single prec) from "FLOAT" function in expressions
302        like: deltaT*FLOAT(myIter) when myIter is large:
303         a) replaced by DFLOAT (if not seen by TAF);
304         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
305    o pkg/aim_v23:
306      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
307        when pickupSuff is set ; do write rolling pickups + at the end of the run.
308    o pkg/atm_ocn_coupler + ocn_compon_interf:
309      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
310        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
311        add corresponding call in DO_OCEANIC_PHYS.
312    o coupler pkgs:
313      Start a new way to set-up optionally-exchanged variables (previously, only
314       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
315       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
316       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
317       compononent param default can be set accordingly).
318      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
319       but rather applies to a group a fields (going both ways like for DIC)
320       and corresponds to an option of coupling config.
321      coupler (pkg/atm_ocn_coupler):
322      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
323        and read namelist directly (without eessup S/R calls) instead of
324        in the very un-flexible old way, 1 param per line, in fixed order;
325      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
326        cleanly in CPL_CHECK_CPLCONFIG
327      - add new coupling-exchange selectors (some not yet active) including
328        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
329                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
330      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
331        component ; called directly from coupler.F, after comp. registrations;
332      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
333         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
334          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
335      components (pkg/atm_ & ocn_compon_interf):
336      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
337        CPP header file in all pkg source files.
338      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
339        ATM/OCN_CHECK_CPLCONFIG;
340      - add error-counter to track errors (e.g., in "data.cpl") and to stop
341        cleanly in ATM/OCN_CHECK_CPLCONFIG;
342      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
343        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
344        before PACKAGES_READPARMS;
345      verification/cpl_aim+ocn/:
346      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
347        "data.cpl" for coupler (in input_cpl).
348    o eesupp/inc:
349      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
350        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
351        to always cumulate tile local-sum in the same order (still uses
352        MPI_Allreduce like standard code).
353      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
354        that are now identical to standard version (in eesupp/inc).
355    o pkg/shelfice:
356      - add SHELFICETransCoeffTFile for initializing spatially varying
357        heat and salt transfer coefficients
358    o pkg/atm_compon_interf & ocn_compon_interf:
359      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
360        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
361      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
362    o pkg/atm_ocn_coupler:
363      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
364    o pkg/rbcs:
365      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
366        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
367      - add a short report (to STDOUT) about RBCS-mask settings.
368    
369    checkpoint65p (2015/10/23)
370    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
371        there is no adjoint test for EVP, we don't know what it does to the adjoint
372        solution, but at least there are no more recomputation warnings left
373    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
374        a chance of giving the same results as a fully converged VP (JFNK) solver
375    o tools/adjoint_options/adjoint_diva:
376      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
377    o pkg/streamice:
378      - spotted bug in streamice_driving_stress using dyG where should have been dxG
379    o pkg/exf:
380      - remove STOP statement that prevented to use wind or (wind-)stress
381        interpolation for constant-in-time forcing fields (wind/stress period = 0).
382    o pkg/seaice:
383      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
384        5 additionals 2D fields and 6 new store directives
385      - change logic in seaice_readparms.F: EVP code can now be turned on in
386        various ways, setting SEAICE_deltaTev is no longer required,
387        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
388        or SEAICEaEVPcoeff
389    o pkg/shelfice/shelfice_thermodynamics.F
390      - redefining uLoc/vLoc to u/v, instead of 2u/v
391    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
392      - this is an intermediate state of a truely converging EVP that has
393        the potential of outperforming implicit VP methods, I do not recommend
394        using it yet.
395      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
396        and all parameters are hardwired
397      - for convergence it still requires very smooth regularisations, that means,
398        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
399        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
400        specific averaging appears to be required, still subject to tuning
401      - still needs cleaning and I need to turn parameter into runtime parameters
402      - add code to compute and print residuals of iteration, compile with
403        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
404    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
405      that entered with r1.54 on Sep04, 2015, -> update results
406    
407    checkpoint65o (2015/09/14)
408    o pkg/mom_vecinv & mom_common:
409      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
410        called from there.
411      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
412        allows to use Vector-Invariant form in deep atmos and anelastic formulation
413    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
414      and Koenig-Beatty+Holland (2012)
415      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
416      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
417      - requires an extra input argument for S/R seaice_calc_viscosities
418      - tensileStrength's depth dependence is different from Itkin et al. (2015)
419        (to be changed and played with, for now exponential)
420    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
421      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
422        by AREA according to Connelly et al. (2004), JPO.
423      - For EVP and the LSR solver, the implicit part of the drag term is
424        the only non-zero term in the denominator when there is no ice (which
425        prevented running the model with zero ice-ocean drag). If
426        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
427        (or zero main diagonals BU/BV) which need to be caught. A practical
428        consequence is that for open water, the momentum equation reduce
429        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
430        they happen to be zero, often leading to a non-zero solution over
431        open water.
432    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
433        efficient EVP method.
434      - introduce area-weighted averages for e12 (analogously to
435        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
436        remain, but also changing the order of terms in the previous average
437        changed the results as much) -> update experiment
438      - add SEAICE_DELTA_SMOOTHREG code
439      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
440        TEM-code
441      - adjust loop bounds so that only required fields are computed
442      - add new averaging code for zetaZ/deltaZ (again similar to
443        seaice_calc_viscosities.F), inactive by default for now (will change
444        results again), but will replace old code eventually
445    o eesupp/src:
446      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
447        to always cumulate tile local-sum in the same order
448        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
449        Still uses MPI_Allreduce (like standard code) but on array of tiles
450        and should be faster than GLOBAL_SUM_SEND_RECV code.
451      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
452        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
453      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
454         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
455         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
456         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
457         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
458    
459    checkpoint65n (2015/07/29)
460    o pkg/thsice:
461      - add a warning when used with pkg/aim but without updating SST
462        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
463    o pkg/offline:
464      - change where Offline-Fields are loaded, from load_fields_driver.F to
465        directly within FORWARD_STEP, just after updating iter number and time;
466      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
467        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
468       These changes allow:
469        a) to recover exactly on-line results using deltaToffline=deltaTClock,
470        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
471        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
472        time-step, both with GM & KPP files and with recomputing these fields;
473        b) no needs to switch on staggerTimeStep anymore;
474        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
475      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
476    o pkg/offline:
477      - change (rarely used) offset-iteration parameter to an offset time (in s):
478        can easily recover previous offset-iter effect by setting offset-time
479        (offlineTimeOffset) to offset-iter x deltaToffline;
480      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
481        in KPP as part of surface buoyancy forcing) in offline run.
482      - fix ptracers KPP non-local term in the case where KPP is re-computed.
483    o OpenAD
484      - Adding preliminary ggl90 test to OpenAD verification.
485        Config. with ggl90 currently diverges after 64 time steps
486        so will need more work to become more stable
487      - Adding preliminary kpp test to OpenAD verification.
488        required small tweakes in kpp_routines.F
489      - Merge and update from Krishna Narayanan's contrib area:
490        * Add one variable for preliminary OpenAD DIVA
491        * Add replacement time-stepping for OpenAD DIVA
492        * genmake2 flag -diva (but only for OpenAD; preliminary)
493        * required modifs for OAD_support
494        successful preliminary test for tutorial_global_oce_biogeo/
495    o pkg/seaice:
496      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
497      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
498        delta with a smooth function in s/r seaice_calc_viscosity
499        (no effect on EVP)
500      - rename local suffix "sqr" into "sq" for more consistent variable names
501    o pkg/seaice:
502        add new parameter SEAICE_deltaMin that is used ***only***
503        for regularizing Delta (and nothing else, like the parameter
504        which is also used for all sorts of things SEAICE_EPS).
505        Defaults to SEAICE_EPS for backward compatibility only.
506    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
507        the wrong key by inialising it before use -> fixes a recomputation
508        problem but does not fix the gradient
509    o pkg/layers:
510      - move resetting of flux arrays to outside the iLa loop
511        (this caused layers_diapycnal to not work with more than one layer coord.)
512      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
513    o pkg/layers:
514      - remove from common block 3D layers fields (used to diagnose transport
515        in tracer coords) and declare them as local arrays in layers_calc.F
516    o pkg/seaice:
517      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
518        in lab_sea forward experiment (changes results -> updated)
519      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
520    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
521       computations; for SEAICE_VECTORIZE_LSR
522      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
523        sweep to the outside,
524      - remove store directives and add "CADJ loop sequential" directives
525        in analogy to model/src/solve_tridiagonal.F
526      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
527        boundaries to yield more readable code. This has also the charming side
528        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
529        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
530        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
531        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
532        an additional option)
533       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
534       but the adjoint gradients (which are affected by this change) still explode.
535    o coupler (atm & ocn _compon_interf):
536      - avoid using Exch2 IO mapping if not suitable.
537    
538    checkpoint65m (2015/06/15)
539    o pkg/layers:
540      - clean-up old parameters setting (from Sep 2012):
541        + remove old parameters setting from common block (declared locally);
542        + stop if any old parameter is mixed with new parameters;
543        + check for valid or consistent parameter setting (e.g., layers_name)
544      - check that layers_bounds for Pot.Density are in the right range;
545        this is supposed to catch un-updated setting after recently shifting
546        potential density field "prho" by -1000 (now in "sigma" scale).
547    o pkg/layers:
548      - Added missing call to layers_fill for keeping track of tottend in
549        pkg/diagnostics/diagnostics_fill_state.F
550    o pkg/layers:
551      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
552        of diapycnal fluxes
553    o pkg/layers:
554      - reverted changes to interpolation to previous treatment; there
555        was never actually a problem
556    o pkg/layers:
557      - fix interpolation of layers tracers in the presence of partial cells
558      - add lots of new functionality to compute water mass transformation
559        (enabled by CPP flag LAYERS_THERMODYNAMICS)
560      - add new calls from main code (diags_oceanic_surf_flux.F,
561        thermodynamics.F, impldiff.F) and gad to save the necessary fields
562        for layers_thermodynamics calculations
563    o pkg/ptracers:
564      - add capability of stepping a passive tracer forward without advection
565        by setting PTRACERS_advScheme to 0.
566    o pkg/diagnostics:
567      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
568    o pkg/layers:
569      - shift potential density field "prho" by -1000 for density layer averaging so
570        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
571        Note that density bin boundaries (layers_bounds in data.layers) have
572        to be set accordingly (i.e., shifted, in sigma scale).
573    o pkg/layers:
574      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
575      - fix calculation of layer non-weighted velocity and layer probability
576      - add diagnostics for pot.density used for layer averaging
577    o pkg/seaice:
578      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
579        positiveness, modify a few comments and improve variable names,
580      - the changed computation of deltaC affects most seaice-related
581        experiments at the truncation level.
582        seaice_itd.thermo is affected by far the most, with
583        only 7 digits of agreement remaining; update experiments.
584    
585    checkpoint65l (2015/05/04)
586    o pkg/shelfice:
587      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
588        factor drKp1 to zero where it is negative (ie. do not use
589        SHELFICEBoundaryLayer if hFacC>1)
590      - the same for factor drLoc in shelfice_forcing.F
591    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
592        with modules in ptracers, when using testreport option "-small_f"
593    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
594      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
595    o verification/testreport
596      - add new option -small_f
597        with this option testreport first makes the target small_f (*.f files)
598        before running make (all). This is useful for explicit inlining when
599        all sources need to be full available.
600    o pkg/exf/exf_interp.F:
601        remove previous changes related to reverse (decreasing) input grids latitude
602    
603    checkpoint65k (2015/04/01)
604    o pkg/ecco:
605        fix missing cosphi initialization; use eccoiter in place of optimcycle;
606        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
607        instead of active read/write
608    o pkg/ctrl:
609        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
610        instead of active read/write.
611    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
612        return if .NOT.useAUTODIFF
613    o pkg/seaice: add CPP brackets (cost function related).
614    o model/src:
615        add useAUTODIFF run time switch.
616    o pkg/exf/exf_interp.F:
617        add code to allow input grids with latitude starting in the north (i.e. when
618        j=1 corresponds to northern edge of field); modify global_with_exf to test
619        this feature.
620    o verification/testreport:
621      - replace "grep -A3" with POSIX conformal sed command, because there are
622        implementations of grep that cannot do contextual searches
623      - replace "cat -n" by "nl" (two occurrences), because not all implementations
624        of "cat" have the option "-n"
625    o model/src:
626        add new file gsw_teos10.F that contains 3 functions, more or less a copy
627        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
628        convert from conservative to potential temperature. For now they are not
629        called anywhere.
630    o pkg/ggl90: make "useIDEMIX" useful
631      - re-organize code in s/r ggl90_calc a little to move computations that
632        are different for idemix into separate loops (changes verification
633        experiment idemix at truncation level, 12 digits remain -> updated)
634      - requires 2 new 2D fields KappaM, verticalShear
635      - make hFacI and recip_hFacI local 3D variables that are passed to
636        s/r ggl90_idemix
637      - fix and improve some comments
638    
639    checkpoint65j (2015/02/25)
640    o pkg/openad
641      - synchronize seawater.F with version in model/src: replace routine
642        body of sw_temp by calling sw_ptmp and fix/add a few comments.
643    o pkg/mnc:
644      - change default value of pickup_read/write_mnc params to FALSE
645        (since few features are missing in reading MNC pickup files).
646    o model/src:
647      - change default (background) vertical diffusivity for salt to be the
648        temperature (background) vertical diffusivity.
649      - change background vertical diffusivity in vertical mixing pkgs ggl90,
650        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
651        This makes ptracers default diffusivity (that uses salt diffKr) more
652        consistent with vertical mixing schemes.
653    o verification/testreport:
654      - fix typo in "-pcls" option ;
655      - put temp files in /tmp (instead of in local dir)
656      - add option "-ncad" to use genmake2 new option "-nocat4ad"
657      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
658    o pkg/ggl90 (idemix code):
659      - apply few fixes ; add some missing "_d 0" ; update output of exp.
660        global_ocean.90x40x15.idemix
661    o OpenAD
662      - enable active file I/O and begin removal of work-around code
663        for OpenAD for handling control variables (memory vs. active files)
664      - new CPP options file OPENAD_OPTIONS.h
665      - revert to genarr2d gradient check for hs94.1x64x5
666      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
667      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
668    o tools/genmake2:
669      - add option for an alternative Makefile (from Martin) where multiple
670        source files are sent to TAF (instead of all in one file).
671    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
672      - code provided by Carsten Eden as an extension of ggl90
673      - so far the code is turned on within ggl90 by setting a CPP-flag at
674        compile time; a runtime flag implementation is not yet complete
675      - tested in new verification experiment global_ocean.90x40x15.idemix
676    o verification:
677      - reduce length of the AD test run by half for experiments
678        global_ocean.cs32x15 (std + thsice) and isomip
679      - enable active file I/O for OpenAD, adjust verifications accordingly
680      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
681    o verification/testreport:
682      - fix two non-POSIX sed statements so that there are no error messages
683        on Mac OS X
684      - replace hostname -s with hostname | sed 's/\..*$//'
685    o model/src/seawater.F:
686      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
687        (following the matlab code), which would have avoided the bug caught
688        by Matt (see below) in the first place
689    o pkg/shelfice:
690      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
691        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
692      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
693        ice-shelf case (i.e., within surface level).
694      - add config summary in shelfice_check.F
695      - remove global variable recip_SHELFICElatentHeat and replace by a local
696        variable recip_latentHeat
697      - introduce diagnostics for friction velocity uStar (in case of
698        SHELFICEuseGammaFrict)
699      - change verification experiment isomip.htd:
700        + start from pickup (as input_ad at nIter0=8640)
701        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
702        + test SHELFICEuseGammaFrict = .TRUE.
703        + test SHELFICEadvDiffHeatFlux = .TRUE.
704    o model/src:
705      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
706        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
707        update output of experiments global_with_exf.yearly and isomip (all 6).
708    o pkg/shelfice:
709      - change setting of kTopC to also be zero where there is no ice-shelf.
710      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
711        ice-shelf is.
712      - first attempt to get RealFreshWaterFlux effects: for now, only without
713        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
714    o pkg/seaice: add the option to prescribe a fixed thickness PDF
715      for thermodynamic calculations
716      - because of divisions of the type 7/7 not exactly equal to 1, this change
717        affects results of some verification experiments by up to 4 digits:
718        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
719        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
720        adjoint: lab_sea, lab_sea.noseaicedyn
721        -> updated
722    
723    checkpoint65i (2015/01/23)
724    o model/src:
725      - change units of frictionHeating field from W to W/m^2
726      - fix bug in frictional heating from stratospheric drag in
727        S/R ATM_PHYS_TENDENCY_APPLY_V
728      - with synchronous time-stepping: move resetting to zero of frictionHeating
729        field from load_fields_driver.F to thermodynamics.F ;
730      - add diagnostics for frictional heating.
731    o model/src & gmredi K3D:
732      - add frictionHeating field to pickup-files (for synchronous time-stepping)
733      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
734      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
735        and name in pickup file).
736      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
737    o model/src:
738      - move (from ini_forcing.F) initialisation of all arrays in header file
739        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
740        (since Nov 2012) with option selectAddFluid=1.
741    o pkg/shelfice:
742      - change units (+ document) of newly added field "shelfIceMassDynTendency"
743      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
744    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
745    o pkg/seaice: two new runtime parameters:
746      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
747        long overdue
748      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
749        parameterization of tensil stress for fast ice (does not do anything yet)
750    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
751        for LSR: move checking overlaps out of JFNK-if-block
752    o pkg/atm_phys:
753      - move copy of grid and dynamical fields out of atm_phys_driver.F into
754        new S/R ATM_PHYS_DYN2PHYS.
755      - fix level height for Linear Free-Surf case (to be consistent with
756        fixed-in-time pressure levels).
757    o pkg/mom_common (bottomdrag):
758      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
759        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
760        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
761    o pkg/shelfice (u/v_drag):
762      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
763      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
764        (now similar to shelfice_u_drag.F)
765      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
766        from mom_vecinv.F (similar to mom_fluxform calls).
767    o pkg/mom_common (bottomdrag):
768      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
769      - add options for alternative discretisation of velocity norm in quadratic
770        bottom drag: averaging of grid-cell-center KE to U.point and V.point
771        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
772        improves when averaging only the other component (e.g. vVel for U bottom
773        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
774      - add options (bottomVisc_pCell) to account for partial-cell in bottom
775        friction (no-slip BC) thus getting the true distance from the bottom;
776        off by default since this also reduces model stability (explicit bottom
777        friction). Changes produce different machine truncation with linear-drag
778        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
779        front_relax (bvp & mxl, 10 & 11 digits).
780    o model/src & mom pkgs:
781      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
782        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
783      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
784        just copy level Nr value to level Nr+1.
785    o doc:
786      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
787    o pkg/shelfice:
788      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
789        SHELFICE.h: move array shelficemass to init_varia, initialise
790        from array shelficemassinit, which is set in init_fixed and
791        has option to be set from file; introduce array
792        shelficeMassDynTend array, set thru file in init_fixed
793      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
794        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
795        pkg/streamice
796      - shelfice_thermodynamics.F: call shelfice_step_icemass if
797        SHELFICEMassStepping = .true.
798      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
799    
800    checkpoint65h (2014/12/17)
801    o verification/global_ocean.90x40x15, global_ocean_ebm:
802      - update to generic controls.
803    o pkg/ctrl:
804      - ctrl_map_ini_genarr.F: test for igen>0
805      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
806      - move gentim2d part of ctrl_map_ini_genarr.F to
807        new separate routine : ctrl_map_ini_gentim2d.F
808      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
809        add time variable weights and cyclic controls (time mean,
810        seasonal cycle, etc) capabilities to gentim2d
811    o pkg/ecco:
812      - move reading of error, conversion to weights from
813        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
814    o global_oce_llc90, cs32:
815      - activte sbo.
816      - CTRL_SIZE.h : add maxCtrlProc.
817      - activate the new genctrl capabilities.
818      - update following reorganization of global_oce_input_fields.tar.gz  
819    o pkg/ctrl/ctrl_ad_diff.list:
820      - add missing ctrl_init_rec.f
821    o tools/OAD_support/keepOriginal:
822      - add ctrl_init_rec.F
823    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
824      - avoid recomputations of xx_gentim2d_dummy.
825    o momentum diagnostics:
826      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
827        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
828    o pkg/seaice/seaice_lsr.F:
829      - fix computation of BU/BV, make sure they are non-zero, only necessary
830        for cubed sphere exchanges and SEAICE_OLx/y>0.
831        This makes calling s/r fill_cs_corner_rl obsolete (removed).
832    o verification/global_ocean.cs32x15/input.seaice
833      - add test for strong implicit coupling and restricted addtive Schwarz
834        methods for LSR
835      - update results/output.seaice.txt
836    o verification/tutorial_global_oce_biogeo:
837      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
838        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
839        update output_adm,_oadm,_tlm.txt
840    o pkg/dic:
841      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
842      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
843        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
844    o verification/tutorial_global_oce_biogeo:
845      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
846        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
847        update output_adm,_oadm,_tlm.txt
848    o eesupp/src:
849      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
850        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
851    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
852      LSR (following Hutchings et al. 2004)
853      - introduce zetaZ as a global variable (requires adjustments in
854        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
855        in seaice_calc_viscosities.F
856      - new flag SEAICEuseStrImpCpl (default off)
857      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
858        momentum equations
859      - JFNK-solver (preconditioner) adjusted to allow using this method
860        (where it does not have any positive effect)
861    o pkg/seaice
862      - add overlap for restrictive additive Schwartz method also to LSR, but
863        turn it off by default (because it only seems to work for non-cubed
864        sphere/llc topologies)
865    o pkg/autodiff
866      - add extra exchanges in addummy_in_steppging also for mnc output
867    o pkg/seaice:
868      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
869        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
870    o pkg/obcs:
871      - add option to specify domain-connected piece Id along OB though files
872        (for now, only used to diagnose PhiVel; default =1 -> global correction)
873      - modify obcs_diag_balance.F to process each connected-part separately;
874        exclude OB where Id = 0 but keep the full divergence there (-> constant
875        Psi along this portion of OB and all inflow derived from grad(Phi))
876      - add example of OB-conect files in verification/so_box_biogeo/input.
877    o pkg/diagnostics:
878      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
879      a) use non zero matrix element across OB and solve for Phi 1 grid point
880         outside OB (i.e, where tracer OBCS are applied).
881      b) global imbalance of inFlow/outFlow across OB: instead of modifying
882         velocity across OB, spread it uniformly along the OB in the RHS.
883    
884    checkpoint65g (2014/11/19)
885    o pkg/diagnostcis:
886      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
887    o pkg/my82,pp81,kl10:
888      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
889        field diffKr as background diffusivity to set minimum diffusivity value.
890    o pkg/seaice:
891      - add new parameter SEAICEuseEVPrev (for revisited EVP by
892        Bouillon et al 2013)
893      - add SEAICE_evpAlpha/Beta to namelist
894      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
895        involve trivial re-ordering of divisions/multiplications that should not
896        have any effects, but ... they do change the results of lab_sea.hb87 so
897        that only 2 digits of agreement remain, in line with the general
898        instability/fragility of the evp-code. For now, I do not care and just
899        update the verification experiment
900    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
901      - remove xx_genarr2d_numsmooth etc
902      - use xx_genarr2d_preproc etc instead
903      - carry out smooth_correl2D at initialization stage rather than during
904        time stepping.
905      - get smoothOpNb from xx_gentim2d_preproc
906    o global_oce_cs32 :
907      - add test of generic ecco capabilities.
908    o pkg/exf/exf_getsurfacefluxes.F :
909      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
910    o pkg/ctrl,ecco :
911      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
912        is defined.
913    o pkg/seaice: add diagnostics for Delta (deformation parameter)
914    o model/src:
915      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
916        diffusivity (background) is specified but ignored.
917    o verification:
918      - in testreport, convert hostname to lower case for default output dir name
919    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
920    o pkg/dic: add modifications from Hajoon:
921      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
922      - light attenuation: add self-shading effect by climatological Chlorophyll
923        (read from file).
924    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
925        compiles when SEAICE_ALLOW_DYNAMICS is undefined
926    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
927        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
928        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
929        approach where CPP_OPTIONS.h includes an omnipotent
930        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
931    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
932        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
933    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
934        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
935        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
936    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
937      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
938      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
939      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
940      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
941    o pkg/ctrl,ecco,exf :
942      - remove variables associated with NON-generic costs,
943        unless ECCO_CTRL_DEPRECATED is defined.
944      - remove NON-generic NON-obcs controls,
945        unless ECCO_CTRL_DEPRECATED is defined.
946    o pkg/ctrl : added ctrl_local_params.h
947    o pkg/ecco : added ecco_local_params.h
948    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
949        experiments, which will progressively be removed once the
950        experiments are revised to use only generic controls/costs.
951    
952    checkpoint65f (2014/10/13)
953    o pkg/ctrl, ecco, seaice : minor changes in headers
954    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
955        cost function and control capabilities added since checkpoint65c.
956    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
957    o pkg/ecco: increase modularity and improve logic
958      - ecco_toolbox.F (new) : basic operations that are often used,
959        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
960        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
961      - cost_gencal.F (new) : determine filnames and records.
962      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
963      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
964        and exploit the above functions leading to more compact code.
965      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
966      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
967        using_ers, using_gfo, using_mdt is now only defined within gencost)
968    o pkg/ecco: extend generic cost capabilities
969      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
970        capabilities via gencost_preproc (+ _c,_i,_r related params),
971        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
972        gencost_outputlevel arguments to cost_generic
973      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
974        and active_read, making room for gencost_preproc to take effect.
975        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
976      - pkg/ecco/cost_generic.F :
977        compute and store misfit maks*(model-data) in localdif that is
978        then used in cost and for output, output misfit if outlev.GT.0
979      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
980        rather gencost_barfile for deciding whether to write barfile
981      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
982      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
983        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
984      - pkg/ecco/ecco_summary.F : report gencost variables
985      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
986    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
987  o pkg/ecco: internal re-organization  o pkg/ecco: internal re-organization
988    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
989      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
990      mv relevant variables definition from ecco_cost.h to ecco.h,      mv relevant variables definition from ecco_cost.h to ecco.h,
991      make sure gencost routines only include ecco.h)      make sure gencost routines only include ecco.h)
992    - throughout : add missing CCP switches, rm unused variables,    - throughout : add missing CCP switches, rm unused variables,
993      and rm un-necessary CPP switches      and rm un-necessary CPP switches
994    - throughout gencost routines : replace modelstartdate with    - throughout gencost routines : replace modelstartdate with
995      gencost_startdate when needed      gencost_startdate when needed
996    - cost_bp_read.F : use arguments, instead of common blocs    - cost_bp_read.F : use arguments, instead of common blocs
997      so that it can be used also by (new) cost_gencost_bpv4.F      so that it can be used also by (new) cost_gencost_bpv4.F
998    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
999    - ecco_phys.F : compute etanFull    - ecco_phys.F : compute etanFull
1000    - ecco_readparms.F : rename using_topex as using_tpj, add    - ecco_readparms.F : rename using_topex as using_tpj, add
# Line 332  o pkg/seaice: more clean up Line 1312  o pkg/seaice: more clean up
1312      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
1313      this experiment):      this experiment):
1314      > size mitgcmuv_ad      > size mitgcmuv_ad
1315      text    data        bss     dec        hex        text    data        bss     dec        hex
1316      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1317      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1318      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1319      text    data        bss     dec        hex      text    data        bss     dec        hex
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