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revision 1.2078 by gforget, Mon Oct 6 14:12:28 2014 UTC revision 1.2248 by mlosch, Fri Apr 29 14:29:04 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/seaice: ITD code
8      - fix picking up from a single category model by initialising
9        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
10      - split a long warning message in seaice_check_pickup.F into two lines,
11        because NEC SX-ACE cannot deal with the long line.
12    o model/src:
13      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
14    o pkg/seaice:
15      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
16    o pkg/seaice:
17      - add basal stress as parameterisation for grounding ice
18        following Lemieux et al. (2015)
19      - turn on by setting new parameter SEAICEbasalDragK2 to a value
20        larger than 0. Lemieux et al. (2015) recommend 15.
21      - The adjoint complains with extra recomputations so there is also a
22        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
23        order to postpone the problem
24      - compile the new code in lab_sea
25    o verification/halfpipe_streamice:
26      - update both TAF and OpenAD adm output (machine truncation differences)
27    
28    checkpoint65v (2016/04/08)
29    o verification/advect_xz:
30      - increase overlap size from 3 to 4 and add new secondary test for PQM
31        advection scheme (with mono & wino limiter).
32      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
33    o model/src:
34      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
35        added phi0Ref) to set vertical axis origin and phiRef origin;
36        keep Ro_SeaLevel for backward compatibility (with a warning).
37       According to coordinate and fluid type:
38        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
39        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
40        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
41        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
42      - remove Ro_SeaLevel from ATM experiment parameter files;
43      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
44        complement; update output.txt (changes at machine truncation level).
45    o pkg/seaice/seaice_evp.F
46      - simplify computation of deltaZ and zetaZ to simple averaging following
47        Bouillon et al. (2013). This removes a lot of code, but also changes
48        verification experiment lab_sea.hb87 -> updated
49    
50    checkpoint65u (2016/03/14)
51    o pkg/generic_advdiff:
52      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
53        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
54        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
55        testing and not for actual use.
56    o model/src:
57      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
58        origin r = rF(1);
59      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
60        in EOS for height coordinate: enable to include NH Pressure or to use
61        more accurate pressure vertical profile; options not linked to EOS type
62        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
63      - start to implement variable gravity (along vertical): for now, only with
64        z-coords (not even z*).
65      - add Ideal Gas equation of state for height coordinate.
66      - update OpenAD output (affected at machine truncation level) of exp:
67        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
68    o pkg/exf:
69      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
70        of exf interpolation (before any rescaling, rotation or interpolation
71        to velocity point) for each field that gets loaded from file. This option
72        identically mimics the input file organization (e.g. record numbers in year
73        by year input files) besides the change in horizontal grid.
74      - add rotateStressOnAgrid run-time switch so that wind stress fields
75        can be provided on the A-grid in zonal/meridional direction and
76        rotated on the fly. This only applies to the case when the exf
77        interpolation is off and rotateStressOnAgrid is false by default.
78    o model/src:
79      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
80        it's also used with pkg/atm_phys) and add few more parameters (but still
81        inactive, src code yet to come)
82    
83    checkpoint65t (2016/02/10)
84    o pkg/atm_phys:
85      - from Ruth Geen: add optical depth dependence on CO2 concentration.
86    o model/src:
87      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
88        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
89        Update output of exp. deep_anelastic (changes at truncation level).
90    o tools:
91      - add a hack in "remove_comments_sed" (used only with TAF) for recent
92        version of OpenMPI (shipped with FC.23): comment out the new header
93        file "mpif-sizeof.h" which causes problems to TAF.
94    o pkg/seaice:
95      - change the termination criterion so that maxits (SEAICElinearIterMax)
96        has an effect
97      - unify iteration parameters for implicit solvers (JFNK and Picard)
98        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
99        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
100        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
101        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
102        SEAICEnonLinTol     replaces JFNKgamma_nonlin
103      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
104      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
105        use with SEAICEuseKrylov
106    o pkg/seaice/seaice_lsr.F
107        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
108        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
109        an effect.
110    o pkg/seaice: add two new parameters
111      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
112        parameter is not in any namelist)
113      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
114        a preconditioner for the non-linear Newton iteration of the JFNK
115        solver
116    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
117      affects some experiments at truncation level:
118      - global_ocean.cs32x15.icedyn (11 digits),
119      - global_ocean.cs32x15.seaice (11 digits),
120      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
121      - also update global_ocean.cs32x15 adjoint and tangent-linear results
122    o pkg/salt_plume & pkg/thsice:
123      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
124        connect salt_plume flux to ATM-OCN coupling pkgs interface:
125       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
126         export to coupler interface) even without compiling pkg/salt_plume ;
127       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
128         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
129    o pkg/dic:
130      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
131        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
132        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
133      - move also update with values from ATM-OCN Coupler in the same new S/R
134        (previously done in ocn_apply_import.F).
135    o tools/adjoint_options:
136      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
137        has been changed on Jan 14, 2016.
138    o pkg/ggl90:
139      - add alternative discretisation of vertical shear (off by default), to
140        compute the mean (@ grid-cell center) of vertical shear compon instead of
141        vertical shear of mean flow (@ grid-cell center).
142      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
143        results on adjacent faces of cubed-sphere grids; this fix the restart.
144    o pkg/atm_compon_interf:
145      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
146        pass last value, stored directly before export to CPL ;
147        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
148      - remove atmSLPr from pickup files (no longer needed for restart)
149    
150    checkpoint65s (2016/01/13)
151    o eesupp & genmake2:
152       - first check for Function ETIME and, if it fails, then check for subroutine
153         ETIME and consistent output; use the appropriate version in timers.F
154    o model/src:
155      - to check restart test, add option to apply EXCH to U,V earlier, just before
156        integr_continuity; turned off by default.
157    o pkg/dic:
158      - remove CPP option USE_ATMOSCO2 (not needed)
159    o tools/tst_2+2:
160      - try to ignore difference between +0 and -0 in binary file, causing test
161        to fail for no good reason.
162    o eesupp & genmake2:
163      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
164        but also check (in genmake2) that test runs and returns meaningful results.
165    o coupler pkgs:
166      Finish implementation of optionally-exchanged variable switches (started on
167       Nov 12) with addition of few more exchanged fields, including 2-way exchange
168       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
169       advection in OCN component; this requires sequential coupling.
170      coupler (pkg/atm_ocn_coupler):
171      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
172        routines (useful for debug).
173      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
174         flux, DIC fields) if corresponding switch is ON.
175      - add option to export RunOff to OCN (to use for DIC river input)
176      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
177      components (pkg/atm_ & ocn_compon_interf):
178      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
179        optionally exchanged fields; add a check & stop in cpl_readparms.F.
180        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
181        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
182      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
183        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
184      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
185      - hold in common block coupler optionally-exchanged variable switch
186        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
187      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
188        this is intended to replace the OCN cplFldtave.* output files (not updated
189        to contain new additional exchanged fields).
190    o pkg/dic:
191      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
192    o pkg/thsice:
193      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
194        and writing of thsice pickup files.
195    o pkg/atm_compon_interf:
196      - move all field individual export-call out of cpl_export_import_data.F
197        into new S/R ATM_EXPORT_FIELDS
198    o pkg/atm_compon_interf:
199      - store state variables (for now, only thSIce fields) just before beeing
200        exported (in cpl_export_import_data.F, like on ocean side) instead of from
201        atm_store_my_data.F like all exported fluxes.
202      - new version of pickup_cpl: write field names into meta file and read meta
203        file to find field postion in pickup. Also only write/read fields meeded for
204        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
205    o pkg/dic:
206      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
207    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
208        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
209        value can be from domain [0,1] to average between the two methods
210    o pkg/atm_phys:
211      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
212        hold fixed in time).
213    
214    checkpoint65r (2015/12/21)
215    o pkg/seaice:
216        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
217        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
218    o pkg/seaice:
219      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
220        when SEAICEscaleSurfStress=.TRUE.,
221      - apply areaW and areaS in S/R seaice_calc_lhs
222    o pkg/atm_phys:
223      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
224        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
225        for individual contribution (convection, LSC cond, radiation)
226      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
227        information); activated with: solar_exponent=0. and wv_exponent=-1.
228    o pkg/ggl90:
229      - within IDEMIX add upper limit for horizontal group velocity to
230        avoid instability problems in the explicit horizontal diffusion term for
231        long time steps or high resolution
232    o pkg/diagnostics:
233      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
234        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
235    o testreport:
236      - remove "-v" (verbose option) in default mpirun command.
237    o pkg/seaice/seaice_growth:
238      - catch potential division by zero in ITD code, does not change
239        verification results
240    o pkg/ecco:
241      - retire old codes to the Attic. The calls to retired functions are
242        left in a commented form in case they ever need to be re-activated.
243      - ecco_check.F: issue warning if any old CPP option is
244        defined that corresponds to retired codes -- then stop.
245    o pkg/atm_compon_interf:
246      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
247        coupler: use last time-step value instead of average over cplSendFrq_iter
248        time-step, similar to what is done for seaIceMass.
249        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
250    o eesupp & genmake2:
251      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
252        <= remove until a fix is found for some ifort version on ia32 machine.
253    o pkg/seaice/seaice_evp:
254      - refine residual computation
255    
256    checkpoint65q (2015/11/18)
257    o pkg/seaice/seaice_evp:
258      - fix residual computations so that they no longer affect the actual
259        simulation code
260      - fix seaice_readparams to be able to actually set new parameters
261        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
262    o model/src:
263      - fix wrong truncation (single prec) from "FLOAT" function in expressions
264        like: deltaT*FLOAT(myIter) when myIter is large:
265         a) replaced by DFLOAT (if not seen by TAF);
266         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
267    o pkg/aim_v23:
268      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
269        when pickupSuff is set ; do write rolling pickups + at the end of the run.
270    o pkg/atm_ocn_coupler + ocn_compon_interf:
271      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
272        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
273        add corresponding call in DO_OCEANIC_PHYS.
274    o coupler pkgs:
275      Start a new way to set-up optionally-exchanged variables (previously, only
276       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
277       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
278       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
279       compononent param default can be set accordingly).
280      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
281       but rather applies to a group a fields (going both ways like for DIC)
282       and corresponds to an option of coupling config.
283      coupler (pkg/atm_ocn_coupler):
284      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
285        and read namelist directly (without eessup S/R calls) instead of
286        in the very un-flexible old way, 1 param per line, in fixed order;
287      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
288        cleanly in CPL_CHECK_CPLCONFIG
289      - add new coupling-exchange selectors (some not yet active) including
290        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
291                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
292      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
293        component ; called directly from coupler.F, after comp. registrations;
294      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
295         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
296          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
297      components (pkg/atm_ & ocn_compon_interf):
298      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
299        CPP header file in all pkg source files.
300      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
301        ATM/OCN_CHECK_CPLCONFIG;
302      - add error-counter to track errors (e.g., in "data.cpl") and to stop
303        cleanly in ATM/OCN_CHECK_CPLCONFIG;
304      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
305        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
306        before PACKAGES_READPARMS;
307      verification/cpl_aim+ocn/:
308      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
309        "data.cpl" for coupler (in input_cpl).
310    o eesupp/inc:
311      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
312        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
313        to always cumulate tile local-sum in the same order (still uses
314        MPI_Allreduce like standard code).
315      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
316        that are now identical to standard version (in eesupp/inc).
317    o pkg/shelfice:
318      - add SHELFICETransCoeffTFile for initializing spatially varying
319        heat and salt transfer coefficients
320    o pkg/atm_compon_interf & ocn_compon_interf:
321      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
322        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
323      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
324    o pkg/atm_ocn_coupler:
325      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
326    o pkg/rbcs:
327      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
328        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
329      - add a short report (to STDOUT) about RBCS-mask settings.
330    
331    checkpoint65p (2015/10/23)
332    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
333        there is no adjoint test for EVP, we don't know what it does to the adjoint
334        solution, but at least there are no more recomputation warnings left
335    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
336        a chance of giving the same results as a fully converged VP (JFNK) solver
337    o tools/adjoint_options/adjoint_diva:
338      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
339    o pkg/streamice:
340      - spotted bug in streamice_driving_stress using dyG where should have been dxG
341    o pkg/exf:
342      - remove STOP statement that prevented to use wind or (wind-)stress
343        interpolation for constant-in-time forcing fields (wind/stress period = 0).
344    o pkg/seaice:
345      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
346        5 additionals 2D fields and 6 new store directives
347      - change logic in seaice_readparms.F: EVP code can now be turned on in
348        various ways, setting SEAICE_deltaTev is no longer required,
349        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
350        or SEAICEaEVPcoeff
351    o pkg/shelfice/shelfice_thermodynamics.F
352      - redefining uLoc/vLoc to u/v, instead of 2u/v
353    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
354      - this is an intermediate state of a truely converging EVP that has
355        the potential of outperforming implicit VP methods, I do not recommend
356        using it yet.
357      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
358        and all parameters are hardwired
359      - for convergence it still requires very smooth regularisations, that means,
360        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
361        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
362        specific averaging appears to be required, still subject to tuning
363      - still needs cleaning and I need to turn parameter into runtime parameters
364      - add code to compute and print residuals of iteration, compile with
365        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
366    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
367      that entered with r1.54 on Sep04, 2015, -> update results
368    
369    checkpoint65o (2015/09/14)
370    o pkg/mom_vecinv & mom_common:
371      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
372        called from there.
373      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
374        allows to use Vector-Invariant form in deep atmos and anelastic formulation
375    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
376      and Koenig-Beatty+Holland (2012)
377      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
378      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
379      - requires an extra input argument for S/R seaice_calc_viscosities
380      - tensileStrength's depth dependence is different from Itkin et al. (2015)
381        (to be changed and played with, for now exponential)
382    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
383      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
384        by AREA according to Connelly et al. (2004), JPO.
385      - For EVP and the LSR solver, the implicit part of the drag term is
386        the only non-zero term in the denominator when there is no ice (which
387        prevented running the model with zero ice-ocean drag). If
388        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
389        (or zero main diagonals BU/BV) which need to be caught. A practical
390        consequence is that for open water, the momentum equation reduce
391        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
392        they happen to be zero, often leading to a non-zero solution over
393        open water.
394    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
395        efficient EVP method.
396      - introduce area-weighted averages for e12 (analogously to
397        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
398        remain, but also changing the order of terms in the previous average
399        changed the results as much) -> update experiment
400      - add SEAICE_DELTA_SMOOTHREG code
401      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
402        TEM-code
403      - adjust loop bounds so that only required fields are computed
404      - add new averaging code for zetaZ/deltaZ (again similar to
405        seaice_calc_viscosities.F), inactive by default for now (will change
406        results again), but will replace old code eventually
407    o eesupp/src:
408      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
409        to always cumulate tile local-sum in the same order
410        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
411        Still uses MPI_Allreduce (like standard code) but on array of tiles
412        and should be faster than GLOBAL_SUM_SEND_RECV code.
413      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
414        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
415      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
416         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
417         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
418         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
419         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
420    
421    checkpoint65n (2015/07/29)
422    o pkg/thsice:
423      - add a warning when used with pkg/aim but without updating SST
424        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
425    o pkg/offline:
426      - change where Offline-Fields are loaded, from load_fields_driver.F to
427        directly within FORWARD_STEP, just after updating iter number and time;
428      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
429        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
430       These changes allow:
431        a) to recover exactly on-line results using deltaToffline=deltaTClock,
432        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
433        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
434        time-step, both with GM & KPP files and with recomputing these fields;
435        b) no needs to switch on staggerTimeStep anymore;
436        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
437      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
438    o pkg/offline:
439      - change (rarely used) offset-iteration parameter to an offset time (in s):
440        can easily recover previous offset-iter effect by setting offset-time
441        (offlineTimeOffset) to offset-iter x deltaToffline;
442      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
443        in KPP as part of surface buoyancy forcing) in offline run.
444      - fix ptracers KPP non-local term in the case where KPP is re-computed.
445    o OpenAD
446      - Adding preliminary ggl90 test to OpenAD verification.
447        Config. with ggl90 currently diverges after 64 time steps
448        so will need more work to become more stable
449      - Adding preliminary kpp test to OpenAD verification.
450        required small tweakes in kpp_routines.F
451      - Merge and update from Krishna Narayanan's contrib area:
452        * Add one variable for preliminary OpenAD DIVA
453        * Add replacement time-stepping for OpenAD DIVA
454        * genmake2 flag -diva (but only for OpenAD; preliminary)
455        * required modifs for OAD_support
456        successful preliminary test for tutorial_global_oce_biogeo/
457    o pkg/seaice:
458      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
459      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
460        delta with a smooth function in s/r seaice_calc_viscosity
461        (no effect on EVP)
462      - rename local suffix "sqr" into "sq" for more consistent variable names
463    o pkg/seaice:
464        add new parameter SEAICE_deltaMin that is used ***only***
465        for regularizing Delta (and nothing else, like the parameter
466        which is also used for all sorts of things SEAICE_EPS).
467        Defaults to SEAICE_EPS for backward compatibility only.
468    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
469        the wrong key by inialising it before use -> fixes a recomputation
470        problem but does not fix the gradient
471    o pkg/layers:
472      - move resetting of flux arrays to outside the iLa loop
473        (this caused layers_diapycnal to not work with more than one layer coord.)
474      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
475    o pkg/layers:
476      - remove from common block 3D layers fields (used to diagnose transport
477        in tracer coords) and declare them as local arrays in layers_calc.F
478    o pkg/seaice:
479      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
480        in lab_sea forward experiment (changes results -> updated)
481      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
482    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
483       computations; for SEAICE_VECTORIZE_LSR
484      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
485        sweep to the outside,
486      - remove store directives and add "CADJ loop sequential" directives
487        in analogy to model/src/solve_tridiagonal.F
488      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
489        boundaries to yield more readable code. This has also the charming side
490        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
491        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
492        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
493        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
494        an additional option)
495       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
496       but the adjoint gradients (which are affected by this change) still explode.
497    o coupler (atm & ocn _compon_interf):
498      - avoid using Exch2 IO mapping if not suitable.
499    
500    checkpoint65m (2015/06/15)
501    o pkg/layers:
502      - clean-up old parameters setting (from Sep 2012):
503        + remove old parameters setting from common block (declared locally);
504        + stop if any old parameter is mixed with new parameters;
505        + check for valid or consistent parameter setting (e.g., layers_name)
506      - check that layers_bounds for Pot.Density are in the right range;
507        this is supposed to catch un-updated setting after recently shifting
508        potential density field "prho" by -1000 (now in "sigma" scale).
509    o pkg/layers:
510      - Added missing call to layers_fill for keeping track of tottend in
511        pkg/diagnostics/diagnostics_fill_state.F
512    o pkg/layers:
513      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
514        of diapycnal fluxes
515    o pkg/layers:
516      - reverted changes to interpolation to previous treatment; there
517        was never actually a problem
518    o pkg/layers:
519      - fix interpolation of layers tracers in the presence of partial cells
520      - add lots of new functionality to compute water mass transformation
521        (enabled by CPP flag LAYERS_THERMODYNAMICS)
522      - add new calls from main code (diags_oceanic_surf_flux.F,
523        thermodynamics.F, impldiff.F) and gad to save the necessary fields
524        for layers_thermodynamics calculations
525    o pkg/ptracers:
526      - add capability of stepping a passive tracer forward without advection
527        by setting PTRACERS_advScheme to 0.
528    o pkg/diagnostics:
529      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
530    o pkg/layers:
531      - shift potential density field "prho" by -1000 for density layer averaging so
532        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
533        Note that density bin boundaries (layers_bounds in data.layers) have
534        to be set accordingly (i.e., shifted, in sigma scale).
535    o pkg/layers:
536      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
537      - fix calculation of layer non-weighted velocity and layer probability
538      - add diagnostics for pot.density used for layer averaging
539    o pkg/seaice:
540      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
541        positiveness, modify a few comments and improve variable names,
542      - the changed computation of deltaC affects most seaice-related
543        experiments at the truncation level.
544        seaice_itd.thermo is affected by far the most, with
545        only 7 digits of agreement remaining; update experiments.
546    
547    checkpoint65l (2015/05/04)
548    o pkg/shelfice:
549      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
550        factor drKp1 to zero where it is negative (ie. do not use
551        SHELFICEBoundaryLayer if hFacC>1)
552      - the same for factor drLoc in shelfice_forcing.F
553    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
554        with modules in ptracers, when using testreport option "-small_f"
555    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
556      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
557    o verification/testreport
558      - add new option -small_f
559        with this option testreport first makes the target small_f (*.f files)
560        before running make (all). This is useful for explicit inlining when
561        all sources need to be full available.
562    o pkg/exf/exf_interp.F:
563        remove previous changes related to reverse (decreasing) input grids latitude
564    
565    checkpoint65k (2015/04/01)
566    o pkg/ecco:
567        fix missing cosphi initialization; use eccoiter in place of optimcycle;
568        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
569        instead of active read/write
570    o pkg/ctrl:
571        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
572        instead of active read/write.
573    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
574        return if .NOT.useAUTODIFF
575    o pkg/seaice: add CPP brackets (cost function related).
576    o model/src:
577        add useAUTODIFF run time switch.
578    o pkg/exf/exf_interp.F:
579        add code to allow input grids with latitude starting in the north (i.e. when
580        j=1 corresponds to northern edge of field); modify global_with_exf to test
581        this feature.
582    o verification/testreport:
583      - replace "grep -A3" with POSIX conformal sed command, because there are
584        implementations of grep that cannot do contextual searches
585      - replace "cat -n" by "nl" (two occurrences), because not all implementations
586        of "cat" have the option "-n"
587    o model/src:
588        add new file gsw_teos10.F that contains 3 functions, more or less a copy
589        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
590        convert from conservative to potential temperature. For now they are not
591        called anywhere.
592    o pkg/ggl90: make "useIDEMIX" useful
593      - re-organize code in s/r ggl90_calc a little to move computations that
594        are different for idemix into separate loops (changes verification
595        experiment idemix at truncation level, 12 digits remain -> updated)
596      - requires 2 new 2D fields KappaM, verticalShear
597      - make hFacI and recip_hFacI local 3D variables that are passed to
598        s/r ggl90_idemix
599      - fix and improve some comments
600    
601    checkpoint65j (2015/02/25)
602    o pkg/openad
603      - synchronize seawater.F with version in model/src: replace routine
604        body of sw_temp by calling sw_ptmp and fix/add a few comments.
605    o pkg/mnc:
606      - change default value of pickup_read/write_mnc params to FALSE
607        (since few features are missing in reading MNC pickup files).
608    o model/src:
609      - change default (background) vertical diffusivity for salt to be the
610        temperature (background) vertical diffusivity.
611      - change background vertical diffusivity in vertical mixing pkgs ggl90,
612        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
613        This makes ptracers default diffusivity (that uses salt diffKr) more
614        consistent with vertical mixing schemes.
615    o verification/testreport:
616      - fix typo in "-pcls" option ;
617      - put temp files in /tmp (instead of in local dir)
618      - add option "-ncad" to use genmake2 new option "-nocat4ad"
619      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
620    o pkg/ggl90 (idemix code):
621      - apply few fixes ; add some missing "_d 0" ; update output of exp.
622        global_ocean.90x40x15.idemix
623    o OpenAD
624      - enable active file I/O and begin removal of work-around code
625        for OpenAD for handling control variables (memory vs. active files)
626      - new CPP options file OPENAD_OPTIONS.h
627      - revert to genarr2d gradient check for hs94.1x64x5
628      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
629      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
630    o tools/genmake2:
631      - add option for an alternative Makefile (from Martin) where multiple
632        source files are sent to TAF (instead of all in one file).
633    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
634      - code provided by Carsten Eden as an extension of ggl90
635      - so far the code is turned on within ggl90 by setting a CPP-flag at
636        compile time; a runtime flag implementation is not yet complete
637      - tested in new verification experiment global_ocean.90x40x15.idemix
638    o verification:
639      - reduce length of the AD test run by half for experiments
640        global_ocean.cs32x15 (std + thsice) and isomip
641      - enable active file I/O for OpenAD, adjust verifications accordingly
642      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
643    o verification/testreport:
644      - fix two non-POSIX sed statements so that there are no error messages
645        on Mac OS X
646      - replace hostname -s with hostname | sed 's/\..*$//'
647    o model/src/seawater.F:
648      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
649        (following the matlab code), which would have avoided the bug caught
650        by Matt (see below) in the first place
651    o pkg/shelfice:
652      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
653        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
654      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
655        ice-shelf case (i.e., within surface level).
656      - add config summary in shelfice_check.F
657      - remove global variable recip_SHELFICElatentHeat and replace by a local
658        variable recip_latentHeat
659      - introduce diagnostics for friction velocity uStar (in case of
660        SHELFICEuseGammaFrict)
661      - change verification experiment isomip.htd:
662        + start from pickup (as input_ad at nIter0=8640)
663        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
664        + test SHELFICEuseGammaFrict = .TRUE.
665        + test SHELFICEadvDiffHeatFlux = .TRUE.
666    o model/src:
667      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
668        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
669        update output of experiments global_with_exf.yearly and isomip (all 6).
670    o pkg/shelfice:
671      - change setting of kTopC to also be zero where there is no ice-shelf.
672      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
673        ice-shelf is.
674      - first attempt to get RealFreshWaterFlux effects: for now, only without
675        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
676    o pkg/seaice: add the option to prescribe a fixed thickness PDF
677      for thermodynamic calculations
678      - because of divisions of the type 7/7 not exactly equal to 1, this change
679        affects results of some verification experiments by up to 4 digits:
680        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
681        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
682        adjoint: lab_sea, lab_sea.noseaicedyn
683        -> updated
684    
685    checkpoint65i (2015/01/23)
686    o model/src:
687      - change units of frictionHeating field from W to W/m^2
688      - fix bug in frictional heating from stratospheric drag in
689        S/R ATM_PHYS_TENDENCY_APPLY_V
690      - with synchronous time-stepping: move resetting to zero of frictionHeating
691        field from load_fields_driver.F to thermodynamics.F ;
692      - add diagnostics for frictional heating.
693    o model/src & gmredi K3D:
694      - add frictionHeating field to pickup-files (for synchronous time-stepping)
695      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
696      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
697        and name in pickup file).
698      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
699    o model/src:
700      - move (from ini_forcing.F) initialisation of all arrays in header file
701        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
702        (since Nov 2012) with option selectAddFluid=1.
703    o pkg/shelfice:
704      - change units (+ document) of newly added field "shelfIceMassDynTendency"
705      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
706    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
707    o pkg/seaice: two new runtime parameters:
708      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
709        long overdue
710      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
711        parameterization of tensil stress for fast ice (does not do anything yet)
712    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
713        for LSR: move checking overlaps out of JFNK-if-block
714    o pkg/atm_phys:
715      - move copy of grid and dynamical fields out of atm_phys_driver.F into
716        new S/R ATM_PHYS_DYN2PHYS.
717      - fix level height for Linear Free-Surf case (to be consistent with
718        fixed-in-time pressure levels).
719    o pkg/mom_common (bottomdrag):
720      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
721        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
722        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
723    o pkg/shelfice (u/v_drag):
724      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
725      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
726        (now similar to shelfice_u_drag.F)
727      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
728        from mom_vecinv.F (similar to mom_fluxform calls).
729    o pkg/mom_common (bottomdrag):
730      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
731      - add options for alternative discretisation of velocity norm in quadratic
732        bottom drag: averaging of grid-cell-center KE to U.point and V.point
733        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
734        improves when averaging only the other component (e.g. vVel for U bottom
735        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
736      - add options (bottomVisc_pCell) to account for partial-cell in bottom
737        friction (no-slip BC) thus getting the true distance from the bottom;
738        off by default since this also reduces model stability (explicit bottom
739        friction). Changes produce different machine truncation with linear-drag
740        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
741        front_relax (bvp & mxl, 10 & 11 digits).
742    o model/src & mom pkgs:
743      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
744        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
745      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
746        just copy level Nr value to level Nr+1.
747    o doc:
748      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
749    o pkg/streamice:
750      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
751        SHELFICE.h: move array shelficemass to init_varia, initialise
752        from array shelficemassinit, which is set in init_fixed and
753        has option to be set from file; introduce array
754        shelficeMassDynTend array, set thru file in init_fixed
755      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
756        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
757        pkg/streamice
758      - shelfice_thermodynamics.F: call shelfice_step_icemass if
759        SHELFICEMassStepping = .true.
760      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
761    
762    checkpoint65h (2014/12/17)
763    o verification/global_ocean.90x40x15, global_ocean_ebm:
764      - update to generic controls.
765    o pkg/ctrl:
766      - ctrl_map_ini_genarr.F: test for igen>0
767      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
768      - move gentim2d part of ctrl_map_ini_genarr.F to
769        new separate routine : ctrl_map_ini_gentim2d.F
770      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
771        add time variable weights and cyclic controls (time mean,
772        seasonal cycle, etc) capabilities to gentim2d
773    o pkg/ecco:
774      - move reading of error, conversion to weights from
775        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
776    o global_oce_llc90, cs32:
777      - activte sbo.
778      - CTRL_SIZE.h : add maxCtrlProc.
779      - activate the new genctrl capabilities.
780      - update following reorganization of global_oce_input_fields.tar.gz  
781    o pkg/ctrl/ctrl_ad_diff.list:
782      - add missing ctrl_init_rec.f
783    o tools/OAD_support/keepOriginal:
784      - add ctrl_init_rec.F
785    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
786      - avoid recomputations of xx_gentim2d_dummy.
787    o momentum diagnostics:
788      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
789        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
790    o pkg/seaice/seaice_lsr.F:
791      - fix computation of BU/BV, make sure they are non-zero, only necessary
792        for cubed sphere exchanges and SEAICE_OLx/y>0.
793        This makes calling s/r fill_cs_corner_rl obsolete (removed).
794    o verification/global_ocean.cs32x15/input.seaice
795      - add test for strong implicit coupling and restricted addtive Schwarz
796        methods for LSR
797      - update results/output.seaice.txt
798    o verification/tutorial_global_oce_biogeo:
799      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
800        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
801        update output_adm,_oadm,_tlm.txt
802    o pkg/dic:
803      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
804      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
805        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
806    o verification/tutorial_global_oce_biogeo:
807      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
808        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
809        update output_adm,_oadm,_tlm.txt
810    o eesupp/src:
811      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
812        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
813    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
814      LSR (following Hutchings et al. 2004)
815      - introduce zetaZ as a global variable (requires adjustments in
816        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
817        in seaice_calc_viscosities.F
818      - new flag SEAICEuseStrImpCpl (default off)
819      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
820        momentum equations
821      - JFNK-solver (preconditioner) adjusted to allow using this method
822        (where it does not have any positive effect)
823    o pkg/seaice
824      - add overlap for restrictive additive Schwartz method also to LSR, but
825        turn it off by default (because it only seems to work for non-cubed
826        sphere/llc topologies)
827    o pkg/autodiff
828      - add extra exchanges in addummy_in_steppging also for mnc output
829    o pkg/seaice:
830      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
831        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
832    o pkg/obcs:
833      - add option to specify domain-connected piece Id along OB though files
834        (for now, only used to diagnose PhiVel; default =1 -> global correction)
835      - modify obcs_diag_balance.F to process each connected-part separately;
836        exclude OB where Id = 0 but keep the full divergence there (-> constant
837        Psi along this portion of OB and all inflow derived from grad(Phi))
838      - add example of OB-conect files in verification/so_box_biogeo/input.
839    o pkg/diagnostics:
840      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
841      a) use non zero matrix element across OB and solve for Phi 1 grid point
842         outside OB (i.e, where tracer OBCS are applied).
843      b) global imbalance of inFlow/outFlow across OB: instead of modifying
844         velocity across OB, spread it uniformly along the OB in the RHS.
845    
846    checkpoint65g (2014/11/19)
847    o pkg/diagnostcis:
848      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
849    o pkg/my82,pp81,kl10:
850      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
851        field diffKr as background diffusivity to set minimum diffusivity value.
852    o pkg/seaice:
853      - add new parameter SEAICEuseEVPrev (for revisited EVP by
854        Bouillon et al 2013)
855      - add SEAICE_evpAlpha/Beta to namelist
856      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
857        involve trivial re-ordering of divisions/multiplications that should not
858        have any effects, but ... they do change the results of lab_sea.hb87 so
859        that only 2 digits of agreement remain, in line with the general
860        instability/fragility of the evp-code. For now, I do not care and just
861        update the verification experiment
862    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
863      - remove xx_genarr2d_numsmooth etc
864      - use xx_genarr2d_preproc etc instead
865      - carry out smooth_correl2D at initialization stage rather than during
866        time stepping.
867      - get smoothOpNb from xx_gentim2d_preproc
868    o global_oce_cs32 :
869      - add test of generic ecco capabilities.
870    o pkg/exf/exf_getsurfacefluxes.F :
871      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
872    o pkg/ctrl,ecco :
873      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
874        is defined.
875    o pkg/seaice: add diagnostics for Delta (deformation parameter)
876    o model/src:
877      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
878        diffusivity (background) is specified but ignored.
879    o verification:
880      - in testreport, convert hostname to lower case for default output dir name
881    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
882    o pkg/dic: add modifications from Hajoon:
883      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
884      - light attenuation: add self-shading effect by climatological Chlorophyll
885        (read from file).
886    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
887        compiles when SEAICE_ALLOW_DYNAMICS is undefined
888    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
889        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
890        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
891        approach where CPP_OPTIONS.h includes an omnipotent
892        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
893    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
894        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
895    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
896        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
897        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
898    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
899      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
900      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
901      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
902      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
903    o pkg/ctrl,ecco,exf :
904      - remove variables associated with NON-generic costs,
905        unless ECCO_CTRL_DEPRECATED is defined.
906      - remove NON-generic NON-obcs controls,
907        unless ECCO_CTRL_DEPRECATED is defined.
908    o pkg/ctrl : added ctrl_local_params.h
909    o pkg/ecco : added ecco_local_params.h
910    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
911        experiments, which will progressively be removed once the
912        experiments are revised to use only generic controls/costs.
913    
914    checkpoint65f (2014/10/13)
915    o pkg/ctrl, ecco, seaice : minor changes in headers
916    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
917        cost function and control capabilities added since checkpoint65c.
918    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
919  o pkg/ecco: increase modularity and improve logic  o pkg/ecco: increase modularity and improve logic
920    - ecco_toolbox.F (new) : basic operations that are often used    - ecco_toolbox.F (new) : basic operations that are often used,
921       (for now, ecco_toolbox.F simply contains function ecco_zero).      including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
922        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
923    - cost_gencal.F (new) : determine filnames and records.    - cost_gencal.F (new) : determine filnames and records.
924    - cost_gendif.F (new) : compute masked model-data difference.    - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
   - cost_genread.F : use ecco_zero to initialize field to 0s.  
925    - cost_generic.F : use spzeroloc rather than hard-coded -9999,    - cost_generic.F : use spzeroloc rather than hard-coded -9999,
926      and exploit the above functions leading to more compact code.      and exploit the above functions leading to more compact code.
927      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
928    - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,    - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
929      using_ers, using_gfo, using_mdt is now only defined within gencost)      using_ers, using_gfo, using_mdt is now only defined within gencost)
930  o pkg/ecco: extend generic cost capabilities  o pkg/ecco: extend generic cost capabilities
931    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost    - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
932      capabilities via gencost_preproc (+ _c,_i,_r related params),      capabilities via gencost_preproc (+ _c,_i,_r related params),
933      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,      gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
934      gencost_outputlevel arguments to cost_generic      gencost_outputlevel arguments to cost_generic
935    - pkg/ecco/cost_genread.F (new) : interface between cost_generic    - pkg/ecco/cost_genread.F (new) : interface between cost_generic
# Line 34  o pkg/ecco: extend generic cost capabili Line 947  o pkg/ecco: extend generic cost capabili
947    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs    - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
948  o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA  o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
949  o pkg/ecco: internal re-organization  o pkg/ecco: internal re-organization
950    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl    - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
951      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,      (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
952      mv relevant variables definition from ecco_cost.h to ecco.h,      mv relevant variables definition from ecco_cost.h to ecco.h,
953      make sure gencost routines only include ecco.h)      make sure gencost routines only include ecco.h)
954    - throughout : add missing CCP switches, rm unused variables,    - throughout : add missing CCP switches, rm unused variables,
955      and rm un-necessary CPP switches      and rm un-necessary CPP switches
956    - throughout gencost routines : replace modelstartdate with    - throughout gencost routines : replace modelstartdate with
957      gencost_startdate when needed      gencost_startdate when needed
958    - cost_bp_read.F : use arguments, instead of common blocs    - cost_bp_read.F : use arguments, instead of common blocs
959      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
960    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0    - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
961    - ecco_phys.F : compute etanFull    - ecco_phys.F : compute etanFull
962    - ecco_readparms.F : rename using_topex as using_tpj, add    - ecco_readparms.F : rename using_topex as using_tpj, add
# Line 361  o pkg/seaice: more clean up Line 1274  o pkg/seaice: more clean up
1274      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
1275      this experiment):      this experiment):
1276      > size mitgcmuv_ad      > size mitgcmuv_ad
1277      text    data        bss     dec        hex        text    data        bss     dec        hex
1278      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1279      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1280      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1281      text    data        bss     dec        hex      text    data        bss     dec        hex
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