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revision 1.2085 by gforget, Tue Oct 21 14:22:26 2014 UTC revision 1.2270 by gforget, Fri Sep 23 18:44:21 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 global_oce_llc90,cs32 : ecco_v4 verification exps now use separate  o pkg/ecco:
8    AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than   - update and cleanup list of CCP options
9    ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,   - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
10    approach where CPP_OPTIONS.h includes an omnipotent     is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
11    ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').   - add checks that retired run-time options are not used, and in relation
12  o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where     to gencost_mask and gencost_errfile
13    ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.   - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
14       gencost_nrecperiod
15     - fix m_eta computation for virtual salt flux case
16     - add m_horflux_vol case (selected via gencost_barfile) that computes
17       transports via cost_gencost_boxmean (gencost_flag=-3)
18     - use gencost_flag more systematically (i.e., avoid using gencost_name)
19       for code switches (aside from physical variable selection)
20    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
21      attempt appears to be a bit of a hack and my need some repair down the road
22    o pkg/exf:
23      - interpolation near South Pole: fix criteria on input field latitude.
24    o pkg/icefront & pkg/exf:
25      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
26        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
27    o pkg/exf:
28      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
29        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
30        (add suffix "_out" instead of a prefix); keep same record number as in
31        input file but always write record 1 first (to avoid a STOP in I/O S/R).
32        Change output file content by writing interpolated field before applying
33        land-sea mask (helpful for debug).
34      - 2 compon. vector interpolation with rotation: apply scaling factor on
35        each compon. (Eastward and Northward) just before rotation.
36    o pkg/bling:
37      - Cleaned package. Removed not needed code and comments.
38      - adjoint example now works
39        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
40    o pkg/ptracers:
41      - add Bruno Deremble's code to complete the linear surface correction
42        for tracer conservation;
43      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
44    
45    checkpoint65y (2016/07/29)
46    o pkg/debug (stats):
47      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
48        proc/thread mapping);
49      - fix Min & Max for case where 1 thread has only empty tiles;
50      - use RL variable to count number of wet grid points (with big domain,
51        can be too large to fit into integer*4).
52    o pkg/monitor:
53      - use RL variable to count number of wet grid points (but used only for del2)
54      - add new routine to compute Advective CFL within tracer time-stepping with
55        writing delayed until next monitor output.
56    o pkg/obcs:
57      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
58    o pkg/cal:
59      - calandar-dump: treat case myTime < timePhase in the same way as in
60        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
61    o pkg/dic & seaice:
62      - fix compilation of ocean component for coupled atm+ocn model with
63        seaice dynamics & dic.
64    
65    checkpoint65x (2016/06/11)
66    o add a license text file in main MITgcm tree.
67    o added pkg/bling:
68      - intermediate complexity biogeochemical model
69      - see bling_description.txt for details
70      - verification experiment is global_oce_biogeo_bling (for now, in
71        Contrib/verification_other/); tested daily on baudelaire with gfortran.
72      - add entry point in pkg/gchem for new pkg "bling".
73    o pkg/seaice: fix tensile stength computation
74      - replace global field tensileStrength by tensileStrFac
75      - tensileStrFac can be computed once in S/R seaice_init_varia
76      - fortunately that does not affect any verification results
77    
78    checkpoint65w (2016/05/12)
79    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
80         with ECCO_CTRL_DEPRECATED defined
81    o verification/global_ocean.cs32x15:
82      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
83        with "selectNHfreeSurf=1".
84    o model/src (non-hydrostatic free-surface):
85      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
86        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
87      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
88        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
89        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
90        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
91      - Update output (changes at machine truncation level) of verification exp:
92        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
93        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
94    o pkg/seaice: ITD code
95      - fix picking up from a single category model by initialising
96        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
97      - split a long warning message in seaice_check_pickup.F into two lines,
98        because NEC SX-ACE cannot deal with the long line.
99    o model/src:
100      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
101    o pkg/seaice:
102      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
103    o pkg/seaice:
104      - add basal stress as parameterisation for grounding ice
105        following Lemieux et al. (2015)
106      - turn on by setting new parameter SEAICEbasalDragK2 to a value
107        larger than 0. Lemieux et al. (2015) recommend 15.
108      - The adjoint complains with extra recomputations so there is also a
109        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
110        order to postpone the problem
111      - compile the new code in lab_sea
112    o verification/halfpipe_streamice:
113      - update both TAF and OpenAD adm output (machine truncation differences)
114    
115    checkpoint65v (2016/04/08)
116    o verification/advect_xz:
117      - increase overlap size from 3 to 4 and add new secondary test for PQM
118        advection scheme (with mono & wino limiter).
119      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
120    o model/src:
121      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
122        added phi0Ref) to set vertical axis origin and phiRef origin;
123        keep Ro_SeaLevel for backward compatibility (with a warning).
124       According to coordinate and fluid type:
125        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
126        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
127        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
128        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
129      - remove Ro_SeaLevel from ATM experiment parameter files;
130      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
131        complement; update output.txt (changes at machine truncation level).
132    o pkg/seaice/seaice_evp.F
133      - simplify computation of deltaZ and zetaZ to simple averaging following
134        Bouillon et al. (2013). This removes a lot of code, but also changes
135        verification experiment lab_sea.hb87 -> updated
136    
137    checkpoint65u (2016/03/14)
138    o pkg/generic_advdiff:
139      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
140        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
141        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
142        testing and not for actual use.
143    o model/src:
144      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
145        origin r = rF(1);
146      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
147        in EOS for height coordinate: enable to include NH Pressure or to use
148        more accurate pressure vertical profile; options not linked to EOS type
149        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
150      - start to implement variable gravity (along vertical): for now, only with
151        z-coords (not even z*).
152      - add Ideal Gas equation of state for height coordinate.
153      - update OpenAD output (affected at machine truncation level) of exp:
154        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
155    o pkg/exf:
156      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
157        of exf interpolation (before any rescaling, rotation or interpolation
158        to velocity point) for each field that gets loaded from file. This option
159        identically mimics the input file organization (e.g. record numbers in year
160        by year input files) besides the change in horizontal grid.
161      - add rotateStressOnAgrid run-time switch so that wind stress fields
162        can be provided on the A-grid in zonal/meridional direction and
163        rotated on the fly. This only applies to the case when the exf
164        interpolation is off and rotateStressOnAgrid is false by default.
165    o model/src:
166      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
167        it's also used with pkg/atm_phys) and add few more parameters (but still
168        inactive, src code yet to come)
169    
170    checkpoint65t (2016/02/10)
171    o pkg/atm_phys:
172      - from Ruth Geen: add optical depth dependence on CO2 concentration.
173    o model/src:
174      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
175        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
176        Update output of exp. deep_anelastic (changes at truncation level).
177    o tools:
178      - add a hack in "remove_comments_sed" (used only with TAF) for recent
179        version of OpenMPI (shipped with FC.23): comment out the new header
180        file "mpif-sizeof.h" which causes problems to TAF.
181    o pkg/seaice:
182      - change the termination criterion so that maxits (SEAICElinearIterMax)
183        has an effect
184      - unify iteration parameters for implicit solvers (JFNK and Picard)
185        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
186        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
187        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
188        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
189        SEAICEnonLinTol     replaces JFNKgamma_nonlin
190      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
191      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
192        use with SEAICEuseKrylov
193    o pkg/seaice/seaice_lsr.F
194        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
195        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
196        an effect.
197    o pkg/seaice: add two new parameters
198      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
199        parameter is not in any namelist)
200      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
201        a preconditioner for the non-linear Newton iteration of the JFNK
202        solver
203    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
204      affects some experiments at truncation level:
205      - global_ocean.cs32x15.icedyn (11 digits),
206      - global_ocean.cs32x15.seaice (11 digits),
207      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
208      - also update global_ocean.cs32x15 adjoint and tangent-linear results
209    o pkg/salt_plume & pkg/thsice:
210      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
211        connect salt_plume flux to ATM-OCN coupling pkgs interface:
212       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
213         export to coupler interface) even without compiling pkg/salt_plume ;
214       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
215         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
216    o pkg/dic:
217      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
218        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
219        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
220      - move also update with values from ATM-OCN Coupler in the same new S/R
221        (previously done in ocn_apply_import.F).
222    o tools/adjoint_options:
223      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
224        has been changed on Jan 14, 2016.
225    o pkg/ggl90:
226      - add alternative discretisation of vertical shear (off by default), to
227        compute the mean (@ grid-cell center) of vertical shear compon instead of
228        vertical shear of mean flow (@ grid-cell center).
229      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
230        results on adjacent faces of cubed-sphere grids; this fix the restart.
231    o pkg/atm_compon_interf:
232      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
233        pass last value, stored directly before export to CPL ;
234        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
235      - remove atmSLPr from pickup files (no longer needed for restart)
236    
237    checkpoint65s (2016/01/13)
238    o eesupp & genmake2:
239       - first check for Function ETIME and, if it fails, then check for subroutine
240         ETIME and consistent output; use the appropriate version in timers.F
241    o model/src:
242      - to check restart test, add option to apply EXCH to U,V earlier, just before
243        integr_continuity; turned off by default.
244    o pkg/dic:
245      - remove CPP option USE_ATMOSCO2 (not needed)
246    o tools/tst_2+2:
247      - try to ignore difference between +0 and -0 in binary file, causing test
248        to fail for no good reason.
249    o eesupp & genmake2:
250      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
251        but also check (in genmake2) that test runs and returns meaningful results.
252    o coupler pkgs:
253      Finish implementation of optionally-exchanged variable switches (started on
254       Nov 12) with addition of few more exchanged fields, including 2-way exchange
255       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
256       advection in OCN component; this requires sequential coupling.
257      coupler (pkg/atm_ocn_coupler):
258      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
259        routines (useful for debug).
260      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
261         flux, DIC fields) if corresponding switch is ON.
262      - add option to export RunOff to OCN (to use for DIC river input)
263      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
264      components (pkg/atm_ & ocn_compon_interf):
265      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
266        optionally exchanged fields; add a check & stop in cpl_readparms.F.
267        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
268        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
269      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
270        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
271      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
272      - hold in common block coupler optionally-exchanged variable switch
273        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
274      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
275        this is intended to replace the OCN cplFldtave.* output files (not updated
276        to contain new additional exchanged fields).
277    o pkg/dic:
278      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
279    o pkg/thsice:
280      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
281        and writing of thsice pickup files.
282    o pkg/atm_compon_interf:
283      - move all field individual export-call out of cpl_export_import_data.F
284        into new S/R ATM_EXPORT_FIELDS
285    o pkg/atm_compon_interf:
286      - store state variables (for now, only thSIce fields) just before beeing
287        exported (in cpl_export_import_data.F, like on ocean side) instead of from
288        atm_store_my_data.F like all exported fluxes.
289      - new version of pickup_cpl: write field names into meta file and read meta
290        file to find field postion in pickup. Also only write/read fields meeded for
291        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
292    o pkg/dic:
293      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
294    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
295        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
296        value can be from domain [0,1] to average between the two methods
297    o pkg/atm_phys:
298      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
299        hold fixed in time).
300    
301    checkpoint65r (2015/12/21)
302    o pkg/seaice:
303        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
304        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
305    o pkg/seaice:
306      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
307        when SEAICEscaleSurfStress=.TRUE.,
308      - apply areaW and areaS in S/R seaice_calc_lhs
309    o pkg/atm_phys:
310      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
311        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
312        for individual contribution (convection, LSC cond, radiation)
313      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
314        information); activated with: solar_exponent=0. and wv_exponent=-1.
315    o pkg/ggl90:
316      - within IDEMIX add upper limit for horizontal group velocity to
317        avoid instability problems in the explicit horizontal diffusion term for
318        long time steps or high resolution
319    o pkg/diagnostics:
320      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
321        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
322    o testreport:
323      - remove "-v" (verbose option) in default mpirun command.
324    o pkg/seaice/seaice_growth:
325      - catch potential division by zero in ITD code, does not change
326        verification results
327    o pkg/ecco:
328      - retire old codes to the Attic. The calls to retired functions are
329        left in a commented form in case they ever need to be re-activated.
330      - ecco_check.F: issue warning if any old CPP option is
331        defined that corresponds to retired codes -- then stop.
332    o pkg/atm_compon_interf:
333      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
334        coupler: use last time-step value instead of average over cplSendFrq_iter
335        time-step, similar to what is done for seaIceMass.
336        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
337    o eesupp & genmake2:
338      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
339        <= remove until a fix is found for some ifort version on ia32 machine.
340    o pkg/seaice/seaice_evp:
341      - refine residual computation
342    
343    checkpoint65q (2015/11/18)
344    o pkg/seaice/seaice_evp:
345      - fix residual computations so that they no longer affect the actual
346        simulation code
347      - fix seaice_readparams to be able to actually set new parameters
348        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
349    o model/src:
350      - fix wrong truncation (single prec) from "FLOAT" function in expressions
351        like: deltaT*FLOAT(myIter) when myIter is large:
352         a) replaced by DFLOAT (if not seen by TAF);
353         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
354    o pkg/aim_v23:
355      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
356        when pickupSuff is set ; do write rolling pickups + at the end of the run.
357    o pkg/atm_ocn_coupler + ocn_compon_interf:
358      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
359        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
360        add corresponding call in DO_OCEANIC_PHYS.
361    o coupler pkgs:
362      Start a new way to set-up optionally-exchanged variables (previously, only
363       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
364       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
365       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
366       compononent param default can be set accordingly).
367      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
368       but rather applies to a group a fields (going both ways like for DIC)
369       and corresponds to an option of coupling config.
370      coupler (pkg/atm_ocn_coupler):
371      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
372        and read namelist directly (without eessup S/R calls) instead of
373        in the very un-flexible old way, 1 param per line, in fixed order;
374      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
375        cleanly in CPL_CHECK_CPLCONFIG
376      - add new coupling-exchange selectors (some not yet active) including
377        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
378                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
379      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
380        component ; called directly from coupler.F, after comp. registrations;
381      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
382         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
383          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
384      components (pkg/atm_ & ocn_compon_interf):
385      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
386        CPP header file in all pkg source files.
387      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
388        ATM/OCN_CHECK_CPLCONFIG;
389      - add error-counter to track errors (e.g., in "data.cpl") and to stop
390        cleanly in ATM/OCN_CHECK_CPLCONFIG;
391      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
392        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
393        before PACKAGES_READPARMS;
394      verification/cpl_aim+ocn/:
395      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
396        "data.cpl" for coupler (in input_cpl).
397    o eesupp/inc:
398      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
399        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
400        to always cumulate tile local-sum in the same order (still uses
401        MPI_Allreduce like standard code).
402      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
403        that are now identical to standard version (in eesupp/inc).
404    o pkg/shelfice:
405      - add SHELFICETransCoeffTFile for initializing spatially varying
406        heat and salt transfer coefficients
407    o pkg/atm_compon_interf & ocn_compon_interf:
408      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
409        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
410      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
411    o pkg/atm_ocn_coupler:
412      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
413    o pkg/rbcs:
414      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
415        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
416      - add a short report (to STDOUT) about RBCS-mask settings.
417    
418    checkpoint65p (2015/10/23)
419    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
420        there is no adjoint test for EVP, we don't know what it does to the adjoint
421        solution, but at least there are no more recomputation warnings left
422    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
423        a chance of giving the same results as a fully converged VP (JFNK) solver
424    o tools/adjoint_options/adjoint_diva:
425      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
426    o pkg/streamice:
427      - spotted bug in streamice_driving_stress using dyG where should have been dxG
428    o pkg/exf:
429      - remove STOP statement that prevented to use wind or (wind-)stress
430        interpolation for constant-in-time forcing fields (wind/stress period = 0).
431    o pkg/seaice:
432      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
433        5 additionals 2D fields and 6 new store directives
434      - change logic in seaice_readparms.F: EVP code can now be turned on in
435        various ways, setting SEAICE_deltaTev is no longer required,
436        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
437        or SEAICEaEVPcoeff
438    o pkg/shelfice/shelfice_thermodynamics.F
439      - redefining uLoc/vLoc to u/v, instead of 2u/v
440    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
441      - this is an intermediate state of a truely converging EVP that has
442        the potential of outperforming implicit VP methods, I do not recommend
443        using it yet.
444      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
445        and all parameters are hardwired
446      - for convergence it still requires very smooth regularisations, that means,
447        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
448        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
449        specific averaging appears to be required, still subject to tuning
450      - still needs cleaning and I need to turn parameter into runtime parameters
451      - add code to compute and print residuals of iteration, compile with
452        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
453    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
454      that entered with r1.54 on Sep04, 2015, -> update results
455    
456    checkpoint65o (2015/09/14)
457    o pkg/mom_vecinv & mom_common:
458      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
459        called from there.
460      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
461        allows to use Vector-Invariant form in deep atmos and anelastic formulation
462    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
463      and Koenig-Beatty+Holland (2012)
464      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
465      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
466      - requires an extra input argument for S/R seaice_calc_viscosities
467      - tensileStrength's depth dependence is different from Itkin et al. (2015)
468        (to be changed and played with, for now exponential)
469    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
470      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
471        by AREA according to Connelly et al. (2004), JPO.
472      - For EVP and the LSR solver, the implicit part of the drag term is
473        the only non-zero term in the denominator when there is no ice (which
474        prevented running the model with zero ice-ocean drag). If
475        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
476        (or zero main diagonals BU/BV) which need to be caught. A practical
477        consequence is that for open water, the momentum equation reduce
478        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
479        they happen to be zero, often leading to a non-zero solution over
480        open water.
481    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
482        efficient EVP method.
483      - introduce area-weighted averages for e12 (analogously to
484        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
485        remain, but also changing the order of terms in the previous average
486        changed the results as much) -> update experiment
487      - add SEAICE_DELTA_SMOOTHREG code
488      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
489        TEM-code
490      - adjust loop bounds so that only required fields are computed
491      - add new averaging code for zetaZ/deltaZ (again similar to
492        seaice_calc_viscosities.F), inactive by default for now (will change
493        results again), but will replace old code eventually
494    o eesupp/src:
495      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
496        to always cumulate tile local-sum in the same order
497        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
498        Still uses MPI_Allreduce (like standard code) but on array of tiles
499        and should be faster than GLOBAL_SUM_SEND_RECV code.
500      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
501        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
502      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
503         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
504         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
505         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
506         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
507    
508    checkpoint65n (2015/07/29)
509    o pkg/thsice:
510      - add a warning when used with pkg/aim but without updating SST
511        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
512    o pkg/offline:
513      - change where Offline-Fields are loaded, from load_fields_driver.F to
514        directly within FORWARD_STEP, just after updating iter number and time;
515      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
516        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
517       These changes allow:
518        a) to recover exactly on-line results using deltaToffline=deltaTClock,
519        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
520        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
521        time-step, both with GM & KPP files and with recomputing these fields;
522        b) no needs to switch on staggerTimeStep anymore;
523        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
524      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
525    o pkg/offline:
526      - change (rarely used) offset-iteration parameter to an offset time (in s):
527        can easily recover previous offset-iter effect by setting offset-time
528        (offlineTimeOffset) to offset-iter x deltaToffline;
529      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
530        in KPP as part of surface buoyancy forcing) in offline run.
531      - fix ptracers KPP non-local term in the case where KPP is re-computed.
532    o OpenAD
533      - Adding preliminary ggl90 test to OpenAD verification.
534        Config. with ggl90 currently diverges after 64 time steps
535        so will need more work to become more stable
536      - Adding preliminary kpp test to OpenAD verification.
537        required small tweakes in kpp_routines.F
538      - Merge and update from Krishna Narayanan's contrib area:
539        * Add one variable for preliminary OpenAD DIVA
540        * Add replacement time-stepping for OpenAD DIVA
541        * genmake2 flag -diva (but only for OpenAD; preliminary)
542        * required modifs for OAD_support
543        successful preliminary test for tutorial_global_oce_biogeo/
544    o pkg/seaice:
545      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
546      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
547        delta with a smooth function in s/r seaice_calc_viscosity
548        (no effect on EVP)
549      - rename local suffix "sqr" into "sq" for more consistent variable names
550    o pkg/seaice:
551        add new parameter SEAICE_deltaMin that is used ***only***
552        for regularizing Delta (and nothing else, like the parameter
553        which is also used for all sorts of things SEAICE_EPS).
554        Defaults to SEAICE_EPS for backward compatibility only.
555    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
556        the wrong key by inialising it before use -> fixes a recomputation
557        problem but does not fix the gradient
558    o pkg/layers:
559      - move resetting of flux arrays to outside the iLa loop
560        (this caused layers_diapycnal to not work with more than one layer coord.)
561      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
562    o pkg/layers:
563      - remove from common block 3D layers fields (used to diagnose transport
564        in tracer coords) and declare them as local arrays in layers_calc.F
565    o pkg/seaice:
566      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
567        in lab_sea forward experiment (changes results -> updated)
568      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
569    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
570       computations; for SEAICE_VECTORIZE_LSR
571      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
572        sweep to the outside,
573      - remove store directives and add "CADJ loop sequential" directives
574        in analogy to model/src/solve_tridiagonal.F
575      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
576        boundaries to yield more readable code. This has also the charming side
577        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
578        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
579        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
580        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
581        an additional option)
582       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
583       but the adjoint gradients (which are affected by this change) still explode.
584    o coupler (atm & ocn _compon_interf):
585      - avoid using Exch2 IO mapping if not suitable.
586    
587    checkpoint65m (2015/06/15)
588    o pkg/layers:
589      - clean-up old parameters setting (from Sep 2012):
590        + remove old parameters setting from common block (declared locally);
591        + stop if any old parameter is mixed with new parameters;
592        + check for valid or consistent parameter setting (e.g., layers_name)
593      - check that layers_bounds for Pot.Density are in the right range;
594        this is supposed to catch un-updated setting after recently shifting
595        potential density field "prho" by -1000 (now in "sigma" scale).
596    o pkg/layers:
597      - Added missing call to layers_fill for keeping track of tottend in
598        pkg/diagnostics/diagnostics_fill_state.F
599    o pkg/layers:
600      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
601        of diapycnal fluxes
602    o pkg/layers:
603      - reverted changes to interpolation to previous treatment; there
604        was never actually a problem
605    o pkg/layers:
606      - fix interpolation of layers tracers in the presence of partial cells
607      - add lots of new functionality to compute water mass transformation
608        (enabled by CPP flag LAYERS_THERMODYNAMICS)
609      - add new calls from main code (diags_oceanic_surf_flux.F,
610        thermodynamics.F, impldiff.F) and gad to save the necessary fields
611        for layers_thermodynamics calculations
612    o pkg/ptracers:
613      - add capability of stepping a passive tracer forward without advection
614        by setting PTRACERS_advScheme to 0.
615    o pkg/diagnostics:
616      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
617    o pkg/layers:
618      - shift potential density field "prho" by -1000 for density layer averaging so
619        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
620        Note that density bin boundaries (layers_bounds in data.layers) have
621        to be set accordingly (i.e., shifted, in sigma scale).
622    o pkg/layers:
623      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
624      - fix calculation of layer non-weighted velocity and layer probability
625      - add diagnostics for pot.density used for layer averaging
626    o pkg/seaice:
627      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
628        positiveness, modify a few comments and improve variable names,
629      - the changed computation of deltaC affects most seaice-related
630        experiments at the truncation level.
631        seaice_itd.thermo is affected by far the most, with
632        only 7 digits of agreement remaining; update experiments.
633    
634    checkpoint65l (2015/05/04)
635    o pkg/shelfice:
636      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
637        factor drKp1 to zero where it is negative (ie. do not use
638        SHELFICEBoundaryLayer if hFacC>1)
639      - the same for factor drLoc in shelfice_forcing.F
640    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
641        with modules in ptracers, when using testreport option "-small_f"
642    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
643      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
644    o verification/testreport
645      - add new option -small_f
646        with this option testreport first makes the target small_f (*.f files)
647        before running make (all). This is useful for explicit inlining when
648        all sources need to be full available.
649    o pkg/exf/exf_interp.F:
650        remove previous changes related to reverse (decreasing) input grids latitude
651    
652    checkpoint65k (2015/04/01)
653    o pkg/ecco:
654        fix missing cosphi initialization; use eccoiter in place of optimcycle;
655        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
656        instead of active read/write
657    o pkg/ctrl:
658        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
659        instead of active read/write.
660    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
661        return if .NOT.useAUTODIFF
662    o pkg/seaice: add CPP brackets (cost function related).
663    o model/src:
664        add useAUTODIFF run time switch.
665    o pkg/exf/exf_interp.F:
666        add code to allow input grids with latitude starting in the north (i.e. when
667        j=1 corresponds to northern edge of field); modify global_with_exf to test
668        this feature.
669    o verification/testreport:
670      - replace "grep -A3" with POSIX conformal sed command, because there are
671        implementations of grep that cannot do contextual searches
672      - replace "cat -n" by "nl" (two occurrences), because not all implementations
673        of "cat" have the option "-n"
674    o model/src:
675        add new file gsw_teos10.F that contains 3 functions, more or less a copy
676        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
677        convert from conservative to potential temperature. For now they are not
678        called anywhere.
679    o pkg/ggl90: make "useIDEMIX" useful
680      - re-organize code in s/r ggl90_calc a little to move computations that
681        are different for idemix into separate loops (changes verification
682        experiment idemix at truncation level, 12 digits remain -> updated)
683      - requires 2 new 2D fields KappaM, verticalShear
684      - make hFacI and recip_hFacI local 3D variables that are passed to
685        s/r ggl90_idemix
686      - fix and improve some comments
687    
688    checkpoint65j (2015/02/25)
689    o pkg/openad
690      - synchronize seawater.F with version in model/src: replace routine
691        body of sw_temp by calling sw_ptmp and fix/add a few comments.
692    o pkg/mnc:
693      - change default value of pickup_read/write_mnc params to FALSE
694        (since few features are missing in reading MNC pickup files).
695    o model/src:
696      - change default (background) vertical diffusivity for salt to be the
697        temperature (background) vertical diffusivity.
698      - change background vertical diffusivity in vertical mixing pkgs ggl90,
699        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
700        This makes ptracers default diffusivity (that uses salt diffKr) more
701        consistent with vertical mixing schemes.
702    o verification/testreport:
703      - fix typo in "-pcls" option ;
704      - put temp files in /tmp (instead of in local dir)
705      - add option "-ncad" to use genmake2 new option "-nocat4ad"
706      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
707    o pkg/ggl90 (idemix code):
708      - apply few fixes ; add some missing "_d 0" ; update output of exp.
709        global_ocean.90x40x15.idemix
710    o OpenAD
711      - enable active file I/O and begin removal of work-around code
712        for OpenAD for handling control variables (memory vs. active files)
713      - new CPP options file OPENAD_OPTIONS.h
714      - revert to genarr2d gradient check for hs94.1x64x5
715      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
716      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
717    o tools/genmake2:
718      - add option for an alternative Makefile (from Martin) where multiple
719        source files are sent to TAF (instead of all in one file).
720    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
721      - code provided by Carsten Eden as an extension of ggl90
722      - so far the code is turned on within ggl90 by setting a CPP-flag at
723        compile time; a runtime flag implementation is not yet complete
724      - tested in new verification experiment global_ocean.90x40x15.idemix
725    o verification:
726      - reduce length of the AD test run by half for experiments
727        global_ocean.cs32x15 (std + thsice) and isomip
728      - enable active file I/O for OpenAD, adjust verifications accordingly
729      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
730    o verification/testreport:
731      - fix two non-POSIX sed statements so that there are no error messages
732        on Mac OS X
733      - replace hostname -s with hostname | sed 's/\..*$//'
734    o model/src/seawater.F:
735      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
736        (following the matlab code), which would have avoided the bug caught
737        by Matt (see below) in the first place
738    o pkg/shelfice:
739      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
740        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
741      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
742        ice-shelf case (i.e., within surface level).
743      - add config summary in shelfice_check.F
744      - remove global variable recip_SHELFICElatentHeat and replace by a local
745        variable recip_latentHeat
746      - introduce diagnostics for friction velocity uStar (in case of
747        SHELFICEuseGammaFrict)
748      - change verification experiment isomip.htd:
749        + start from pickup (as input_ad at nIter0=8640)
750        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
751        + test SHELFICEuseGammaFrict = .TRUE.
752        + test SHELFICEadvDiffHeatFlux = .TRUE.
753    o model/src:
754      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
755        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
756        update output of experiments global_with_exf.yearly and isomip (all 6).
757    o pkg/shelfice:
758      - change setting of kTopC to also be zero where there is no ice-shelf.
759      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
760        ice-shelf is.
761      - first attempt to get RealFreshWaterFlux effects: for now, only without
762        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
763    o pkg/seaice: add the option to prescribe a fixed thickness PDF
764      for thermodynamic calculations
765      - because of divisions of the type 7/7 not exactly equal to 1, this change
766        affects results of some verification experiments by up to 4 digits:
767        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
768        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
769        adjoint: lab_sea, lab_sea.noseaicedyn
770        -> updated
771    
772    checkpoint65i (2015/01/23)
773    o model/src:
774      - change units of frictionHeating field from W to W/m^2
775      - fix bug in frictional heating from stratospheric drag in
776        S/R ATM_PHYS_TENDENCY_APPLY_V
777      - with synchronous time-stepping: move resetting to zero of frictionHeating
778        field from load_fields_driver.F to thermodynamics.F ;
779      - add diagnostics for frictional heating.
780    o model/src & gmredi K3D:
781      - add frictionHeating field to pickup-files (for synchronous time-stepping)
782      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
783      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
784        and name in pickup file).
785      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
786    o model/src:
787      - move (from ini_forcing.F) initialisation of all arrays in header file
788        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
789        (since Nov 2012) with option selectAddFluid=1.
790    o pkg/shelfice:
791      - change units (+ document) of newly added field "shelfIceMassDynTendency"
792      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
793    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
794    o pkg/seaice: two new runtime parameters:
795      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
796        long overdue
797      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
798        parameterization of tensil stress for fast ice (does not do anything yet)
799    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
800        for LSR: move checking overlaps out of JFNK-if-block
801    o pkg/atm_phys:
802      - move copy of grid and dynamical fields out of atm_phys_driver.F into
803        new S/R ATM_PHYS_DYN2PHYS.
804      - fix level height for Linear Free-Surf case (to be consistent with
805        fixed-in-time pressure levels).
806    o pkg/mom_common (bottomdrag):
807      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
808        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
809        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
810    o pkg/shelfice (u/v_drag):
811      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
812      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
813        (now similar to shelfice_u_drag.F)
814      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
815        from mom_vecinv.F (similar to mom_fluxform calls).
816    o pkg/mom_common (bottomdrag):
817      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
818      - add options for alternative discretisation of velocity norm in quadratic
819        bottom drag: averaging of grid-cell-center KE to U.point and V.point
820        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
821        improves when averaging only the other component (e.g. vVel for U bottom
822        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
823      - add options (bottomVisc_pCell) to account for partial-cell in bottom
824        friction (no-slip BC) thus getting the true distance from the bottom;
825        off by default since this also reduces model stability (explicit bottom
826        friction). Changes produce different machine truncation with linear-drag
827        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
828        front_relax (bvp & mxl, 10 & 11 digits).
829    o model/src & mom pkgs:
830      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
831        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
832      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
833        just copy level Nr value to level Nr+1.
834    o doc:
835      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
836    o pkg/shelfice:
837      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
838        SHELFICE.h: move array shelficemass to init_varia, initialise
839        from array shelficemassinit, which is set in init_fixed and
840        has option to be set from file; introduce array
841        shelficeMassDynTend array, set thru file in init_fixed
842      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
843        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
844        pkg/streamice
845      - shelfice_thermodynamics.F: call shelfice_step_icemass if
846        SHELFICEMassStepping = .true.
847      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
848    
849    checkpoint65h (2014/12/17)
850    o verification/global_ocean.90x40x15, global_ocean_ebm:
851      - update to generic controls.
852    o pkg/ctrl:
853      - ctrl_map_ini_genarr.F: test for igen>0
854      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
855      - move gentim2d part of ctrl_map_ini_genarr.F to
856        new separate routine : ctrl_map_ini_gentim2d.F
857      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
858        add time variable weights and cyclic controls (time mean,
859        seasonal cycle, etc) capabilities to gentim2d
860    o pkg/ecco:
861      - move reading of error, conversion to weights from
862        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
863    o global_oce_llc90, cs32:
864      - activte sbo.
865      - CTRL_SIZE.h : add maxCtrlProc.
866      - activate the new genctrl capabilities.
867      - update following reorganization of global_oce_input_fields.tar.gz  
868    o pkg/ctrl/ctrl_ad_diff.list:
869      - add missing ctrl_init_rec.f
870    o tools/OAD_support/keepOriginal:
871      - add ctrl_init_rec.F
872    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
873      - avoid recomputations of xx_gentim2d_dummy.
874    o momentum diagnostics:
875      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
876        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
877    o pkg/seaice/seaice_lsr.F:
878      - fix computation of BU/BV, make sure they are non-zero, only necessary
879        for cubed sphere exchanges and SEAICE_OLx/y>0.
880        This makes calling s/r fill_cs_corner_rl obsolete (removed).
881    o verification/global_ocean.cs32x15/input.seaice
882      - add test for strong implicit coupling and restricted addtive Schwarz
883        methods for LSR
884      - update results/output.seaice.txt
885    o verification/tutorial_global_oce_biogeo:
886      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
887        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
888        update output_adm,_oadm,_tlm.txt
889    o pkg/dic:
890      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
891      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
892        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
893    o verification/tutorial_global_oce_biogeo:
894      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
895        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
896        update output_adm,_oadm,_tlm.txt
897    o eesupp/src:
898      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
899        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
900    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
901      LSR (following Hutchings et al. 2004)
902      - introduce zetaZ as a global variable (requires adjustments in
903        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
904        in seaice_calc_viscosities.F
905      - new flag SEAICEuseStrImpCpl (default off)
906      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
907        momentum equations
908      - JFNK-solver (preconditioner) adjusted to allow using this method
909        (where it does not have any positive effect)
910    o pkg/seaice
911      - add overlap for restrictive additive Schwartz method also to LSR, but
912        turn it off by default (because it only seems to work for non-cubed
913        sphere/llc topologies)
914    o pkg/autodiff
915      - add extra exchanges in addummy_in_steppging also for mnc output
916    o pkg/seaice:
917      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
918        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
919    o pkg/obcs:
920      - add option to specify domain-connected piece Id along OB though files
921        (for now, only used to diagnose PhiVel; default =1 -> global correction)
922      - modify obcs_diag_balance.F to process each connected-part separately;
923        exclude OB where Id = 0 but keep the full divergence there (-> constant
924        Psi along this portion of OB and all inflow derived from grad(Phi))
925      - add example of OB-conect files in verification/so_box_biogeo/input.
926    o pkg/diagnostics:
927      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
928      a) use non zero matrix element across OB and solve for Phi 1 grid point
929         outside OB (i.e, where tracer OBCS are applied).
930      b) global imbalance of inFlow/outFlow across OB: instead of modifying
931         velocity across OB, spread it uniformly along the OB in the RHS.
932    
933    checkpoint65g (2014/11/19)
934    o pkg/diagnostcis:
935      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
936    o pkg/my82,pp81,kl10:
937      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
938        field diffKr as background diffusivity to set minimum diffusivity value.
939    o pkg/seaice:
940      - add new parameter SEAICEuseEVPrev (for revisited EVP by
941        Bouillon et al 2013)
942      - add SEAICE_evpAlpha/Beta to namelist
943      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
944        involve trivial re-ordering of divisions/multiplications that should not
945        have any effects, but ... they do change the results of lab_sea.hb87 so
946        that only 2 digits of agreement remain, in line with the general
947        instability/fragility of the evp-code. For now, I do not care and just
948        update the verification experiment
949    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
950      - remove xx_genarr2d_numsmooth etc
951      - use xx_genarr2d_preproc etc instead
952      - carry out smooth_correl2D at initialization stage rather than during
953        time stepping.
954      - get smoothOpNb from xx_gentim2d_preproc
955    o global_oce_cs32 :
956      - add test of generic ecco capabilities.
957    o pkg/exf/exf_getsurfacefluxes.F :
958      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
959    o pkg/ctrl,ecco :
960      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
961        is defined.
962    o pkg/seaice: add diagnostics for Delta (deformation parameter)
963    o model/src:
964      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
965        diffusivity (background) is specified but ignored.
966    o verification:
967      - in testreport, convert hostname to lower case for default output dir name
968    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
969    o pkg/dic: add modifications from Hajoon:
970      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
971      - light attenuation: add self-shading effect by climatological Chlorophyll
972        (read from file).
973    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
974        compiles when SEAICE_ALLOW_DYNAMICS is undefined
975    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
976        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
977        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
978        approach where CPP_OPTIONS.h includes an omnipotent
979        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
980    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
981        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
982  o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF  o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
983    to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included      to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
984    (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)      (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
985  o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :  o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
986    add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed    add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
987    - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h    - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
988    - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h    - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
989    - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc    - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
990  o pkg/ctrl,ecco,exf :  o pkg/ctrl,ecco,exf :
991    - remove variables associated with NON-generic costs,    - remove variables associated with NON-generic costs,
992      unless ECCO_CTRL_DEPRECATED is defined.      unless ECCO_CTRL_DEPRECATED is defined.
993    - remove NON-generic NON-obcs controls,    - remove NON-generic NON-obcs controls,
994      unless ECCO_CTRL_DEPRECATED is defined.      unless ECCO_CTRL_DEPRECATED is defined.
995  o pkg/ctrl : added ctrl_local_params.h  o pkg/ctrl : added ctrl_local_params.h
996  o pkg/ecco : added ecco_local_params.h  o pkg/ecco : added ecco_local_params.h
997  o verification : added ECCO_CTRL_DEPRECATED to most as and oad  o verification : added ECCO_CTRL_DEPRECATED to most as and oad
998    experiments, which will progressively be removed once the      experiments, which will progressively be removed once the
999    experiments are revised to use only generic controls/costs.      experiments are revised to use only generic controls/costs.
1000    
1001  checkpoint65f (2014/10/13)  checkpoint65f (2014/10/13)
1002  o pkg/ctrl, ecco, seaice : minor changes in headers  o pkg/ctrl, ecco, seaice : minor changes in headers
1003  o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic  o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
1004    cost function and control capabilities added since checkpoint65c.      cost function and control capabilities added since checkpoint65c.
1005  o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.  o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
1006  o pkg/ecco: increase modularity and improve logic  o pkg/ecco: increase modularity and improve logic
1007    - ecco_toolbox.F (new) : basic operations that are often used,    - ecco_toolbox.F (new) : basic operations that are often used,
# Line 393  o pkg/seaice: more clean up Line 1361  o pkg/seaice: more clean up
1361      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
1362      this experiment):      this experiment):
1363      > size mitgcmuv_ad      > size mitgcmuv_ad
1364      text    data        bss     dec        hex        text    data        bss     dec        hex
1365      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1366      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1367      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1368      text    data        bss     dec        hex      text    data        bss     dec        hex
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