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revision 1.2040 by jmc, Wed Aug 6 23:19:25 2014 UTC revision 1.2239 by jmc, Mon Mar 14 13:31:47 2016 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65u (2016/03/14)
8    o pkg/generic_advdiff:
9      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
10        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
11        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
12        testing and not for actual use.
13    o model/src:
14      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
15        origin r = rF(1);
16      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
17        in EOS for height coordinate: enable to include NH Pressure or to use
18        more accurate pressure vertical profile; options not linked to EOS type
19        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
20      - start to implement variable gravity (along vertical): for now, only with
21        z-coords (not even z*).
22      - add Ideal Gas equation of state for height coordinate.
23      - update OpenAD output (affected at machine truncation level) of exp:
24        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
25    o pkg/exf:
26      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
27        of exf interpolation (before any rescaling, rotation or interpolation
28        to velocity point) for each field that gets loaded from file. This option
29        identically mimics the input file organization (e.g. record numbers in year
30        by year input files) besides the change in horizontal grid.
31      - add rotateStressOnAgrid run-time switch so that wind stress fields
32        can be provided on the A-grid in zonal/meridional direction and
33        rotated on the fly. This only applies to the case when the exf
34        interpolation is off and rotateStressOnAgrid is false by default.
35    o model/src:
36      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
37        it's also used with pkg/atm_phys) and add few more parameters (but still
38        inactive, src code yet to come)
39    
40    checkpoint65t (2016/02/10)
41    o pkg/atm_phys:
42      - from Ruth Geen: add optical depth dependence on CO2 concentration.
43    o model/src:
44      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
45        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
46        Update output of exp. deep_anelastic (changes at truncation level).
47    o tools:
48      - add a hack in "remove_comments_sed" (used only with TAF) for recent
49        version of OpenMPI (shipped with FC.23): comment out the new header
50        file "mpif-sizeof.h" which causes problems to TAF.
51    o pkg/seaice:
52      - change the termination criterion so that maxits (SEAICElinearIterMax)
53        has an effect
54      - unify iteration parameters for implicit solvers (JFNK and Picard)
55        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
56        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
57        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
58        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
59        SEAICEnonLinTol     replaces JFNKgamma_nonlin
60      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
61      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
62        use with SEAICEuseKrylov
63    o pkg/seaice/seaice_lsr.F
64        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
65        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
66        an effect.
67    o pkg/seaice: add two new parameters
68      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
69        parameter is not in any namelist)
70      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
71        a preconditioner for the non-linear Newton iteration of the JFNK
72        solver
73    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
74      affects some experiments at truncation level:
75      - global_ocean.cs32x15.icedyn (11 digits),
76      - global_ocean.cs32x15.seaice (11 digits),
77      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
78      - also update global_ocean.cs32x15 adjoint and tangent-linear results
79    o pkg/salt_plume & pkg/thsice:
80      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
81        connect salt_plume flux to ATM-OCN coupling pkgs interface:
82       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
83         export to coupler interface) even without compiling pkg/salt_plume ;
84       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
85         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
86    o pkg/dic:
87      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
88        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
89        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
90      - move also update with values from ATM-OCN Coupler in the same new S/R
91        (previously done in ocn_apply_import.F).
92    o tools/adjoint_options:
93      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
94        has been changed on Jan 14, 2016.
95    o pkg/ggl90:
96      - add alternative discretisation of vertical shear (off by default), to
97        compute the mean (@ grid-cell center) of vertical shear compon instead of
98        vertical shear of mean flow (@ grid-cell center).
99      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
100        results on adjacent faces of cubed-sphere grids; this fix the restart.
101    o pkg/atm_compon_interf:
102      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
103        pass last value, stored directly before export to CPL ;
104        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
105      - remove atmSLPr from pickup files (no longer needed for restart)
106    
107    checkpoint65s (2016/01/13)
108    o eesupp & genmake2:
109       - first check for Function ETIME and, if it fails, then check for subroutine
110         ETIME and consistent output; use the appropriate version in timers.F
111    o model/src:
112      - to check restart test, add option to apply EXCH to U,V earlier, just before
113        integr_continuity; turned off by default.
114    o pkg/dic:
115      - remove CPP option USE_ATMOSCO2 (not needed)
116    o tools/tst_2+2:
117      - try to ignore difference between +0 and -0 in binary file, causing test
118        to fail for no good reason.
119    o eesupp & genmake2:
120      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
121        but also check (in genmake2) that test runs and returns meaningful results.
122    o coupler pkgs:
123      Finish implementation of optionally-exchanged variable switches (started on
124       Nov 12) with addition of few more exchanged fields, including 2-way exchange
125       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
126       advection in OCN component; this requires sequential coupling.
127      coupler (pkg/atm_ocn_coupler):
128      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
129        routines (useful for debug).
130      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
131         flux, DIC fields) if corresponding switch is ON.
132      - add option to export RunOff to OCN (to use for DIC river input)
133      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
134      components (pkg/atm_ & ocn_compon_interf):
135      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
136        optionally exchanged fields; add a check & stop in cpl_readparms.F.
137        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
138        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
139      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
140        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
141      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
142      - hold in common block coupler optionally-exchanged variable switch
143        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
144      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
145        this is intended to replace the OCN cplFldtave.* output files (not updated
146        to contain new additional exchanged fields).
147    o pkg/dic:
148      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
149    o pkg/thsice:
150      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
151        and writing of thsice pickup files.
152    o pkg/atm_compon_interf:
153      - move all field individual export-call out of cpl_export_import_data.F
154        into new S/R ATM_EXPORT_FIELDS
155    o pkg/atm_compon_interf:
156      - store state variables (for now, only thSIce fields) just before beeing
157        exported (in cpl_export_import_data.F, like on ocean side) instead of from
158        atm_store_my_data.F like all exported fluxes.
159      - new version of pickup_cpl: write field names into meta file and read meta
160        file to find field postion in pickup. Also only write/read fields meeded for
161        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
162    o pkg/dic:
163      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
164    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
165        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
166        value can be from domain [0,1] to average between the two methods
167    o pkg/atm_phys:
168      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
169        hold fixed in time).
170    
171    checkpoint65r (2015/12/21)
172    o pkg/seaice:
173        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
174        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
175    o pkg/seaice:
176      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
177        when SEAICEscaleSurfStress=.TRUE.,
178      - apply areaW and areaS in S/R seaice_calc_lhs
179    o pkg/atm_phys:
180      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
181        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
182        for individual contribution (convection, LSC cond, radiation)
183      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
184        information); activated with: solar_exponent=0. and wv_exponent=-1.
185    o pkg/ggl90:
186      - within IDEMIX add upper limit for horizontal group velocity to
187        avoid instability problems in the explicit horizontal diffusion term for
188        long time steps or high resolution
189    o pkg/diagnostics:
190      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
191        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
192    o testreport:
193      - remove "-v" (verbose option) in default mpirun command.
194    o pkg/seaice/seaice_growth:
195      - catch potential division by zero in ITD code, does not change
196        verification results
197    o pkg/ecco:
198      - retire old codes to the Attic. The calls to retired functions are
199        left in a commented form in case they ever need to be re-activated.
200      - ecco_check.F: issue warning if any old CPP option is
201        defined that corresponds to retired codes -- then stop.
202    o pkg/atm_compon_interf:
203      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
204        coupler: use last time-step value instead of average over cplSendFrq_iter
205        time-step, similar to what is done for seaIceMass.
206        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
207    o eesupp & genmake2:
208      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
209        <= remove until a fix is found for some ifort version on ia32 machine.
210    o pkg/seaice/seaice_evp:
211      - refine residual computation
212    
213    checkpoint65q (2015/11/18)
214    o pkg/seaice/seaice_evp:
215      - fix residual computations so that they no longer affect the actual
216        simulation code
217      - fix seaice_readparams to be able to actually set new parameters
218        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
219    o model/src:
220      - fix wrong truncation (single prec) from "FLOAT" function in expressions
221        like: deltaT*FLOAT(myIter) when myIter is large:
222         a) replaced by DFLOAT (if not seen by TAF);
223         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
224    o pkg/aim_v23:
225      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
226        when pickupSuff is set ; do write rolling pickups + at the end of the run.
227    o pkg/atm_ocn_coupler + ocn_compon_interf:
228      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
229        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
230        add corresponding call in DO_OCEANIC_PHYS.
231    o coupler pkgs:
232      Start a new way to set-up optionally-exchanged variables (previously, only
233       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
234       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
235       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
236       compononent param default can be set accordingly).
237      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
238       but rather applies to a group a fields (going both ways like for DIC)
239       and corresponds to an option of coupling config.
240      coupler (pkg/atm_ocn_coupler):
241      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
242        and read namelist directly (without eessup S/R calls) instead of
243        in the very un-flexible old way, 1 param per line, in fixed order;
244      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
245        cleanly in CPL_CHECK_CPLCONFIG
246      - add new coupling-exchange selectors (some not yet active) including
247        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
248                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
249      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
250        component ; called directly from coupler.F, after comp. registrations;
251      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
252         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
253          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
254      components (pkg/atm_ & ocn_compon_interf):
255      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
256        CPP header file in all pkg source files.
257      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
258        ATM/OCN_CHECK_CPLCONFIG;
259      - add error-counter to track errors (e.g., in "data.cpl") and to stop
260        cleanly in ATM/OCN_CHECK_CPLCONFIG;
261      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
262        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
263        before PACKAGES_READPARMS;
264      verification/cpl_aim+ocn/:
265      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
266        "data.cpl" for coupler (in input_cpl).
267    o eesupp/inc:
268      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
269        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
270        to always cumulate tile local-sum in the same order (still uses
271        MPI_Allreduce like standard code).
272      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
273        that are now identical to standard version (in eesupp/inc).
274    o pkg/shelfice:
275      - add SHELFICETransCoeffTFile for initializing spatially varying
276        heat and salt transfer coefficients
277    o pkg/atm_compon_interf & ocn_compon_interf:
278      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
279        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
280      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
281    o pkg/atm_ocn_coupler:
282      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
283    o pkg/rbcs:
284      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
285        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
286      - add a short report (to STDOUT) about RBCS-mask settings.
287    
288    checkpoint65p (2015/10/23)
289    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
290        there is no adjoint test for EVP, we don't know what it does to the adjoint
291        solution, but at least there are no more recomputation warnings left
292    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
293        a chance of giving the same results as a fully converged VP (JFNK) solver
294    o tools/adjoint_options/adjoint_diva:
295      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
296    o pkg/streamice:
297      - spotted bug in streamice_driving_stress using dyG where should have been dxG
298    o pkg/exf:
299      - remove STOP statement that prevented to use wind or (wind-)stress
300        interpolation for constant-in-time forcing fields (wind/stress period = 0).
301    o pkg/seaice:
302      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
303        5 additionals 2D fields and 6 new store directives
304      - change logic in seaice_readparms.F: EVP code can now be turned on in
305        various ways, setting SEAICE_deltaTev is no longer required,
306        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
307        or SEAICEaEVPcoeff
308    o pkg/shelfice/shelfice_thermodynamics.F
309      - redefining uLoc/vLoc to u/v, instead of 2u/v
310    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
311      - this is an intermediate state of a truely converging EVP that has
312        the potential of outperforming implicit VP methods, I do not recommend
313        using it yet.
314      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
315        and all parameters are hardwired
316      - for convergence it still requires very smooth regularisations, that means,
317        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
318        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
319        specific averaging appears to be required, still subject to tuning
320      - still needs cleaning and I need to turn parameter into runtime parameters
321      - add code to compute and print residuals of iteration, compile with
322        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
323    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
324      that entered with r1.54 on Sep04, 2015, -> update results
325    
326    checkpoint65o (2015/09/14)
327    o pkg/mom_vecinv & mom_common:
328      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
329        called from there.
330      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
331        allows to use Vector-Invariant form in deep atmos and anelastic formulation
332    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
333      and Koenig-Beatty+Holland (2012)
334      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
335      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
336      - requires an extra input argument for S/R seaice_calc_viscosities
337      - tensileStrength's depth dependence is different from Itkin et al. (2015)
338        (to be changed and played with, for now exponential)
339    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
340      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
341        by AREA according to Connelly et al. (2004), JPO.
342      - For EVP and the LSR solver, the implicit part of the drag term is
343        the only non-zero term in the denominator when there is no ice (which
344        prevented running the model with zero ice-ocean drag). If
345        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
346        (or zero main diagonals BU/BV) which need to be caught. A practical
347        consequence is that for open water, the momentum equation reduce
348        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
349        they happen to be zero, often leading to a non-zero solution over
350        open water.
351    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
352        efficient EVP method.
353      - introduce area-weighted averages for e12 (analogously to
354        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
355        remain, but also changing the order of terms in the previous average
356        changed the results as much) -> update experiment
357      - add SEAICE_DELTA_SMOOTHREG code
358      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
359        TEM-code
360      - adjust loop bounds so that only required fields are computed
361      - add new averaging code for zetaZ/deltaZ (again similar to
362        seaice_calc_viscosities.F), inactive by default for now (will change
363        results again), but will replace old code eventually
364    o eesupp/src:
365      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
366        to always cumulate tile local-sum in the same order
367        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
368        Still uses MPI_Allreduce (like standard code) but on array of tiles
369        and should be faster than GLOBAL_SUM_SEND_RECV code.
370      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
371        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
372      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
373         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
374         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
375         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
376         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
377    
378    checkpoint65n (2015/07/29)
379    o pkg/thsice:
380      - add a warning when used with pkg/aim but without updating SST
381        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
382    o pkg/offline:
383      - change where Offline-Fields are loaded, from load_fields_driver.F to
384        directly within FORWARD_STEP, just after updating iter number and time;
385      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
386        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
387       These changes allow:
388        a) to recover exactly on-line results using deltaToffline=deltaTClock,
389        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
390        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
391        time-step, both with GM & KPP files and with recomputing these fields;
392        b) no needs to switch on staggerTimeStep anymore;
393        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
394      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
395    o pkg/offline:
396      - change (rarely used) offset-iteration parameter to an offset time (in s):
397        can easily recover previous offset-iter effect by setting offset-time
398        (offlineTimeOffset) to offset-iter x deltaToffline;
399      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
400        in KPP as part of surface buoyancy forcing) in offline run.
401      - fix ptracers KPP non-local term in the case where KPP is re-computed.
402    o OpenAD
403      - Adding preliminary ggl90 test to OpenAD verification.
404        Config. with ggl90 currently diverges after 64 time steps
405        so will need more work to become more stable
406      - Adding preliminary kpp test to OpenAD verification.
407        required small tweakes in kpp_routines.F
408      - Merge and update from Krishna Narayanan's contrib area:
409        * Add one variable for preliminary OpenAD DIVA
410        * Add replacement time-stepping for OpenAD DIVA
411        * genmake2 flag -diva (but only for OpenAD; preliminary)
412        * required modifs for OAD_support
413        successful preliminary test for tutorial_global_oce_biogeo/
414    o pkg/seaice:
415      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
416      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
417        delta with a smooth function in s/r seaice_calc_viscosity
418        (no effect on EVP)
419      - rename local suffix "sqr" into "sq" for more consistent variable names
420    o pkg/seaice:
421        add new parameter SEAICE_deltaMin that is used ***only***
422        for regularizing Delta (and nothing else, like the parameter
423        which is also used for all sorts of things SEAICE_EPS).
424        Defaults to SEAICE_EPS for backward compatibility only.
425    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
426        the wrong key by inialising it before use -> fixes a recomputation
427        problem but does not fix the gradient
428    o pkg/layers:
429      - move resetting of flux arrays to outside the iLa loop
430        (this caused layers_diapycnal to not work with more than one layer coord.)
431      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
432    o pkg/layers:
433      - remove from common block 3D layers fields (used to diagnose transport
434        in tracer coords) and declare them as local arrays in layers_calc.F
435    o pkg/seaice:
436      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
437        in lab_sea forward experiment (changes results -> updated)
438      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
439    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
440       computations; for SEAICE_VECTORIZE_LSR
441      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
442        sweep to the outside,
443      - remove store directives and add "CADJ loop sequential" directives
444        in analogy to model/src/solve_tridiagonal.F
445      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
446        boundaries to yield more readable code. This has also the charming side
447        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
448        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
449        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
450        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
451        an additional option)
452       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
453       but the adjoint gradients (which are affected by this change) still explode.
454    o coupler (atm & ocn _compon_interf):
455      - avoid using Exch2 IO mapping if not suitable.
456    
457    checkpoint65m (2015/06/15)
458    o pkg/layers:
459      - clean-up old parameters setting (from Sep 2012):
460        + remove old parameters setting from common block (declared locally);
461        + stop if any old parameter is mixed with new parameters;
462        + check for valid or consistent parameter setting (e.g., layers_name)
463      - check that layers_bounds for Pot.Density are in the right range;
464        this is supposed to catch un-updated setting after recently shifting
465        potential density field "prho" by -1000 (now in "sigma" scale).
466    o pkg/layers:
467      - Added missing call to layers_fill for keeping track of tottend in
468        pkg/diagnostics/diagnostics_fill_state.F
469    o pkg/layers:
470      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
471        of diapycnal fluxes
472    o pkg/layers:
473      - reverted changes to interpolation to previous treatment; there
474        was never actually a problem
475    o pkg/layers:
476      - fix interpolation of layers tracers in the presence of partial cells
477      - add lots of new functionality to compute water mass transformation
478        (enabled by CPP flag LAYERS_THERMODYNAMICS)
479      - add new calls from main code (diags_oceanic_surf_flux.F,
480        thermodynamics.F, impldiff.F) and gad to save the necessary fields
481        for layers_thermodynamics calculations
482    o pkg/ptracers:
483      - add capability of stepping a passive tracer forward without advection
484        by setting PTRACERS_advScheme to 0.
485    o pkg/diagnostics:
486      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
487    o pkg/layers:
488      - shift potential density field "prho" by -1000 for density layer averaging so
489        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
490        Note that density bin boundaries (layers_bounds in data.layers) have
491        to be set accordingly (i.e., shifted, in sigma scale).
492    o pkg/layers:
493      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
494      - fix calculation of layer non-weighted velocity and layer probability
495      - add diagnostics for pot.density used for layer averaging
496    o pkg/seaice:
497      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
498        positiveness, modify a few comments and improve variable names,
499      - the changed computation of deltaC affects most seaice-related
500        experiments at the truncation level.
501        seaice_itd.thermo is affected by far the most, with
502        only 7 digits of agreement remaining; update experiments.
503    
504    checkpoint65l (2015/05/04)
505    o pkg/shelfice:
506      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
507        factor drKp1 to zero where it is negative (ie. do not use
508        SHELFICEBoundaryLayer if hFacC>1)
509      - the same for factor drLoc in shelfice_forcing.F
510    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
511        with modules in ptracers, when using testreport option "-small_f"
512    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
513      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
514    o verification/testreport
515      - add new option -small_f
516        with this option testreport first makes the target small_f (*.f files)
517        before running make (all). This is useful for explicit inlining when
518        all sources need to be full available.
519    o pkg/exf/exf_interp.F:
520        remove previous changes related to reverse (decreasing) input grids latitude
521    
522    checkpoint65k (2015/04/01)
523    o pkg/ecco:
524        fix missing cosphi initialization; use eccoiter in place of optimcycle;
525        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
526        instead of active read/write
527    o pkg/ctrl:
528        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
529        instead of active read/write.
530    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
531        return if .NOT.useAUTODIFF
532    o pkg/seaice: add CPP brackets (cost function related).
533    o model/src:
534        add useAUTODIFF run time switch.
535    o pkg/exf/exf_interp.F:
536        add code to allow input grids with latitude starting in the north (i.e. when
537        j=1 corresponds to northern edge of field); modify global_with_exf to test
538        this feature.
539    o verification/testreport:
540      - replace "grep -A3" with POSIX conformal sed command, because there are
541        implementations of grep that cannot do contextual searches
542      - replace "cat -n" by "nl" (two occurrences), because not all implementations
543        of "cat" have the option "-n"
544    o model/src:
545        add new file gsw_teos10.F that contains 3 functions, more or less a copy
546        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
547        convert from conservative to potential temperature. For now they are not
548        called anywhere.
549    o pkg/ggl90: make "useIDEMIX" useful
550      - re-organize code in s/r ggl90_calc a little to move computations that
551        are different for idemix into separate loops (changes verification
552        experiment idemix at truncation level, 12 digits remain -> updated)
553      - requires 2 new 2D fields KappaM, verticalShear
554      - make hFacI and recip_hFacI local 3D variables that are passed to
555        s/r ggl90_idemix
556      - fix and improve some comments
557    
558    checkpoint65j (2015/02/25)
559    o pkg/openad
560      - synchronize seawater.F with version in model/src: replace routine
561        body of sw_temp by calling sw_ptmp and fix/add a few comments.
562    o pkg/mnc:
563      - change default value of pickup_read/write_mnc params to FALSE
564        (since few features are missing in reading MNC pickup files).
565    o model/src:
566      - change default (background) vertical diffusivity for salt to be the
567        temperature (background) vertical diffusivity.
568      - change background vertical diffusivity in vertical mixing pkgs ggl90,
569        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
570        This makes ptracers default diffusivity (that uses salt diffKr) more
571        consistent with vertical mixing schemes.
572    o verification/testreport:
573      - fix typo in "-pcls" option ;
574      - put temp files in /tmp (instead of in local dir)
575      - add option "-ncad" to use genmake2 new option "-nocat4ad"
576      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
577    o pkg/ggl90 (idemix code):
578      - apply few fixes ; add some missing "_d 0" ; update output of exp.
579        global_ocean.90x40x15.idemix
580    o OpenAD
581      - enable active file I/O and begin removal of work-around code
582        for OpenAD for handling control variables (memory vs. active files)
583      - new CPP options file OPENAD_OPTIONS.h
584      - revert to genarr2d gradient check for hs94.1x64x5
585      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
586      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
587    o tools/genmake2:
588      - add option for an alternative Makefile (from Martin) where multiple
589        source files are sent to TAF (instead of all in one file).
590    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
591      - code provided by Carsten Eden as an extension of ggl90
592      - so far the code is turned on within ggl90 by setting a CPP-flag at
593        compile time; a runtime flag implementation is not yet complete
594      - tested in new verification experiment global_ocean.90x40x15.idemix
595    o verification:
596      - reduce length of the AD test run by half for experiments
597        global_ocean.cs32x15 (std + thsice) and isomip
598      - enable active file I/O for OpenAD, adjust verifications accordingly
599      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
600    o verification/testreport:
601      - fix two non-POSIX sed statements so that there are no error messages
602        on Mac OS X
603      - replace hostname -s with hostname | sed 's/\..*$//'
604    o model/src/seawater.F:
605      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
606        (following the matlab code), which would have avoided the bug caught
607        by Matt (see below) in the first place
608    o pkg/shelfice:
609      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
610        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
611      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
612        ice-shelf case (i.e., within surface level).
613      - add config summary in shelfice_check.F
614      - remove global variable recip_SHELFICElatentHeat and replace by a local
615        variable recip_latentHeat
616      - introduce diagnostics for friction velocity uStar (in case of
617        SHELFICEuseGammaFrict)
618      - change verification experiment isomip.htd:
619        + start from pickup (as input_ad at nIter0=8640)
620        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
621        + test SHELFICEuseGammaFrict = .TRUE.
622        + test SHELFICEadvDiffHeatFlux = .TRUE.
623    o model/src:
624      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
625        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
626        update output of experiments global_with_exf.yearly and isomip (all 6).
627    o pkg/shelfice:
628      - change setting of kTopC to also be zero where there is no ice-shelf.
629      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
630        ice-shelf is.
631      - first attempt to get RealFreshWaterFlux effects: for now, only without
632        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
633    o pkg/seaice: add the option to prescribe a fixed thickness PDF
634      for thermodynamic calculations
635      - because of divisions of the type 7/7 not exactly equal to 1, this change
636        affects results of some verification experiments by up to 4 digits:
637        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
638        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
639        adjoint: lab_sea, lab_sea.noseaicedyn
640        -> updated
641    
642    checkpoint65i (2015/01/23)
643    o model/src:
644      - change units of frictionHeating field from W to W/m^2
645      - fix bug in frictional heating from stratospheric drag in
646        S/R ATM_PHYS_TENDENCY_APPLY_V
647      - with synchronous time-stepping: move resetting to zero of frictionHeating
648        field from load_fields_driver.F to thermodynamics.F ;
649      - add diagnostics for frictional heating.
650    o model/src & gmredi K3D:
651      - add frictionHeating field to pickup-files (for synchronous time-stepping)
652      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
653      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
654        and name in pickup file).
655      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
656    o model/src:
657      - move (from ini_forcing.F) initialisation of all arrays in header file
658        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
659        (since Nov 2012) with option selectAddFluid=1.
660    o pkg/shelfice:
661      - change units (+ document) of newly added field "shelfIceMassDynTendency"
662      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
663    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
664    o pkg/seaice: two new runtime parameters:
665      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
666        long overdue
667      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
668        parameterization of tensil stress for fast ice (does not do anything yet)
669    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
670        for LSR: move checking overlaps out of JFNK-if-block
671    o pkg/atm_phys:
672      - move copy of grid and dynamical fields out of atm_phys_driver.F into
673        new S/R ATM_PHYS_DYN2PHYS.
674      - fix level height for Linear Free-Surf case (to be consistent with
675        fixed-in-time pressure levels).
676    o pkg/mom_common (bottomdrag):
677      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
678        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
679        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
680    o pkg/shelfice (u/v_drag):
681      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
682      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
683        (now similar to shelfice_u_drag.F)
684      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
685        from mom_vecinv.F (similar to mom_fluxform calls).
686    o pkg/mom_common (bottomdrag):
687      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
688      - add options for alternative discretisation of velocity norm in quadratic
689        bottom drag: averaging of grid-cell-center KE to U.point and V.point
690        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
691        improves when averaging only the other component (e.g. vVel for U bottom
692        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
693      - add options (bottomVisc_pCell) to account for partial-cell in bottom
694        friction (no-slip BC) thus getting the true distance from the bottom;
695        off by default since this also reduces model stability (explicit bottom
696        friction). Changes produce different machine truncation with linear-drag
697        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
698        front_relax (bvp & mxl, 10 & 11 digits).
699    o model/src & mom pkgs:
700      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
701        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
702      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
703        just copy level Nr value to level Nr+1.
704    o doc:
705      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
706    o pkg/streamice:
707      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
708        SHELFICE.h: move array shelficemass to init_varia, initialise
709        from array shelficemassinit, which is set in init_fixed and
710        has option to be set from file; introduce array
711        shelficeMassDynTend array, set thru file in init_fixed
712      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
713        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
714        pkg/streamice
715      - shelfice_thermodynamics.F: call shelfice_step_icemass if
716        SHELFICEMassStepping = .true.
717      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
718    
719    checkpoint65h (2014/12/17)
720    o verification/global_ocean.90x40x15, global_ocean_ebm:
721      - update to generic controls.
722    o pkg/ctrl:
723      - ctrl_map_ini_genarr.F: test for igen>0
724      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
725      - move gentim2d part of ctrl_map_ini_genarr.F to
726        new separate routine : ctrl_map_ini_gentim2d.F
727      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
728        add time variable weights and cyclic controls (time mean,
729        seasonal cycle, etc) capabilities to gentim2d
730    o pkg/ecco:
731      - move reading of error, conversion to weights from
732        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
733    o global_oce_llc90, cs32:
734      - activte sbo.
735      - CTRL_SIZE.h : add maxCtrlProc.
736      - activate the new genctrl capabilities.
737      - update following reorganization of global_oce_input_fields.tar.gz  
738    o pkg/ctrl/ctrl_ad_diff.list:
739      - add missing ctrl_init_rec.f
740    o tools/OAD_support/keepOriginal:
741      - add ctrl_init_rec.F
742    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
743      - avoid recomputations of xx_gentim2d_dummy.
744    o momentum diagnostics:
745      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
746        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
747    o pkg/seaice/seaice_lsr.F:
748      - fix computation of BU/BV, make sure they are non-zero, only necessary
749        for cubed sphere exchanges and SEAICE_OLx/y>0.
750        This makes calling s/r fill_cs_corner_rl obsolete (removed).
751    o verification/global_ocean.cs32x15/input.seaice
752      - add test for strong implicit coupling and restricted addtive Schwarz
753        methods for LSR
754      - update results/output.seaice.txt
755    o verification/tutorial_global_oce_biogeo:
756      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
757        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
758        update output_adm,_oadm,_tlm.txt
759    o pkg/dic:
760      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
761      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
762        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
763    o verification/tutorial_global_oce_biogeo:
764      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
765        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
766        update output_adm,_oadm,_tlm.txt
767    o eesupp/src:
768      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
769        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
770    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
771      LSR (following Hutchings et al. 2004)
772      - introduce zetaZ as a global variable (requires adjustments in
773        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
774        in seaice_calc_viscosities.F
775      - new flag SEAICEuseStrImpCpl (default off)
776      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
777        momentum equations
778      - JFNK-solver (preconditioner) adjusted to allow using this method
779        (where it does not have any positive effect)
780    o pkg/seaice
781      - add overlap for restrictive additive Schwartz method also to LSR, but
782        turn it off by default (because it only seems to work for non-cubed
783        sphere/llc topologies)
784    o pkg/autodiff
785      - add extra exchanges in addummy_in_steppging also for mnc output
786    o pkg/seaice:
787      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
788        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
789    o pkg/obcs:
790      - add option to specify domain-connected piece Id along OB though files
791        (for now, only used to diagnose PhiVel; default =1 -> global correction)
792      - modify obcs_diag_balance.F to process each connected-part separately;
793        exclude OB where Id = 0 but keep the full divergence there (-> constant
794        Psi along this portion of OB and all inflow derived from grad(Phi))
795      - add example of OB-conect files in verification/so_box_biogeo/input.
796    o pkg/diagnostics:
797      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
798      a) use non zero matrix element across OB and solve for Phi 1 grid point
799         outside OB (i.e, where tracer OBCS are applied).
800      b) global imbalance of inFlow/outFlow across OB: instead of modifying
801         velocity across OB, spread it uniformly along the OB in the RHS.
802    
803    checkpoint65g (2014/11/19)
804    o pkg/diagnostcis:
805      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
806    o pkg/my82,pp81,kl10:
807      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
808        field diffKr as background diffusivity to set minimum diffusivity value.
809    o pkg/seaice:
810      - add new parameter SEAICEuseEVPrev (for revisited EVP by
811        Bouillon et al 2013)
812      - add SEAICE_evpAlpha/Beta to namelist
813      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
814        involve trivial re-ordering of divisions/multiplications that should not
815        have any effects, but ... they do change the results of lab_sea.hb87 so
816        that only 2 digits of agreement remain, in line with the general
817        instability/fragility of the evp-code. For now, I do not care and just
818        update the verification experiment
819    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
820      - remove xx_genarr2d_numsmooth etc
821      - use xx_genarr2d_preproc etc instead
822      - carry out smooth_correl2D at initialization stage rather than during
823        time stepping.
824      - get smoothOpNb from xx_gentim2d_preproc
825    o global_oce_cs32 :
826      - add test of generic ecco capabilities.
827    o pkg/exf/exf_getsurfacefluxes.F :
828      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
829    o pkg/ctrl,ecco :
830      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
831        is defined.
832    o pkg/seaice: add diagnostics for Delta (deformation parameter)
833    o model/src:
834      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
835        diffusivity (background) is specified but ignored.
836    o verification:
837      - in testreport, convert hostname to lower case for default output dir name
838    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
839    o pkg/dic: add modifications from Hajoon:
840      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
841      - light attenuation: add self-shading effect by climatological Chlorophyll
842        (read from file).
843    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
844        compiles when SEAICE_ALLOW_DYNAMICS is undefined
845    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
846        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
847        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
848        approach where CPP_OPTIONS.h includes an omnipotent
849        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
850    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
851        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
852    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
853        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
854        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
855    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
856      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
857      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
858      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
859      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
860    o pkg/ctrl,ecco,exf :
861      - remove variables associated with NON-generic costs,
862        unless ECCO_CTRL_DEPRECATED is defined.
863      - remove NON-generic NON-obcs controls,
864        unless ECCO_CTRL_DEPRECATED is defined.
865    o pkg/ctrl : added ctrl_local_params.h
866    o pkg/ecco : added ecco_local_params.h
867    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
868        experiments, which will progressively be removed once the
869        experiments are revised to use only generic controls/costs.
870    
871    checkpoint65f (2014/10/13)
872    o pkg/ctrl, ecco, seaice : minor changes in headers
873    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
874        cost function and control capabilities added since checkpoint65c.
875    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
876    o pkg/ecco: increase modularity and improve logic
877      - ecco_toolbox.F (new) : basic operations that are often used,
878        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
879        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
880      - cost_gencal.F (new) : determine filnames and records.
881      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
882      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
883        and exploit the above functions leading to more compact code.
884      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
885      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
886        using_ers, using_gfo, using_mdt is now only defined within gencost)
887    o pkg/ecco: extend generic cost capabilities
888      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
889        capabilities via gencost_preproc (+ _c,_i,_r related params),
890        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
891        gencost_outputlevel arguments to cost_generic
892      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
893        and active_read, making room for gencost_preproc to take effect.
894        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
895      - pkg/ecco/cost_generic.F :
896        compute and store misfit maks*(model-data) in localdif that is
897        then used in cost and for output, output misfit if outlev.GT.0
898      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
899        rather gencost_barfile for deciding whether to write barfile
900      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
901      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
902        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
903      - pkg/ecco/ecco_summary.F : report gencost variables
904      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
905    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
906    o pkg/ecco: internal re-organization
907      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
908        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
909        mv relevant variables definition from ecco_cost.h to ecco.h,
910        make sure gencost routines only include ecco.h)
911      - throughout : add missing CCP switches, rm unused variables,
912        and rm un-necessary CPP switches
913      - throughout gencost routines : replace modelstartdate with
914        gencost_startdate when needed
915      - cost_bp_read.F : use arguments, instead of common blocs
916        so that it can be used also by (new) cost_gencost_bpv4.F
917      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
918      - ecco_phys.F : compute etanFull
919      - ecco_readparms.F : rename using_topex as using_tpj, add
920        bpv4-grace to gencost list, initialize added parameters
921      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
922    
923    checkpoint65e (2014/09/28)
924    o pkg/obcs:
925      - replaced the just-added CPP options with run-time variables
926        (see pkg/obcs/OBCS_PARAMS.h for details)
927    o pkg/obcs:
928      - add additional CPP options for sponge boundary layers
929        (see pkg/obcs/OBCS_OPTIONS.h for details)
930    o pkg/atm_phys:
931      - implement simple (obliquity only, assuming circular planet orbit)
932        seasonal cycle for incoming insolation ; used when run-time parameter
933        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
934    o pkg/exf, pkg/ecco, pkg/ctrl:
935      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
936      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
937      - implement gentim2d for xx_tauu, xx_tauv
938    o pkg/ctrl, pkg/ecco :
939      - fix and complement the generic controls implementation
940    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
941        pkg/shelfice/shelfice_thermodynamics.F,
942        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
943        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
944      - add weight in CTRL_GET_GEN calls
945    o pkg/ctrl :
946      - ctrl_get_gen.F : add weight as input parameter, and apply
947        it directly rather than using smooth_correl2Dw (to be retired).
948      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
949    o pkg/ctrl :
950      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
951        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
952      - re-activate ctrl_summary (call in ctrl_init.F)
953    o pkg/ctrl/ctrl_cost_gen.F :
954      - fix CCP brackets, remove un-necessary myiter, mytime
955    o pkg/ecco, pkg/ctrl :
956      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
957      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
958      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
959      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
960    
961    checkpoint65d (2014/09/15)
962    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
963      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
964        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
965    o pkg/ctrl/ctrl_map_ini_genarr.F :
966      - remove compilation failure
967      - replace hard coded example
968      - use ctrl_map_ini_gen2D, 3D
969    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
970      - on/off switch based upon xx_genarr2d_weight,3d
971    o src/packages_init_variables.F :
972      - regroup pkg/estimation calls
973      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
974        (moved to ctrl_init_variables)
975    o cost/cost_init_varia.F :
976      - remove ecco_cost_init_varia
977        (moved to ecco_init_varia)
978    o ctrl/ctrl_init_variables.F :
979      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
980      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
981    o ctrl/ctrl_map_ini.F :
982      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
983        (moved to ctrl_init_variables)
984    o ctrl/ctrl_map_ini_ecco.F :
985      - remove ECCO_PHYS (mv to ecco_init_varia)
986      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
987    o ecco/ecco_ad_diff.list :
988      - add ecco_init_varia.f
989    o ecco/ecco_init_varia.F
990      - new routine
991    o pkg/streamice:
992      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
993        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
994      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
995    o pkg/generic_advdiff:
996      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
997    o pkg/exf:
998      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
999         xxg_precip capability
1000      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
1001    o pkg/ctrl:
1002      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
1003    o model/src/load_fields_driver.F :
1004      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
1005        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
1006    o OpenAD verification experiments:
1007      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
1008        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
1009        for now, only in pkgs used in OpenAD verification experiments.
1010      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
1011        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
1012        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
1013        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
1014    o OpenAD verification tests:
1015      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
1016      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
1017        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
1018      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
1019        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
1020    o model/src & generic_advdiff:
1021      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
1022        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
1023        dynamics requires valid tracer forcing only over tile interior but, for
1024        some diagnostics, may need to extend it over 1 point in tile halo region.
1025      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
1026        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
1027        setting in temp/salt/ptracer_integrate.F
1028    o pkg/dic:
1029      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
1030        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
1031        in gchem_forcing_sep.F
1032    o pkg/autodiff & obcs:
1033      - add storage of current OB values for U & V (was already done for T & S).
1034    
1035    checkpoint65c (2014/08/30)
1036    o pkg/dic:
1037      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
1038        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
1039        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
1040    o verification:
1041      - new experiment testing OBCS and DIC pkgs, using params & output from
1042        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
1043        passage: take OBCS from the last year of a 2 yrs simulation and initial
1044        conditions from t=1.yr while keeping the same forcing.
1045    o model/src:
1046      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
1047        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
1048    o pkg/diagnostics (Stats-Diags):
1049      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
1050        a) refine region where stats are computed, excluding where arrhFac=0 ;
1051        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
1052        c) extend regional stats over the region edges (for U or V pt location).
1053    o pkg/gchem:
1054      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
1055        pkg/dic is currently changing/updating ptracers values beyond the OB).
1056    o verification (hs94):
1057      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
1058        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
1059        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
1060        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
1061    o pkg/ptracers:
1062      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
1063        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
1064      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
1065        with AB-2 code (so that it get tested).
1066    o model/src:
1067      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
1068        with AB-2 code (previously only available with AB-3 code).
1069        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
1070        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
1071        there, by calling CYCLE_AB_TRACER).
1072    o pkg/generic_advdiff:
1073      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
1074        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
1075        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
1076        S/R temp/salt/ptracers_integrate.F
1077    o model/src & pkg/ptracers:
1078      - remove common block variables gT,gS (in DYNVARS.h), except when
1079         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
1080      - remove common block variable gPtr.
1081    o model/src & pkgs:
1082      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
1083         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
1084         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
1085         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
1086      + change accordingly all calling S/R.
1087      - use local temperature/salinity/ptracer tendency array (without bi,bj)
1088        in S/R temp/salt/ptracers_integrate.F
1089    o pkg/seaice:
1090      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
1091        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
1092      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
1093        in seaice_lsr
1094      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
1095        in s/r seaice_lsr_calc_coeffs
1096    o pkg/mdsio:
1097      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
1098        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
1099        too long (e.g., > MAX_LEN_FNAM/2 )
1100    
1101    checkpoint65b (2014/08/12)
1102    o pkg/matrix:
1103      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
1104    o model/src:
1105      - fix initialisation of geothermalFile; compile geothermal-flux code in
1106        natl_box verification experiment.
1107    o model/src & pkg/down_slope:
1108      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
1109      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
1110        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
1111        results at machine truncation level: update output of experiments
1112        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
1113    o pkg/diagnostics (Stats-Diags):
1114      - do not cumulate the full volume when DIAGNOSTICS_FILL is
1115        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
1116        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
1117        times (but Min,Max and StD are still wrong).
1118    o model/src:
1119      - add geothermal flux forcing: read in ini_forcing.F as time-constant
1120        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
1121    o model/src:
1122      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
1123        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
1124        arrays are already updated while adjustments (filters, conv.adjustment) are
1125        still applied later, in S/R TRACERS_CORRECTION_STEP.
1126  o model/src:  o model/src:
1127    - store in common bloc array "rhoInSitu" the virtual potential temperature    - store in common bloc array "rhoInSitu" the virtual potential temperature
1128      anomaly that is used to compute geopotential: this make the atmos code      anomaly that is used to compute geopotential: this make the atmos code
# Line 82  o model/src: Line 1201  o model/src:
1201    - collect T & S forcing tendency into local 2-D array (passed as argument to    - collect T & S forcing tendency into local 2-D array (passed as argument to
1202      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.      apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
1203      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
1204      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1205      moist correction due to vertical advection).      correction due to vertical advection).
1206    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1207      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1208      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),      seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
# Line 112  o pkg/seaice: more clean up Line 1231  o pkg/seaice: more clean up
1231      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
1232      this experiment):      this experiment):
1233      > size mitgcmuv_ad      > size mitgcmuv_ad
1234      text    data        bss     dec        hex        text    data        bss     dec        hex
1235      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1236      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1237      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1238      text    data        bss     dec        hex      text    data        bss     dec        hex
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