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revision 1.2107 by jmc, Wed Dec 17 17:58:39 2014 UTC revision 1.2227 by mlosch, Thu Jan 21 16:04:00 2016 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
8      affects some experiments at truncation level:
9      - global_ocean.cs32x15.icedyn (11 digits),
10      - global_ocean.cs32x15.seaice (11 digits),
11      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
12      - also update global_ocean.cs32x15 adjoint and tangent-linear results
13    o pkg/salt_plume & pkg/thsice:
14      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
15        connect salt_plume flux to ATM-OCN coupling pkgs interface:
16       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
17         export to coupler interface) even without compiling pkg/salt_plume ;
18       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
19         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
20    o pkg/dic:
21      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
22        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
23        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
24      - move also update with values from ATM-OCN Coupler in the same new S/R
25        (previously done in ocn_apply_import.F).
26    o tools/adjoint_options:
27      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
28        has been changed on Jan 14, 2016.
29    o pkg/ggl90:
30      - add alternative discretisation of vertical shear (off by default), to
31        compute the mean (@ grid-cell center) of vertical shear compon instead of
32        vertical shear of mean flow (@ grid-cell center).
33      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
34        results on adjacent faces of cubed-sphere grids; this fix the restart.
35    o pkg/atm_compon_interf:
36      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
37        pass last value, stored directly before export to CPL ;
38        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
39      - remove atmSLPr from pickup files (no longer needed for restart)
40    
41    checkpoint65s (2016/01/13)
42    o eesupp & genmake2:
43       - first check for Function ETIME and, if it fails, then check for subroutine
44         ETIME and consistent output; use the appropriate version in timers.F
45    o model/src:
46      - to check restart test, add option to apply EXCH to U,V earlier, just before
47        integr_continuity; turned off by default.
48    o pkg/dic:
49      - remove CPP option USE_ATMOSCO2 (not needed)
50    o tools/tst_2+2:
51      - try to ignore difference between +0 and -0 in binary file, causing test
52        to fail for no good reason.
53    o eesupp & genmake2:
54      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
55        but also check (in genmake2) that test runs and returns meaningful results.
56    o coupler pkgs:
57      Finish implementation of optionally-exchanged variable switches (started on
58       Nov 12) with addition of few more exchanged fields, including 2-way exchange
59       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
60       advection in OCN component; this requires sequential coupling.
61      coupler (pkg/atm_ocn_coupler):
62      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
63        routines (useful for debug).
64      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
65         flux, DIC fields) if corresponding switch is ON.
66      - add option to export RunOff to OCN (to use for DIC river input)
67      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
68      components (pkg/atm_ & ocn_compon_interf):
69      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
70        optionally exchanged fields; add a check & stop in cpl_readparms.F.
71        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
72        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
73      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
74        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
75      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
76      - hold in common block coupler optionally-exchanged variable switch
77        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
78      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
79        this is intended to replace the OCN cplFldtave.* output files (not updated
80        to contain new additional exchanged fields).
81    o pkg/dic:
82      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
83    o pkg/thsice:
84      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
85        and writing of thsice pickup files.
86    o pkg/atm_compon_interf:
87      - move all field individual export-call out of cpl_export_import_data.F
88        into new S/R ATM_EXPORT_FIELDS
89    o pkg/atm_compon_interf:
90      - store state variables (for now, only thSIce fields) just before beeing
91        exported (in cpl_export_import_data.F, like on ocean side) instead of from
92        atm_store_my_data.F like all exported fluxes.
93      - new version of pickup_cpl: write field names into meta file and read meta
94        file to find field postion in pickup. Also only write/read fields meeded for
95        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
96    o pkg/dic:
97      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
98    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
99        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
100        value can be from domain [0,1] to average between the two methods
101    o pkg/atm_phys:
102      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
103        hold fixed in time).
104    
105    checkpoint65r (2015/12/21)
106    o pkg/seaice:
107        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
108        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
109    o pkg/seaice:
110      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
111        when SEAICEscaleSurfStress=.TRUE.,
112      - apply areaW and areaS in S/R seaice_calc_lhs
113    o pkg/atm_phys:
114      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
115        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
116        for individual contribution (convection, LSC cond, radiation)
117      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
118        information); activated with: solar_exponent=0. and wv_exponent=-1.
119    o pkg/ggl90:
120      - within IDEMIX add upper limit for horizontal group velocity to
121        avoid instability problems in the explicit horizontal diffusion term for
122        long time steps or high resolution
123    o pkg/diagnostics:
124      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
125        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
126    o testreport:
127      - remove "-v" (verbose option) in default mpirun command.
128    o pkg/seaice/seaice_growth:
129      - catch potential division by zero in ITD code, does not change
130        verification results
131    o pkg/ecco:
132      - retire old codes to the Attic. The calls to retired functions are
133        left in a commented form in case they ever need to be re-activated.
134      - ecco_check.F: issue warning if any old CPP option is
135        defined that corresponds to retired codes -- then stop.
136    o pkg/atm_compon_interf:
137      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
138        coupler: use last time-step value instead of average over cplSendFrq_iter
139        time-step, similar to what is done for seaIceMass.
140        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
141    o eesupp & genmake2:
142      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
143        <= remove until a fix is found for some ifort version on ia32 machine.
144    o pkg/seaice/seaice_evp:
145      - refine residual computation
146    
147    checkpoint65q (2015/11/18)
148    o pkg/seaice/seaice_evp:
149      - fix residual computations so that they no longer affect the actual
150        simulation code
151      - fix seaice_readparams to be able to actually set new parameters
152        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
153    o model/src:
154      - fix wrong truncation (single prec) from "FLOAT" function in expressions
155        like: deltaT*FLOAT(myIter) when myIter is large:
156         a) replaced by DFLOAT (if not seen by TAF);
157         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
158    o pkg/aim_v23:
159      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
160        when pickupSuff is set ; do write rolling pickups + at the end of the run.
161    o pkg/atm_ocn_coupler + ocn_compon_interf:
162      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
163        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
164        add corresponding call in DO_OCEANIC_PHYS.
165    o coupler pkgs:
166      Start a new way to set-up optionally-exchanged variables (previously, only
167       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
168       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
169       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
170       compononent param default can be set accordingly).
171      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
172       but rather applies to a group a fields (going both ways like for DIC)
173       and corresponds to an option of coupling config.
174      coupler (pkg/atm_ocn_coupler):
175      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
176        and read namelist directly (without eessup S/R calls) instead of
177        in the very un-flexible old way, 1 param per line, in fixed order;
178      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
179        cleanly in CPL_CHECK_CPLCONFIG
180      - add new coupling-exchange selectors (some not yet active) including
181        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
182                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
183      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
184        component ; called directly from coupler.F, after comp. registrations;
185      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
186         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
187          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
188      components (pkg/atm_ & ocn_compon_interf):
189      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
190        CPP header file in all pkg source files.
191      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
192        ATM/OCN_CHECK_CPLCONFIG;
193      - add error-counter to track errors (e.g., in "data.cpl") and to stop
194        cleanly in ATM/OCN_CHECK_CPLCONFIG;
195      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
196        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
197        before PACKAGES_READPARMS;
198      verification/cpl_aim+ocn/:
199      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
200        "data.cpl" for coupler (in input_cpl).
201    o eesupp/inc:
202      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
203        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
204        to always cumulate tile local-sum in the same order (still uses
205        MPI_Allreduce like standard code).
206      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
207        that are now identical to standard version (in eesupp/inc).
208    o pkg/shelfice:
209      - add SHELFICETransCoeffTFile for initializing spatially varying
210        heat and salt transfer coefficients
211    o pkg/atm_compon_interf & ocn_compon_interf:
212      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
213        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
214      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
215    o pkg/atm_ocn_coupler:
216      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
217    o pkg/rbcs:
218      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
219        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
220      - add a short report (to STDOUT) about RBCS-mask settings.
221    
222    checkpoint65p (2015/10/23)
223    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
224        there is no adjoint test for EVP, we don't know what it does to the adjoint
225        solution, but at least there are no more recomputation warnings left
226    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
227        a chance of giving the same results as a fully converged VP (JFNK) solver
228    o tools/adjoint_options/adjoint_diva:
229      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
230    o pkg/streamice:
231      - spotted bug in streamice_driving_stress using dyG where should have been dxG
232    o pkg/exf:
233      - remove STOP statement that prevented to use wind or (wind-)stress
234        interpolation for constant-in-time forcing fields (wind/stress period = 0).
235    o pkg/seaice:
236      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
237        5 additionals 2D fields and 6 new store directives
238      - change logic in seaice_readparms.F: EVP code can now be turned on in
239        various ways, setting SEAICE_deltaTev is no longer required,
240        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
241        or SEAICEaEVPcoeff
242    o pkg/shelfice/shelfice_thermodynamics.F
243      - redefining uLoc/vLoc to u/v, instead of 2u/v
244    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
245      - this is an intermediate state of a truely converging EVP that has
246        the potential of outperforming implicit VP methods, I do not recommend
247        using it yet.
248      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
249        and all parameters are hardwired
250      - for convergence it still requires very smooth regularisations, that means,
251        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
252        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
253        specific averaging appears to be required, still subject to tuning
254      - still needs cleaning and I need to turn parameter into runtime parameters
255      - add code to compute and print residuals of iteration, compile with
256        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
257    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
258      that entered with r1.54 on Sep04, 2015, -> update results
259    
260    checkpoint65o (2015/09/14)
261    o pkg/mom_vecinv & mom_common:
262      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
263        called from there.
264      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
265        allows to use Vector-Invariant form in deep atmos and anelastic formulation
266    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
267      and Koenig-Beatty+Holland (2012)
268      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
269      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
270      - requires an extra input argument for S/R seaice_calc_viscosities
271      - tensileStrength's depth dependence is different from Itkin et al. (2015)
272        (to be changed and played with, for now exponential)
273    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
274      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
275        by AREA according to Connelly et al. (2004), JPO.
276      - For EVP and the LSR solver, the implicit part of the drag term is
277        the only non-zero term in the denominator when there is no ice (which
278        prevented running the model with zero ice-ocean drag). If
279        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
280        (or zero main diagonals BU/BV) which need to be caught. A practical
281        consequence is that for open water, the momentum equation reduce
282        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
283        they happen to be zero, often leading to a non-zero solution over
284        open water.
285    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
286        efficient EVP method.
287      - introduce area-weighted averages for e12 (analogously to
288        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
289        remain, but also changing the order of terms in the previous average
290        changed the results as much) -> update experiment
291      - add SEAICE_DELTA_SMOOTHREG code
292      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
293        TEM-code
294      - adjust loop bounds so that only required fields are computed
295      - add new averaging code for zetaZ/deltaZ (again similar to
296        seaice_calc_viscosities.F), inactive by default for now (will change
297        results again), but will replace old code eventually
298    o eesupp/src:
299      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
300        to always cumulate tile local-sum in the same order
301        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
302        Still uses MPI_Allreduce (like standard code) but on array of tiles
303        and should be faster than GLOBAL_SUM_SEND_RECV code.
304      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
305        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
306      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
307         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
308         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
309         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
310         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
311    
312    checkpoint65n (2015/07/29)
313    o pkg/thsice:
314      - add a warning when used with pkg/aim but without updating SST
315        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
316    o pkg/offline:
317      - change where Offline-Fields are loaded, from load_fields_driver.F to
318        directly within FORWARD_STEP, just after updating iter number and time;
319      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
320        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
321       These changes allow:
322        a) to recover exactly on-line results using deltaToffline=deltaTClock,
323        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
324        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
325        time-step, both with GM & KPP files and with recomputing these fields;
326        b) no needs to switch on staggerTimeStep anymore;
327        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
328      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
329    o pkg/offline:
330      - change (rarely used) offset-iteration parameter to an offset time (in s):
331        can easily recover previous offset-iter effect by setting offset-time
332        (offlineTimeOffset) to offset-iter x deltaToffline;
333      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
334        in KPP as part of surface buoyancy forcing) in offline run.
335      - fix ptracers KPP non-local term in the case where KPP is re-computed.
336    o OpenAD
337      - Adding preliminary ggl90 test to OpenAD verification.
338        Config. with ggl90 currently diverges after 64 time steps
339        so will need more work to become more stable
340      - Adding preliminary kpp test to OpenAD verification.
341        required small tweakes in kpp_routines.F
342      - Merge and update from Krishna Narayanan's contrib area:
343        * Add one variable for preliminary OpenAD DIVA
344        * Add replacement time-stepping for OpenAD DIVA
345        * genmake2 flag -diva (but only for OpenAD; preliminary)
346        * required modifs for OAD_support
347        successful preliminary test for tutorial_global_oce_biogeo/
348    o pkg/seaice:
349      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
350      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
351        delta with a smooth function in s/r seaice_calc_viscosity
352        (no effect on EVP)
353      - rename local suffix "sqr" into "sq" for more consistent variable names
354    o pkg/seaice:
355        add new parameter SEAICE_deltaMin that is used ***only***
356        for regularizing Delta (and nothing else, like the parameter
357        which is also used for all sorts of things SEAICE_EPS).
358        Defaults to SEAICE_EPS for backward compatibility only.
359    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
360        the wrong key by inialising it before use -> fixes a recomputation
361        problem but does not fix the gradient
362    o pkg/layers:
363      - move resetting of flux arrays to outside the iLa loop
364        (this caused layers_diapycnal to not work with more than one layer coord.)
365      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
366    o pkg/layers:
367      - remove from common block 3D layers fields (used to diagnose transport
368        in tracer coords) and declare them as local arrays in layers_calc.F
369    o pkg/seaice:
370      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
371        in lab_sea forward experiment (changes results -> updated)
372      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
373    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
374       computations; for SEAICE_VECTORIZE_LSR
375      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
376        sweep to the outside,
377      - remove store directives and add "CADJ loop sequential" directives
378        in analogy to model/src/solve_tridiagonal.F
379      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
380        boundaries to yield more readable code. This has also the charming side
381        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
382        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
383        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
384        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
385        an additional option)
386       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
387       but the adjoint gradients (which are affected by this change) still explode.
388    o coupler (atm & ocn _compon_interf):
389      - avoid using Exch2 IO mapping if not suitable.
390    
391    checkpoint65m (2015/06/15)
392    o pkg/layers:
393      - clean-up old parameters setting (from Sep 2012):
394        + remove old parameters setting from common block (declared locally);
395        + stop if any old parameter is mixed with new parameters;
396        + check for valid or consistent parameter setting (e.g., layers_name)
397      - check that layers_bounds for Pot.Density are in the right range;
398        this is supposed to catch un-updated setting after recently shifting
399        potential density field "prho" by -1000 (now in "sigma" scale).
400    o pkg/layers:
401      - Added missing call to layers_fill for keeping track of tottend in
402        pkg/diagnostics/diagnostics_fill_state.F
403    o pkg/layers:
404      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
405        of diapycnal fluxes
406    o pkg/layers:
407      - reverted changes to interpolation to previous treatment; there
408        was never actually a problem
409    o pkg/layers:
410      - fix interpolation of layers tracers in the presence of partial cells
411      - add lots of new functionality to compute water mass transformation
412        (enabled by CPP flag LAYERS_THERMODYNAMICS)
413      - add new calls from main code (diags_oceanic_surf_flux.F,
414        thermodynamics.F, impldiff.F) and gad to save the necessary fields
415        for layers_thermodynamics calculations
416    o pkg/ptracers:
417      - add capability of stepping a passive tracer forward without advection
418        by setting PTRACERS_advScheme to 0.
419    o pkg/diagnostics:
420      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
421    o pkg/layers:
422      - shift potential density field "prho" by -1000 for density layer averaging so
423        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
424        Note that density bin boundaries (layers_bounds in data.layers) have
425        to be set accordingly (i.e., shifted, in sigma scale).
426    o pkg/layers:
427      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
428      - fix calculation of layer non-weighted velocity and layer probability
429      - add diagnostics for pot.density used for layer averaging
430    o pkg/seaice:
431      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
432        positiveness, modify a few comments and improve variable names,
433      - the changed computation of deltaC affects most seaice-related
434        experiments at the truncation level.
435        seaice_itd.thermo is affected by far the most, with
436        only 7 digits of agreement remaining; update experiments.
437    
438    checkpoint65l (2015/05/04)
439    o pkg/shelfice:
440      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
441        factor drKp1 to zero where it is negative (ie. do not use
442        SHELFICEBoundaryLayer if hFacC>1)
443      - the same for factor drLoc in shelfice_forcing.F
444    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
445        with modules in ptracers, when using testreport option "-small_f"
446    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
447      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
448    o verification/testreport
449      - add new option -small_f
450        with this option testreport first makes the target small_f (*.f files)
451        before running make (all). This is useful for explicit inlining when
452        all sources need to be full available.
453    o pkg/exf/exf_interp.F:
454        remove previous changes related to reverse (decreasing) input grids latitude
455    
456    checkpoint65k (2015/04/01)
457    o pkg/ecco:
458        fix missing cosphi initialization; use eccoiter in place of optimcycle;
459        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
460        instead of active read/write
461    o pkg/ctrl:
462        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
463        instead of active read/write.
464    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
465        return if .NOT.useAUTODIFF
466    o pkg/seaice: add CPP brackets (cost function related).
467    o model/src:
468        add useAUTODIFF run time switch.
469    o pkg/exf/exf_interp.F:
470        add code to allow input grids with latitude starting in the north (i.e. when
471        j=1 corresponds to northern edge of field); modify global_with_exf to test
472        this feature.
473    o verification/testreport:
474      - replace "grep -A3" with POSIX conformal sed command, because there are
475        implementations of grep that cannot do contextual searches
476      - replace "cat -n" by "nl" (two occurrences), because not all implementations
477        of "cat" have the option "-n"
478    o model/src:
479        add new file gsw_teos10.F that contains 3 functions, more or less a copy
480        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
481        convert from conservative to potential temperature. For now they are not
482        called anywhere.
483    o pkg/ggl90: make "useIDEMIX" useful
484      - re-organize code in s/r ggl90_calc a little to move computations that
485        are different for idemix into separate loops (changes verification
486        experiment idemix at truncation level, 12 digits remain -> updated)
487      - requires 2 new 2D fields KappaM, verticalShear
488      - make hFacI and recip_hFacI local 3D variables that are passed to
489        s/r ggl90_idemix
490      - fix and improve some comments
491    
492    checkpoint65j (2015/02/25)
493    o pkg/openad
494      - synchronize seawater.F with version in model/src: replace routine
495        body of sw_temp by calling sw_ptmp and fix/add a few comments.
496    o pkg/mnc:
497      - change default value of pickup_read/write_mnc params to FALSE
498        (since few features are missing in reading MNC pickup files).
499    o model/src:
500      - change default (background) vertical diffusivity for salt to be the
501        temperature (background) vertical diffusivity.
502      - change background vertical diffusivity in vertical mixing pkgs ggl90,
503        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
504        This makes ptracers default diffusivity (that uses salt diffKr) more
505        consistent with vertical mixing schemes.
506    o verification/testreport:
507      - fix typo in "-pcls" option ;
508      - put temp files in /tmp (instead of in local dir)
509      - add option "-ncad" to use genmake2 new option "-nocat4ad"
510      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
511    o pkg/ggl90 (idemix code):
512      - apply few fixes ; add some missing "_d 0" ; update output of exp.
513        global_ocean.90x40x15.idemix
514    o OpenAD
515      - enable active file I/O and begin removal of work-around code
516        for OpenAD for handling control variables (memory vs. active files)
517      - new CPP options file OPENAD_OPTIONS.h
518      - revert to genarr2d gradient check for hs94.1x64x5
519      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
520      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
521    o tools/genmake2:
522      - add option for an alternative Makefile (from Martin) where multiple
523        source files are sent to TAF (instead of all in one file).
524    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
525      - code provided by Carsten Eden as an extension of ggl90
526      - so far the code is turned on within ggl90 by setting a CPP-flag at
527        compile time; a runtime flag implementation is not yet complete
528      - tested in new verification experiment global_ocean.90x40x15.idemix
529    o verification:
530      - reduce length of the AD test run by half for experiments
531        global_ocean.cs32x15 (std + thsice) and isomip
532      - enable active file I/O for OpenAD, adjust verifications accordingly
533      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
534    o verification/testreport:
535      - fix two non-POSIX sed statements so that there are no error messages
536        on Mac OS X
537      - replace hostname -s with hostname | sed 's/\..*$//'
538    o model/src/seawater.F:
539      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
540        (following the matlab code), which would have avoided the bug caught
541        by Matt (see below) in the first place
542    o pkg/shelfice:
543      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
544        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
545      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
546        ice-shelf case (i.e., within surface level).
547      - add config summary in shelfice_check.F
548      - remove global variable recip_SHELFICElatentHeat and replace by a local
549        variable recip_latentHeat
550      - introduce diagnostics for friction velocity uStar (in case of
551        SHELFICEuseGammaFrict)
552      - change verification experiment isomip.htd:
553        + start from pickup (as input_ad at nIter0=8640)
554        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
555        + test SHELFICEuseGammaFrict = .TRUE.
556        + test SHELFICEadvDiffHeatFlux = .TRUE.
557    o model/src:
558      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
559        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
560        update output of experiments global_with_exf.yearly and isomip (all 6).
561    o pkg/shelfice:
562      - change setting of kTopC to also be zero where there is no ice-shelf.
563      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
564        ice-shelf is.
565      - first attempt to get RealFreshWaterFlux effects: for now, only without
566        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
567    o pkg/seaice: add the option to prescribe a fixed thickness PDF
568      for thermodynamic calculations
569      - because of divisions of the type 7/7 not exactly equal to 1, this change
570        affects results of some verification experiments by up to 4 digits:
571        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
572        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
573        adjoint: lab_sea, lab_sea.noseaicedyn
574        -> updated
575    
576    checkpoint65i (2015/01/23)
577    o model/src:
578      - change units of frictionHeating field from W to W/m^2
579      - fix bug in frictional heating from stratospheric drag in
580        S/R ATM_PHYS_TENDENCY_APPLY_V
581      - with synchronous time-stepping: move resetting to zero of frictionHeating
582        field from load_fields_driver.F to thermodynamics.F ;
583      - add diagnostics for frictional heating.
584    o model/src & gmredi K3D:
585      - add frictionHeating field to pickup-files (for synchronous time-stepping)
586      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
587      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
588        and name in pickup file).
589      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
590    o model/src:
591      - move (from ini_forcing.F) initialisation of all arrays in header file
592        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
593        (since Nov 2012) with option selectAddFluid=1.
594    o pkg/shelfice:
595      - change units (+ document) of newly added field "shelfIceMassDynTendency"
596      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
597    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
598    o pkg/seaice: two new runtime parameters:
599      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
600        long overdue
601      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
602        parameterization of tensil stress for fast ice (does not do anything yet)
603    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
604        for LSR: move checking overlaps out of JFNK-if-block
605    o pkg/atm_phys:
606      - move copy of grid and dynamical fields out of atm_phys_driver.F into
607        new S/R ATM_PHYS_DYN2PHYS.
608      - fix level height for Linear Free-Surf case (to be consistent with
609        fixed-in-time pressure levels).
610    o pkg/mom_common (bottomdrag):
611      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
612        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
613        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
614    o pkg/shelfice (u/v_drag):
615      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
616      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
617        (now similar to shelfice_u_drag.F)
618      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
619        from mom_vecinv.F (similar to mom_fluxform calls).
620    o pkg/mom_common (bottomdrag):
621      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
622      - add options for alternative discretisation of velocity norm in quadratic
623        bottom drag: averaging of grid-cell-center KE to U.point and V.point
624        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
625        improves when averaging only the other component (e.g. vVel for U bottom
626        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
627      - add options (bottomVisc_pCell) to account for partial-cell in bottom
628        friction (no-slip BC) thus getting the true distance from the bottom;
629        off by default since this also reduces model stability (explicit bottom
630        friction). Changes produce different machine truncation with linear-drag
631        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
632        front_relax (bvp & mxl, 10 & 11 digits).
633    o model/src & mom pkgs:
634      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
635        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
636      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
637        just copy level Nr value to level Nr+1.
638    o doc:
639      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
640    o pkg/streamice:
641      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
642        SHELFICE.h: move array shelficemass to init_varia, initialise
643        from array shelficemassinit, which is set in init_fixed and
644        has option to be set from file; introduce array
645        shelficeMassDynTend array, set thru file in init_fixed
646      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
647        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
648        pkg/streamice
649      - shelfice_thermodynamics.F: call shelfice_step_icemass if
650        SHELFICEMassStepping = .true.
651      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
652    
653  checkpoint65h (2014/12/17)  checkpoint65h (2014/12/17)
654  o verification/global_ocean.90x40x15, global_ocean_ebm:  o verification/global_ocean.90x40x15, global_ocean_ebm:
655    - update to generic controls.    - update to generic controls.

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