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revision 1.2031 by jmc, Thu Jul 24 18:21:25 2014 UTC revision 1.2202 by jmc, Wed Nov 18 14:58:09 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65q (2015/11/18)
8    o pkg/seaice/seaice_evp:
9      - fix residual computations so that they no longer affect the actual
10        simulation code
11      - fix seaice_readparams to be able to actually set new parameters
12        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
13    o model/src:
14      - fix wrong truncation (single prec) from "FLOAT" function in expressions
15        like: deltaT*FLOAT(myIter) when myIter is large:
16         a) replaced by DFLOAT (if not seen by TAF);
17         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
18    o pkg/aim_v23:
19      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
20        when pickupSuff is set ; do write rolling pickups + at the end of the run.
21    o pkg/atm_ocn_coupler + ocn_compon_interf:
22      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
23        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
24        add corresponding call in DO_OCEANIC_PHYS.
25    o coupler pkgs:
26      Start a new way to set-up optionally-exchanged variables (previously, only
27       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
28       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
29       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
30       compononent param default can be set accordingly).
31      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
32       but rather applies to a group a fields (going both ways like for DIC)
33       and corresponds to an option of coupling config.
34      coupler (pkg/atm_ocn_coupler):
35      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
36        and read namelist directly (without eessup S/R calls) instead of
37        in the very un-flexible old way, 1 param per line, in fixed order;
38      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
39        cleanly in CPL_CHECK_CPLCONFIG
40      - add new coupling-exchange selectors (some not yet active) including
41        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
42                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
43      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
44        component ; called directly from coupler.F, after comp. registrations;
45      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
46         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
47          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
48      components (pkg/atm_ & ocn_compon_interf):
49      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
50        CPP header file in all pkg source files.
51      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
52        ATM/OCN_CHECK_CPLCONFIG;
53      - add error-counter to track errors (e.g., in "data.cpl") and to stop
54        cleanly in ATM/OCN_CHECK_CPLCONFIG;
55      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
56        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
57        before PACKAGES_READPARMS;
58      verification/cpl_aim+ocn/:
59      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
60        "data.cpl" for coupler (in input_cpl).
61    o eesupp/inc:
62      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
63        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
64        to always cumulate tile local-sum in the same order (still uses
65        MPI_Allreduce like standard code).
66      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
67        that are now identical to standard version (in eesupp/inc).
68    o pkg/shelfice:
69      - add SHELFICETransCoeffTFile for initializing spatially varying
70        heat and salt transfer coefficients
71    o pkg/atm_compon_interf & ocn_compon_interf:
72      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
73        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
74      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
75    o pkg/atm_ocn_coupler:
76      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
77    o pkg/rbcs:
78      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
79        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
80      - add a short report (to STDOUT) about RBCS-mask settings.
81    
82    checkpoint65p (2015/10/23)
83    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
84        there is no adjoint test for EVP, we don't know what it does to the adjoint
85        solution, but at least there are no more recomputation warnings left
86    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
87        a chance of giving the same results as a fully converged VP (JFNK) solver
88    o tools/adjoint_options/adjoint_diva:
89      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
90    o pkg/streamice:
91      - spotted bug in streamice_driving_stress using dyG where should have been dxG
92    o pkg/exf:
93      - remove STOP statement that prevented to use wind or (wind-)stress
94        interpolation for constant-in-time forcing fields (wind/stress period = 0).
95    o pkg/seaice:
96      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
97        5 additionals 2D fields and 6 new store directives
98      - change logic in seaice_readparms.F: EVP code can now be turned on in
99        various ways, setting SEAICE_deltaTev is no longer required,
100        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
101        or SEAICEaEVPcoeff
102    o pkg/shelfice/shelfice_thermodynamics.F
103      - redefining uLoc/vLoc to u/v, instead of 2u/v
104    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
105      - this is an intermediate state of a truely converging EVP that has
106        the potential of outperforming implicit VP methods, I do not recommend
107        using it yet.
108      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
109        and all parameters are hardwired
110      - for convergence it still requires very smooth regularisations, that means,
111        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
112        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
113        specific averaging appears to be required, still subject to tuning
114      - still needs cleaning and I need to turn parameter into runtime parameters
115      - add code to compute and print residuals of iteration, compile with
116        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
117    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
118      that entered with r1.54 on Sep04, 2015, -> update results
119    
120    checkpoint65o (2015/09/14)
121    o pkg/mom_vecinv & mom_common:
122      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
123        called from there.
124      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
125        allows to use Vector-Invariant form in deep atmos and anelastic formulation
126    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
127      and Koenig-Beatty+Holland (2012)
128      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
129      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
130      - requires an extra input argument for S/R seaice_calc_viscosities
131      - tensileStrength's depth dependence is different from Itkin et al. (2015)
132        (to be changed and played with, for now exponential)
133    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
134      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
135        by AREA according to Connelly et al. (2004), JPO.
136      - For EVP and the LSR solver, the implicit part of the drag term is
137        the only non-zero term in the denominator when there is no ice (which
138        prevented running the model with zero ice-ocean drag). If
139        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
140        (or zero main diagonals BU/BV) which need to be caught. A practical
141        consequence is that for open water, the momentum equation reduce
142        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
143        they happen to be zero, often leading to a non-zero solution over
144        open water.
145    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
146        efficient EVP method.
147      - introduce area-weighted averages for e12 (analogously to
148        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
149        remain, but also changing the order of terms in the previous average
150        changed the results as much) -> update experiment
151      - add SEAICE_DELTA_SMOOTHREG code
152      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
153        TEM-code
154      - adjust loop bounds so that only required fields are computed
155      - add new averaging code for zetaZ/deltaZ (again similar to
156        seaice_calc_viscosities.F), inactive by default for now (will change
157        results again), but will replace old code eventually
158    o eesupp/src:
159      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
160        to always cumulate tile local-sum in the same order
161        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
162        Still uses MPI_Allreduce (like standard code) but on array of tiles
163        and should be faster than GLOBAL_SUM_SEND_RECV code.
164      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
165        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
166      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
167         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
168         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
169         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
170         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
171    
172    checkpoint65n (2015/07/29)
173    o pkg/thsice:
174      - add a warning when used with pkg/aim but without updating SST
175        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
176    o pkg/offline:
177      - change where Offline-Fields are loaded, from load_fields_driver.F to
178        directly within FORWARD_STEP, just after updating iter number and time;
179      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
180        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
181       These changes allow:
182        a) to recover exactly on-line results using deltaToffline=deltaTClock,
183        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
184        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
185        time-step, both with GM & KPP files and with recomputing these fields;
186        b) no needs to switch on staggerTimeStep anymore;
187        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
188      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
189    o pkg/offline:
190      - change (rarely used) offset-iteration parameter to an offset time (in s):
191        can easily recover previous offset-iter effect by setting offset-time
192        (offlineTimeOffset) to offset-iter x deltaToffline;
193      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
194        in KPP as part of surface buoyancy forcing) in offline run.
195      - fix ptracers KPP non-local term in the case where KPP is re-computed.
196    o OpenAD
197      - Adding preliminary ggl90 test to OpenAD verification.
198        Config. with ggl90 currently diverges after 64 time steps
199        so will need more work to become more stable
200      - Adding preliminary kpp test to OpenAD verification.
201        required small tweakes in kpp_routines.F
202      - Merge and update from Krishna Narayanan's contrib area:
203        * Add one variable for preliminary OpenAD DIVA
204        * Add replacement time-stepping for OpenAD DIVA
205        * genmake2 flag -diva (but only for OpenAD; preliminary)
206        * required modifs for OAD_support
207        successful preliminary test for tutorial_global_oce_biogeo/
208    o pkg/seaice:
209      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
210      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
211        delta with a smooth function in s/r seaice_calc_viscosity
212        (no effect on EVP)
213      - rename local suffix "sqr" into "sq" for more consistent variable names
214    o pkg/seaice:
215        add new parameter SEAICE_deltaMin that is used ***only***
216        for regularizing Delta (and nothing else, like the parameter
217        which is also used for all sorts of things SEAICE_EPS).
218        Defaults to SEAICE_EPS for backward compatibility only.
219    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
220        the wrong key by inialising it before use -> fixes a recomputation
221        problem but does not fix the gradient
222    o pkg/layers:
223      - move resetting of flux arrays to outside the iLa loop
224        (this caused layers_diapycnal to not work with more than one layer coord.)
225      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
226    o pkg/layers:
227      - remove from common block 3D layers fields (used to diagnose transport
228        in tracer coords) and declare them as local arrays in layers_calc.F
229    o pkg/seaice:
230      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
231        in lab_sea forward experiment (changes results -> updated)
232      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
233    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
234       computations; for SEAICE_VECTORIZE_LSR
235      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
236        sweep to the outside,
237      - remove store directives and add "CADJ loop sequential" directives
238        in analogy to model/src/solve_tridiagonal.F
239      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
240        boundaries to yield more readable code. This has also the charming side
241        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
242        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
243        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
244        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
245        an additional option)
246       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
247       but the adjoint gradients (which are affected by this change) still explode.
248    o coupler (atm & ocn _compon_interf):
249      - avoid using Exch2 IO mapping if not suitable.
250    
251    checkpoint65m (2015/06/15)
252    o pkg/layers:
253      - clean-up old parameters setting (from Sep 2012):
254        + remove old parameters setting from common block (declared locally);
255        + stop if any old parameter is mixed with new parameters;
256        + check for valid or consistent parameter setting (e.g., layers_name)
257      - check that layers_bounds for Pot.Density are in the right range;
258        this is supposed to catch un-updated setting after recently shifting
259        potential density field "prho" by -1000 (now in "sigma" scale).
260    o pkg/layers:
261      - Added missing call to layers_fill for keeping track of tottend in
262        pkg/diagnostics/diagnostics_fill_state.F
263    o pkg/layers:
264      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
265        of diapycnal fluxes
266    o pkg/layers:
267      - reverted changes to interpolation to previous treatment; there
268        was never actually a problem
269    o pkg/layers:
270      - fix interpolation of layers tracers in the presence of partial cells
271      - add lots of new functionality to compute water mass transformation
272        (enabled by CPP flag LAYERS_THERMODYNAMICS)
273      - add new calls from main code (diags_oceanic_surf_flux.F,
274        thermodynamics.F, impldiff.F) and gad to save the necessary fields
275        for layers_thermodynamics calculations
276    o pkg/ptracers:
277      - add capability of stepping a passive tracer forward without advection
278        by setting PTRACERS_advScheme to 0.
279    o pkg/diagnostics:
280      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
281    o pkg/layers:
282      - shift potential density field "prho" by -1000 for density layer averaging so
283        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
284        Note that density bin boundaries (layers_bounds in data.layers) have
285        to be set accordingly (i.e., shifted, in sigma scale).
286    o pkg/layers:
287      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
288      - fix calculation of layer non-weighted velocity and layer probability
289      - add diagnostics for pot.density used for layer averaging
290    o pkg/seaice:
291      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
292        positiveness, modify a few comments and improve variable names,
293      - the changed computation of deltaC affects most seaice-related
294        experiments at the truncation level.
295        seaice_itd.thermo is affected by far the most, with
296        only 7 digits of agreement remaining; update experiments.
297    
298    checkpoint65l (2015/05/04)
299    o pkg/shelfice:
300      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
301        factor drKp1 to zero where it is negative (ie. do not use
302        SHELFICEBoundaryLayer if hFacC>1)
303      - the same for factor drLoc in shelfice_forcing.F
304    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
305        with modules in ptracers, when using testreport option "-small_f"
306    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
307      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
308    o verification/testreport
309      - add new option -small_f
310        with this option testreport first makes the target small_f (*.f files)
311        before running make (all). This is useful for explicit inlining when
312        all sources need to be full available.
313    o pkg/exf/exf_interp.F:
314        remove previous changes related to reverse (decreasing) input grids latitude
315    
316    checkpoint65k (2015/04/01)
317    o pkg/ecco:
318        fix missing cosphi initialization; use eccoiter in place of optimcycle;
319        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
320        instead of active read/write
321    o pkg/ctrl:
322        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
323        instead of active read/write.
324    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
325        return if .NOT.useAUTODIFF
326    o pkg/seaice: add CPP brackets (cost function related).
327    o model/src:
328        add useAUTODIFF run time switch.
329    o pkg/exf/exf_interp.F:
330        add code to allow input grids with latitude starting in the north (i.e. when
331        j=1 corresponds to northern edge of field); modify global_with_exf to test
332        this feature.
333    o verification/testreport:
334      - replace "grep -A3" with POSIX conformal sed command, because there are
335        implementations of grep that cannot do contextual searches
336      - replace "cat -n" by "nl" (two occurrences), because not all implementations
337        of "cat" have the option "-n"
338    o model/src:
339        add new file gsw_teos10.F that contains 3 functions, more or less a copy
340        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
341        convert from conservative to potential temperature. For now they are not
342        called anywhere.
343    o pkg/ggl90: make "useIDEMIX" useful
344      - re-organize code in s/r ggl90_calc a little to move computations that
345        are different for idemix into separate loops (changes verification
346        experiment idemix at truncation level, 12 digits remain -> updated)
347      - requires 2 new 2D fields KappaM, verticalShear
348      - make hFacI and recip_hFacI local 3D variables that are passed to
349        s/r ggl90_idemix
350      - fix and improve some comments
351    
352    checkpoint65j (2015/02/25)
353    o pkg/openad
354      - synchronize seawater.F with version in model/src: replace routine
355        body of sw_temp by calling sw_ptmp and fix/add a few comments.
356    o pkg/mnc:
357      - change default value of pickup_read/write_mnc params to FALSE
358        (since few features are missing in reading MNC pickup files).
359    o model/src:
360      - change default (background) vertical diffusivity for salt to be the
361        temperature (background) vertical diffusivity.
362      - change background vertical diffusivity in vertical mixing pkgs ggl90,
363        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
364        This makes ptracers default diffusivity (that uses salt diffKr) more
365        consistent with vertical mixing schemes.
366    o verification/testreport:
367      - fix typo in "-pcls" option ;
368      - put temp files in /tmp (instead of in local dir)
369      - add option "-ncad" to use genmake2 new option "-nocat4ad"
370      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
371    o pkg/ggl90 (idemix code):
372      - apply few fixes ; add some missing "_d 0" ; update output of exp.
373        global_ocean.90x40x15.idemix
374    o OpenAD
375      - enable active file I/O and begin removal of work-around code
376        for OpenAD for handling control variables (memory vs. active files)
377      - new CPP options file OPENAD_OPTIONS.h
378      - revert to genarr2d gradient check for hs94.1x64x5
379      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
380      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
381    o tools/genmake2:
382      - add option for an alternative Makefile (from Martin) where multiple
383        source files are sent to TAF (instead of all in one file).
384    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
385      - code provided by Carsten Eden as an extension of ggl90
386      - so far the code is turned on within ggl90 by setting a CPP-flag at
387        compile time; a runtime flag implementation is not yet complete
388      - tested in new verification experiment global_ocean.90x40x15.idemix
389    o verification:
390      - reduce length of the AD test run by half for experiments
391        global_ocean.cs32x15 (std + thsice) and isomip
392      - enable active file I/O for OpenAD, adjust verifications accordingly
393      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
394    o verification/testreport:
395      - fix two non-POSIX sed statements so that there are no error messages
396        on Mac OS X
397      - replace hostname -s with hostname | sed 's/\..*$//'
398    o model/src/seawater.F:
399      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
400        (following the matlab code), which would have avoided the bug caught
401        by Matt (see below) in the first place
402    o pkg/shelfice:
403      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
404        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
405      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
406        ice-shelf case (i.e., within surface level).
407      - add config summary in shelfice_check.F
408      - remove global variable recip_SHELFICElatentHeat and replace by a local
409        variable recip_latentHeat
410      - introduce diagnostics for friction velocity uStar (in case of
411        SHELFICEuseGammaFrict)
412      - change verification experiment isomip.htd:
413        + start from pickup (as input_ad at nIter0=8640)
414        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
415        + test SHELFICEuseGammaFrict = .TRUE.
416        + test SHELFICEadvDiffHeatFlux = .TRUE.
417    o model/src:
418      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
419        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
420        update output of experiments global_with_exf.yearly and isomip (all 6).
421    o pkg/shelfice:
422      - change setting of kTopC to also be zero where there is no ice-shelf.
423      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
424        ice-shelf is.
425      - first attempt to get RealFreshWaterFlux effects: for now, only without
426        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
427    o pkg/seaice: add the option to prescribe a fixed thickness PDF
428      for thermodynamic calculations
429      - because of divisions of the type 7/7 not exactly equal to 1, this change
430        affects results of some verification experiments by up to 4 digits:
431        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
432        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
433        adjoint: lab_sea, lab_sea.noseaicedyn
434        -> updated
435    
436    checkpoint65i (2015/01/23)
437    o model/src:
438      - change units of frictionHeating field from W to W/m^2
439      - fix bug in frictional heating from stratospheric drag in
440        S/R ATM_PHYS_TENDENCY_APPLY_V
441      - with synchronous time-stepping: move resetting to zero of frictionHeating
442        field from load_fields_driver.F to thermodynamics.F ;
443      - add diagnostics for frictional heating.
444    o model/src & gmredi K3D:
445      - add frictionHeating field to pickup-files (for synchronous time-stepping)
446      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
447      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
448        and name in pickup file).
449      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
450    o model/src:
451      - move (from ini_forcing.F) initialisation of all arrays in header file
452        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
453        (since Nov 2012) with option selectAddFluid=1.
454    o pkg/shelfice:
455      - change units (+ document) of newly added field "shelfIceMassDynTendency"
456      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
457    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
458    o pkg/seaice: two new runtime parameters:
459      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
460        long overdue
461      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
462        parameterization of tensil stress for fast ice (does not do anything yet)
463    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
464        for LSR: move checking overlaps out of JFNK-if-block
465    o pkg/atm_phys:
466      - move copy of grid and dynamical fields out of atm_phys_driver.F into
467        new S/R ATM_PHYS_DYN2PHYS.
468      - fix level height for Linear Free-Surf case (to be consistent with
469        fixed-in-time pressure levels).
470    o pkg/mom_common (bottomdrag):
471      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
472        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
473        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
474    o pkg/shelfice (u/v_drag):
475      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
476      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
477        (now similar to shelfice_u_drag.F)
478      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
479        from mom_vecinv.F (similar to mom_fluxform calls).
480    o pkg/mom_common (bottomdrag):
481      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
482      - add options for alternative discretisation of velocity norm in quadratic
483        bottom drag: averaging of grid-cell-center KE to U.point and V.point
484        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
485        improves when averaging only the other component (e.g. vVel for U bottom
486        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
487      - add options (bottomVisc_pCell) to account for partial-cell in bottom
488        friction (no-slip BC) thus getting the true distance from the bottom;
489        off by default since this also reduces model stability (explicit bottom
490        friction). Changes produce different machine truncation with linear-drag
491        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
492        front_relax (bvp & mxl, 10 & 11 digits).
493    o model/src & mom pkgs:
494      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
495        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
496      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
497        just copy level Nr value to level Nr+1.
498    o doc:
499      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
500    o pkg/streamice:
501      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
502        SHELFICE.h: move array shelficemass to init_varia, initialise
503        from array shelficemassinit, which is set in init_fixed and
504        has option to be set from file; introduce array
505        shelficeMassDynTend array, set thru file in init_fixed
506      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
507        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
508        pkg/streamice
509      - shelfice_thermodynamics.F: call shelfice_step_icemass if
510        SHELFICEMassStepping = .true.
511      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
512    
513    checkpoint65h (2014/12/17)
514    o verification/global_ocean.90x40x15, global_ocean_ebm:
515      - update to generic controls.
516    o pkg/ctrl:
517      - ctrl_map_ini_genarr.F: test for igen>0
518      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
519      - move gentim2d part of ctrl_map_ini_genarr.F to
520        new separate routine : ctrl_map_ini_gentim2d.F
521      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
522        add time variable weights and cyclic controls (time mean,
523        seasonal cycle, etc) capabilities to gentim2d
524    o pkg/ecco:
525      - move reading of error, conversion to weights from
526        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
527    o global_oce_llc90, cs32:
528      - activte sbo.
529      - CTRL_SIZE.h : add maxCtrlProc.
530      - activate the new genctrl capabilities.
531      - update following reorganization of global_oce_input_fields.tar.gz  
532    o pkg/ctrl/ctrl_ad_diff.list:
533      - add missing ctrl_init_rec.f
534    o tools/OAD_support/keepOriginal:
535      - add ctrl_init_rec.F
536    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
537      - avoid recomputations of xx_gentim2d_dummy.
538    o momentum diagnostics:
539      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
540        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
541    o pkg/seaice/seaice_lsr.F:
542      - fix computation of BU/BV, make sure they are non-zero, only necessary
543        for cubed sphere exchanges and SEAICE_OLx/y>0.
544        This makes calling s/r fill_cs_corner_rl obsolete (removed).
545    o verification/global_ocean.cs32x15/input.seaice
546      - add test for strong implicit coupling and restricted addtive Schwarz
547        methods for LSR
548      - update results/output.seaice.txt
549    o verification/tutorial_global_oce_biogeo:
550      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
551        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
552        update output_adm,_oadm,_tlm.txt
553    o pkg/dic:
554      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
555      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
556        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
557    o verification/tutorial_global_oce_biogeo:
558      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
559        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
560        update output_adm,_oadm,_tlm.txt
561    o eesupp/src:
562      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
563        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
564    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
565      LSR (following Hutchings et al. 2004)
566      - introduce zetaZ as a global variable (requires adjustments in
567        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
568        in seaice_calc_viscosities.F
569      - new flag SEAICEuseStrImpCpl (default off)
570      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
571        momentum equations
572      - JFNK-solver (preconditioner) adjusted to allow using this method
573        (where it does not have any positive effect)
574    o pkg/seaice
575      - add overlap for restrictive additive Schwartz method also to LSR, but
576        turn it off by default (because it only seems to work for non-cubed
577        sphere/llc topologies)
578    o pkg/autodiff
579      - add extra exchanges in addummy_in_steppging also for mnc output
580    o pkg/seaice:
581      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
582        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
583    o pkg/obcs:
584      - add option to specify domain-connected piece Id along OB though files
585        (for now, only used to diagnose PhiVel; default =1 -> global correction)
586      - modify obcs_diag_balance.F to process each connected-part separately;
587        exclude OB where Id = 0 but keep the full divergence there (-> constant
588        Psi along this portion of OB and all inflow derived from grad(Phi))
589      - add example of OB-conect files in verification/so_box_biogeo/input.
590    o pkg/diagnostics:
591      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
592      a) use non zero matrix element across OB and solve for Phi 1 grid point
593         outside OB (i.e, where tracer OBCS are applied).
594      b) global imbalance of inFlow/outFlow across OB: instead of modifying
595         velocity across OB, spread it uniformly along the OB in the RHS.
596    
597    checkpoint65g (2014/11/19)
598    o pkg/diagnostcis:
599      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
600    o pkg/my82,pp81,kl10:
601      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
602        field diffKr as background diffusivity to set minimum diffusivity value.
603    o pkg/seaice:
604      - add new parameter SEAICEuseEVPrev (for revisited EVP by
605        Bouillon et al 2013)
606      - add SEAICE_evpAlpha/Beta to namelist
607      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
608        involve trivial re-ordering of divisions/multiplications that should not
609        have any effects, but ... they do change the results of lab_sea.hb87 so
610        that only 2 digits of agreement remain, in line with the general
611        instability/fragility of the evp-code. For now, I do not care and just
612        update the verification experiment
613    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
614      - remove xx_genarr2d_numsmooth etc
615      - use xx_genarr2d_preproc etc instead
616      - carry out smooth_correl2D at initialization stage rather than during
617        time stepping.
618      - get smoothOpNb from xx_gentim2d_preproc
619    o global_oce_cs32 :
620      - add test of generic ecco capabilities.
621    o pkg/exf/exf_getsurfacefluxes.F :
622      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
623    o pkg/ctrl,ecco :
624      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
625        is defined.
626    o pkg/seaice: add diagnostics for Delta (deformation parameter)
627    o model/src:
628      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
629        diffusivity (background) is specified but ignored.
630    o verification:
631      - in testreport, convert hostname to lower case for default output dir name
632    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
633    o pkg/dic: add modifications from Hajoon:
634      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
635      - light attenuation: add self-shading effect by climatological Chlorophyll
636        (read from file).
637    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
638        compiles when SEAICE_ALLOW_DYNAMICS is undefined
639    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
640        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
641        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
642        approach where CPP_OPTIONS.h includes an omnipotent
643        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
644    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
645        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
646    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
647        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
648        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
649    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
650      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
651      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
652      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
653      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
654    o pkg/ctrl,ecco,exf :
655      - remove variables associated with NON-generic costs,
656        unless ECCO_CTRL_DEPRECATED is defined.
657      - remove NON-generic NON-obcs controls,
658        unless ECCO_CTRL_DEPRECATED is defined.
659    o pkg/ctrl : added ctrl_local_params.h
660    o pkg/ecco : added ecco_local_params.h
661    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
662        experiments, which will progressively be removed once the
663        experiments are revised to use only generic controls/costs.
664    
665    checkpoint65f (2014/10/13)
666    o pkg/ctrl, ecco, seaice : minor changes in headers
667    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
668        cost function and control capabilities added since checkpoint65c.
669    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
670    o pkg/ecco: increase modularity and improve logic
671      - ecco_toolbox.F (new) : basic operations that are often used,
672        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
673        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
674      - cost_gencal.F (new) : determine filnames and records.
675      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
676      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
677        and exploit the above functions leading to more compact code.
678      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
679      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
680        using_ers, using_gfo, using_mdt is now only defined within gencost)
681    o pkg/ecco: extend generic cost capabilities
682      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
683        capabilities via gencost_preproc (+ _c,_i,_r related params),
684        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
685        gencost_outputlevel arguments to cost_generic
686      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
687        and active_read, making room for gencost_preproc to take effect.
688        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
689      - pkg/ecco/cost_generic.F :
690        compute and store misfit maks*(model-data) in localdif that is
691        then used in cost and for output, output misfit if outlev.GT.0
692      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
693        rather gencost_barfile for deciding whether to write barfile
694      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
695      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
696        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
697      - pkg/ecco/ecco_summary.F : report gencost variables
698      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
699    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
700    o pkg/ecco: internal re-organization
701      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
702        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
703        mv relevant variables definition from ecco_cost.h to ecco.h,
704        make sure gencost routines only include ecco.h)
705      - throughout : add missing CCP switches, rm unused variables,
706        and rm un-necessary CPP switches
707      - throughout gencost routines : replace modelstartdate with
708        gencost_startdate when needed
709      - cost_bp_read.F : use arguments, instead of common blocs
710        so that it can be used also by (new) cost_gencost_bpv4.F
711      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
712      - ecco_phys.F : compute etanFull
713      - ecco_readparms.F : rename using_topex as using_tpj, add
714        bpv4-grace to gencost list, initialize added parameters
715      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
716    
717    checkpoint65e (2014/09/28)
718    o pkg/obcs:
719      - replaced the just-added CPP options with run-time variables
720        (see pkg/obcs/OBCS_PARAMS.h for details)
721    o pkg/obcs:
722      - add additional CPP options for sponge boundary layers
723        (see pkg/obcs/OBCS_OPTIONS.h for details)
724    o pkg/atm_phys:
725      - implement simple (obliquity only, assuming circular planet orbit)
726        seasonal cycle for incoming insolation ; used when run-time parameter
727        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
728    o pkg/exf, pkg/ecco, pkg/ctrl:
729      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
730      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
731      - implement gentim2d for xx_tauu, xx_tauv
732    o pkg/ctrl, pkg/ecco :
733      - fix and complement the generic controls implementation
734    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
735        pkg/shelfice/shelfice_thermodynamics.F,
736        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
737        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
738      - add weight in CTRL_GET_GEN calls
739    o pkg/ctrl :
740      - ctrl_get_gen.F : add weight as input parameter, and apply
741        it directly rather than using smooth_correl2Dw (to be retired).
742      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
743    o pkg/ctrl :
744      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
745        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
746      - re-activate ctrl_summary (call in ctrl_init.F)
747    o pkg/ctrl/ctrl_cost_gen.F :
748      - fix CCP brackets, remove un-necessary myiter, mytime
749    o pkg/ecco, pkg/ctrl :
750      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
751      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
752      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
753      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
754    
755    checkpoint65d (2014/09/15)
756    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
757      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
758        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
759    o pkg/ctrl/ctrl_map_ini_genarr.F :
760      - remove compilation failure
761      - replace hard coded example
762      - use ctrl_map_ini_gen2D, 3D
763    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
764      - on/off switch based upon xx_genarr2d_weight,3d
765    o src/packages_init_variables.F :
766      - regroup pkg/estimation calls
767      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
768        (moved to ctrl_init_variables)
769    o cost/cost_init_varia.F :
770      - remove ecco_cost_init_varia
771        (moved to ecco_init_varia)
772    o ctrl/ctrl_init_variables.F :
773      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
774      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
775    o ctrl/ctrl_map_ini.F :
776      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
777        (moved to ctrl_init_variables)
778    o ctrl/ctrl_map_ini_ecco.F :
779      - remove ECCO_PHYS (mv to ecco_init_varia)
780      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
781    o ecco/ecco_ad_diff.list :
782      - add ecco_init_varia.f
783    o ecco/ecco_init_varia.F
784      - new routine
785    o pkg/streamice:
786      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
787        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
788      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
789    o pkg/generic_advdiff:
790      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
791    o pkg/exf:
792      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
793         xxg_precip capability
794      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
795    o pkg/ctrl:
796      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
797    o model/src/load_fields_driver.F :
798      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
799        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
800    o OpenAD verification experiments:
801      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
802        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
803        for now, only in pkgs used in OpenAD verification experiments.
804      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
805        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
806        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
807        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
808    o OpenAD verification tests:
809      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
810      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
811        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
812      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
813        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
814    o model/src & generic_advdiff:
815      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
816        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
817        dynamics requires valid tracer forcing only over tile interior but, for
818        some diagnostics, may need to extend it over 1 point in tile halo region.
819      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
820        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
821        setting in temp/salt/ptracer_integrate.F
822    o pkg/dic:
823      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
824        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
825        in gchem_forcing_sep.F
826    o pkg/autodiff & obcs:
827      - add storage of current OB values for U & V (was already done for T & S).
828    
829    checkpoint65c (2014/08/30)
830    o pkg/dic:
831      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
832        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
833        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
834    o verification:
835      - new experiment testing OBCS and DIC pkgs, using params & output from
836        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
837        passage: take OBCS from the last year of a 2 yrs simulation and initial
838        conditions from t=1.yr while keeping the same forcing.
839    o model/src:
840      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
841        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
842    o pkg/diagnostics (Stats-Diags):
843      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
844        a) refine region where stats are computed, excluding where arrhFac=0 ;
845        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
846        c) extend regional stats over the region edges (for U or V pt location).
847    o pkg/gchem:
848      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
849        pkg/dic is currently changing/updating ptracers values beyond the OB).
850    o verification (hs94):
851      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
852        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
853        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
854        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
855    o pkg/ptracers:
856      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
857        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
858      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
859        with AB-2 code (so that it get tested).
860    o model/src:
861      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
862        with AB-2 code (previously only available with AB-3 code).
863        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
864        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
865        there, by calling CYCLE_AB_TRACER).
866    o pkg/generic_advdiff:
867      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
868        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
869        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
870        S/R temp/salt/ptracers_integrate.F
871    o model/src & pkg/ptracers:
872      - remove common block variables gT,gS (in DYNVARS.h), except when
873         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
874      - remove common block variable gPtr.
875    o model/src & pkgs:
876      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
877         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
878         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
879         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
880      + change accordingly all calling S/R.
881      - use local temperature/salinity/ptracer tendency array (without bi,bj)
882        in S/R temp/salt/ptracers_integrate.F
883    o pkg/seaice:
884      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
885        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
886      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
887        in seaice_lsr
888      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
889        in s/r seaice_lsr_calc_coeffs
890    o pkg/mdsio:
891      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
892        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
893        too long (e.g., > MAX_LEN_FNAM/2 )
894    
895    checkpoint65b (2014/08/12)
896    o pkg/matrix:
897      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
898    o model/src:
899      - fix initialisation of geothermalFile; compile geothermal-flux code in
900        natl_box verification experiment.
901    o model/src & pkg/down_slope:
902      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
903      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
904        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
905        results at machine truncation level: update output of experiments
906        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
907    o pkg/diagnostics (Stats-Diags):
908      - do not cumulate the full volume when DIAGNOSTICS_FILL is
909        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
910        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
911        times (but Min,Max and StD are still wrong).
912    o model/src:
913      - add geothermal flux forcing: read in ini_forcing.F as time-constant
914        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
915    o model/src:
916      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
917        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
918        arrays are already updated while adjustments (filters, conv.adjustment) are
919        still applied later, in S/R TRACERS_CORRECTION_STEP.
920    o model/src:
921      - store in common bloc array "rhoInSitu" the virtual potential temperature
922        anomaly that is used to compute geopotential: this make the atmos code
923        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
924    o pkg/seaice/seaice_lsr.F
925      - rename integer variable ilcall to ipass (that's what it is called
926        in the residual diagnostics
927      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
928        default) for improved non-linear convergence of the first few steps
929      - adjust a few comments and add new ones to explain some of the store
930        directives
931    o pkg/generic_advdiff (& ptracers):
932      - re-work the code to check for valid advection scheme and for minimum
933        size of overlap (now stored in local common bloc in gad_advscheme.F)
934    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
935      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
936      - add an auxilliary variable "bet" and fix store directives and keys in
937        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
938        less exact gradients in my tests); but there are still
939        recomputation warning (although gradients are sort of OK), when
940        SEAICE_LSR_VECTORIZE is not defined, so this flag and
941        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
942      - update verification experiments lab_sea.
943      - change some comments in S/R seaice_calc_viscosities
944    o model/src:
945      - if staggerTimeStep=T, always apply exchange to velocity field in
946        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
947        (independent of using multi-dim advection or not); no effect on FWD run
948        but affects AD results (at machine truncation level): update output of
949        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
950        and isomip (oad: 12.d).
951    o pkg/generic_advdiff:
952      - stop if doAB_onGtGs is set to FALSE but ignored
953      - refine warning related to stability of tracer time-stepping
954        regarding internal wave dynamics.
955      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
956        on staggerTimeStep & implicitIntGravWave (will now get a warning
957        if potentially unstable).
958    o pkg/kl10:
959      - add new pkg "kl10" for mixing due to internal wave breaking, from
960        http://www.sciencedirect.com/science/article/pii/S1463500310000144
961        (contribution from Jody Klymak), tested in verification experiment
962        verification/internal_wave/input.kl10/
963    o isomip experiment:
964      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
965        (input.htd) and update the output.
966    o cd_code experiments:
967      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
968        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
969        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
970        update the corresponding output.
971    o pkg/seaice:
972      - reduce the number of include files and store directives in
973        S/R seaice_lsr_tridiagu/v
974      - change the order of loops in one case in S/R seaice_lsr_tridiagv
975        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
976        get rid off one store directive (a TAF bug?)
977      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
978        S/R seaice_lsr_tridiagv to change the loop range for consistency
979      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
980      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
981        S/R seaice_lsr_tridiagu/v (requires update of
982        offline_exf_seaice/input.dyn_jfnk)
983    
984    checkpoint65a (2014/07/27)
985  o model/src:  o model/src:
986    - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than    - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
987      surrounding hFacC=1 @ edge of a step with different kSurfC on either side      surrounding hFacC=1 @ edge of a step with different kSurfC on either side
988      (topo in p-coords, ice-shelf in z-coords); update output of experiment      (topo in p-coords, ice-shelf in z-coords); update output of experiments
989      tutorial_global_oce_in_p.      tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
990  o model/src:  o model/src:
991    - collect momentum forcing tendency into local 2-D array (passed as argument    - collect momentum forcing tendency into local 2-D array (passed as argument
992      to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE      to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
# Line 17  o model/src: Line 995  o model/src:
995    - 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
996      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.
997      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
998      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
999      moist correction due to vertical advection).      correction due to vertical advection).
1000    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1001      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1002      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 47  o pkg/seaice: more clean up Line 1025  o pkg/seaice: more clean up
1025      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
1026      this experiment):      this experiment):
1027      > size mitgcmuv_ad      > size mitgcmuv_ad
1028      text    data        bss     dec        hex        text    data        bss     dec        hex
1029      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1030      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1031      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1032      text    data        bss     dec        hex      text    data        bss     dec        hex
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