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revision 1.2032 by jmc, Sun Jul 27 18:04:14 2014 UTC revision 1.2214 by jmc, Mon Dec 21 13:38:57 2015 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65r (2015/12/21)
8    o pkg/seaice:
9        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
10        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
11    o pkg/seaice:
12      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
13        when SEAICEscaleSurfStress=.TRUE.,
14      - apply areaW and areaS in S/R seaice_calc_lhs
15    o pkg/atm_phys:
16      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
17        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
18        for individual contribution (convection, LSC cond, radiation)
19      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
20        information); activated with: solar_exponent=0. and wv_exponent=-1.
21    o pkg/ggl90:
22      - within IDEMIX add upper limit for horizontal group velocity to
23        avoid instability problems in the explicit horizontal diffusion term for
24        long time steps or high resolution
25    o pkg/diagnostics:
26      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
27        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
28    o testreport:
29      - remove "-v" (verbose option) in default mpirun command.
30    o pkg/seaice/seaice_growth:
31      - catch potential division by zero in ITD code, does not change
32        verification results
33    o pkg/ecco:
34      - retire old codes to the Attic. The calls to retired functions are
35        left in a commented form in case they ever need to be re-activated.
36      - ecco_check.F: issue warning if any old CPP option is
37        defined that corresponds to retired codes -- then stop.
38    o pkg/atm_compon_interf:
39      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
40        coupler: use last time-step value instead of average over cplSendFrq_iter
41        time-step, similar to what is done for seaIceMass.
42        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
43    o eesupp & genmake2:
44      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
45        <= remove until a fix is found for some ifort version on ia32 machine.
46    o pkg/seaice/seaice_evp:
47      - refine residual computation
48    
49    checkpoint65q (2015/11/18)
50    o pkg/seaice/seaice_evp:
51      - fix residual computations so that they no longer affect the actual
52        simulation code
53      - fix seaice_readparams to be able to actually set new parameters
54        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
55    o model/src:
56      - fix wrong truncation (single prec) from "FLOAT" function in expressions
57        like: deltaT*FLOAT(myIter) when myIter is large:
58         a) replaced by DFLOAT (if not seen by TAF);
59         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
60    o pkg/aim_v23:
61      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
62        when pickupSuff is set ; do write rolling pickups + at the end of the run.
63    o pkg/atm_ocn_coupler + ocn_compon_interf:
64      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
65        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
66        add corresponding call in DO_OCEANIC_PHYS.
67    o coupler pkgs:
68      Start a new way to set-up optionally-exchanged variables (previously, only
69       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
70       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
71       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
72       compononent param default can be set accordingly).
73      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
74       but rather applies to a group a fields (going both ways like for DIC)
75       and corresponds to an option of coupling config.
76      coupler (pkg/atm_ocn_coupler):
77      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
78        and read namelist directly (without eessup S/R calls) instead of
79        in the very un-flexible old way, 1 param per line, in fixed order;
80      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
81        cleanly in CPL_CHECK_CPLCONFIG
82      - add new coupling-exchange selectors (some not yet active) including
83        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
84                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
85      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
86        component ; called directly from coupler.F, after comp. registrations;
87      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
88         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
89          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
90      components (pkg/atm_ & ocn_compon_interf):
91      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
92        CPP header file in all pkg source files.
93      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
94        ATM/OCN_CHECK_CPLCONFIG;
95      - add error-counter to track errors (e.g., in "data.cpl") and to stop
96        cleanly in ATM/OCN_CHECK_CPLCONFIG;
97      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
98        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
99        before PACKAGES_READPARMS;
100      verification/cpl_aim+ocn/:
101      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
102        "data.cpl" for coupler (in input_cpl).
103    o eesupp/inc:
104      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
105        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
106        to always cumulate tile local-sum in the same order (still uses
107        MPI_Allreduce like standard code).
108      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
109        that are now identical to standard version (in eesupp/inc).
110    o pkg/shelfice:
111      - add SHELFICETransCoeffTFile for initializing spatially varying
112        heat and salt transfer coefficients
113    o pkg/atm_compon_interf & ocn_compon_interf:
114      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
115        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
116      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
117    o pkg/atm_ocn_coupler:
118      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
119    o pkg/rbcs:
120      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
121        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
122      - add a short report (to STDOUT) about RBCS-mask settings.
123    
124    checkpoint65p (2015/10/23)
125    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
126        there is no adjoint test for EVP, we don't know what it does to the adjoint
127        solution, but at least there are no more recomputation warnings left
128    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
129        a chance of giving the same results as a fully converged VP (JFNK) solver
130    o tools/adjoint_options/adjoint_diva:
131      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
132    o pkg/streamice:
133      - spotted bug in streamice_driving_stress using dyG where should have been dxG
134    o pkg/exf:
135      - remove STOP statement that prevented to use wind or (wind-)stress
136        interpolation for constant-in-time forcing fields (wind/stress period = 0).
137    o pkg/seaice:
138      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
139        5 additionals 2D fields and 6 new store directives
140      - change logic in seaice_readparms.F: EVP code can now be turned on in
141        various ways, setting SEAICE_deltaTev is no longer required,
142        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
143        or SEAICEaEVPcoeff
144    o pkg/shelfice/shelfice_thermodynamics.F
145      - redefining uLoc/vLoc to u/v, instead of 2u/v
146    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
147      - this is an intermediate state of a truely converging EVP that has
148        the potential of outperforming implicit VP methods, I do not recommend
149        using it yet.
150      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
151        and all parameters are hardwired
152      - for convergence it still requires very smooth regularisations, that means,
153        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
154        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
155        specific averaging appears to be required, still subject to tuning
156      - still needs cleaning and I need to turn parameter into runtime parameters
157      - add code to compute and print residuals of iteration, compile with
158        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
159    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
160      that entered with r1.54 on Sep04, 2015, -> update results
161    
162    checkpoint65o (2015/09/14)
163    o pkg/mom_vecinv & mom_common:
164      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
165        called from there.
166      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
167        allows to use Vector-Invariant form in deep atmos and anelastic formulation
168    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
169      and Koenig-Beatty+Holland (2012)
170      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
171      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
172      - requires an extra input argument for S/R seaice_calc_viscosities
173      - tensileStrength's depth dependence is different from Itkin et al. (2015)
174        (to be changed and played with, for now exponential)
175    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
176      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
177        by AREA according to Connelly et al. (2004), JPO.
178      - For EVP and the LSR solver, the implicit part of the drag term is
179        the only non-zero term in the denominator when there is no ice (which
180        prevented running the model with zero ice-ocean drag). If
181        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
182        (or zero main diagonals BU/BV) which need to be caught. A practical
183        consequence is that for open water, the momentum equation reduce
184        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
185        they happen to be zero, often leading to a non-zero solution over
186        open water.
187    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
188        efficient EVP method.
189      - introduce area-weighted averages for e12 (analogously to
190        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
191        remain, but also changing the order of terms in the previous average
192        changed the results as much) -> update experiment
193      - add SEAICE_DELTA_SMOOTHREG code
194      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
195        TEM-code
196      - adjust loop bounds so that only required fields are computed
197      - add new averaging code for zetaZ/deltaZ (again similar to
198        seaice_calc_viscosities.F), inactive by default for now (will change
199        results again), but will replace old code eventually
200    o eesupp/src:
201      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
202        to always cumulate tile local-sum in the same order
203        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
204        Still uses MPI_Allreduce (like standard code) but on array of tiles
205        and should be faster than GLOBAL_SUM_SEND_RECV code.
206      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
207        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
208      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
209         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
210         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
211         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
212         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
213    
214    checkpoint65n (2015/07/29)
215    o pkg/thsice:
216      - add a warning when used with pkg/aim but without updating SST
217        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
218    o pkg/offline:
219      - change where Offline-Fields are loaded, from load_fields_driver.F to
220        directly within FORWARD_STEP, just after updating iter number and time;
221      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
222        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
223       These changes allow:
224        a) to recover exactly on-line results using deltaToffline=deltaTClock,
225        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
226        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
227        time-step, both with GM & KPP files and with recomputing these fields;
228        b) no needs to switch on staggerTimeStep anymore;
229        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
230      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
231    o pkg/offline:
232      - change (rarely used) offset-iteration parameter to an offset time (in s):
233        can easily recover previous offset-iter effect by setting offset-time
234        (offlineTimeOffset) to offset-iter x deltaToffline;
235      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
236        in KPP as part of surface buoyancy forcing) in offline run.
237      - fix ptracers KPP non-local term in the case where KPP is re-computed.
238    o OpenAD
239      - Adding preliminary ggl90 test to OpenAD verification.
240        Config. with ggl90 currently diverges after 64 time steps
241        so will need more work to become more stable
242      - Adding preliminary kpp test to OpenAD verification.
243        required small tweakes in kpp_routines.F
244      - Merge and update from Krishna Narayanan's contrib area:
245        * Add one variable for preliminary OpenAD DIVA
246        * Add replacement time-stepping for OpenAD DIVA
247        * genmake2 flag -diva (but only for OpenAD; preliminary)
248        * required modifs for OAD_support
249        successful preliminary test for tutorial_global_oce_biogeo/
250    o pkg/seaice:
251      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
252      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
253        delta with a smooth function in s/r seaice_calc_viscosity
254        (no effect on EVP)
255      - rename local suffix "sqr" into "sq" for more consistent variable names
256    o pkg/seaice:
257        add new parameter SEAICE_deltaMin that is used ***only***
258        for regularizing Delta (and nothing else, like the parameter
259        which is also used for all sorts of things SEAICE_EPS).
260        Defaults to SEAICE_EPS for backward compatibility only.
261    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
262        the wrong key by inialising it before use -> fixes a recomputation
263        problem but does not fix the gradient
264    o pkg/layers:
265      - move resetting of flux arrays to outside the iLa loop
266        (this caused layers_diapycnal to not work with more than one layer coord.)
267      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
268    o pkg/layers:
269      - remove from common block 3D layers fields (used to diagnose transport
270        in tracer coords) and declare them as local arrays in layers_calc.F
271    o pkg/seaice:
272      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
273        in lab_sea forward experiment (changes results -> updated)
274      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
275    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
276       computations; for SEAICE_VECTORIZE_LSR
277      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
278        sweep to the outside,
279      - remove store directives and add "CADJ loop sequential" directives
280        in analogy to model/src/solve_tridiagonal.F
281      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
282        boundaries to yield more readable code. This has also the charming side
283        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
284        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
285        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
286        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
287        an additional option)
288       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
289       but the adjoint gradients (which are affected by this change) still explode.
290    o coupler (atm & ocn _compon_interf):
291      - avoid using Exch2 IO mapping if not suitable.
292    
293    checkpoint65m (2015/06/15)
294    o pkg/layers:
295      - clean-up old parameters setting (from Sep 2012):
296        + remove old parameters setting from common block (declared locally);
297        + stop if any old parameter is mixed with new parameters;
298        + check for valid or consistent parameter setting (e.g., layers_name)
299      - check that layers_bounds for Pot.Density are in the right range;
300        this is supposed to catch un-updated setting after recently shifting
301        potential density field "prho" by -1000 (now in "sigma" scale).
302    o pkg/layers:
303      - Added missing call to layers_fill for keeping track of tottend in
304        pkg/diagnostics/diagnostics_fill_state.F
305    o pkg/layers:
306      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
307        of diapycnal fluxes
308    o pkg/layers:
309      - reverted changes to interpolation to previous treatment; there
310        was never actually a problem
311    o pkg/layers:
312      - fix interpolation of layers tracers in the presence of partial cells
313      - add lots of new functionality to compute water mass transformation
314        (enabled by CPP flag LAYERS_THERMODYNAMICS)
315      - add new calls from main code (diags_oceanic_surf_flux.F,
316        thermodynamics.F, impldiff.F) and gad to save the necessary fields
317        for layers_thermodynamics calculations
318    o pkg/ptracers:
319      - add capability of stepping a passive tracer forward without advection
320        by setting PTRACERS_advScheme to 0.
321    o pkg/diagnostics:
322      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
323    o pkg/layers:
324      - shift potential density field "prho" by -1000 for density layer averaging so
325        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
326        Note that density bin boundaries (layers_bounds in data.layers) have
327        to be set accordingly (i.e., shifted, in sigma scale).
328    o pkg/layers:
329      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
330      - fix calculation of layer non-weighted velocity and layer probability
331      - add diagnostics for pot.density used for layer averaging
332    o pkg/seaice:
333      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
334        positiveness, modify a few comments and improve variable names,
335      - the changed computation of deltaC affects most seaice-related
336        experiments at the truncation level.
337        seaice_itd.thermo is affected by far the most, with
338        only 7 digits of agreement remaining; update experiments.
339    
340    checkpoint65l (2015/05/04)
341    o pkg/shelfice:
342      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
343        factor drKp1 to zero where it is negative (ie. do not use
344        SHELFICEBoundaryLayer if hFacC>1)
345      - the same for factor drLoc in shelfice_forcing.F
346    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
347        with modules in ptracers, when using testreport option "-small_f"
348    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
349      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
350    o verification/testreport
351      - add new option -small_f
352        with this option testreport first makes the target small_f (*.f files)
353        before running make (all). This is useful for explicit inlining when
354        all sources need to be full available.
355    o pkg/exf/exf_interp.F:
356        remove previous changes related to reverse (decreasing) input grids latitude
357    
358    checkpoint65k (2015/04/01)
359    o pkg/ecco:
360        fix missing cosphi initialization; use eccoiter in place of optimcycle;
361        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
362        instead of active read/write
363    o pkg/ctrl:
364        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
365        instead of active read/write.
366    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
367        return if .NOT.useAUTODIFF
368    o pkg/seaice: add CPP brackets (cost function related).
369    o model/src:
370        add useAUTODIFF run time switch.
371    o pkg/exf/exf_interp.F:
372        add code to allow input grids with latitude starting in the north (i.e. when
373        j=1 corresponds to northern edge of field); modify global_with_exf to test
374        this feature.
375    o verification/testreport:
376      - replace "grep -A3" with POSIX conformal sed command, because there are
377        implementations of grep that cannot do contextual searches
378      - replace "cat -n" by "nl" (two occurrences), because not all implementations
379        of "cat" have the option "-n"
380    o model/src:
381        add new file gsw_teos10.F that contains 3 functions, more or less a copy
382        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
383        convert from conservative to potential temperature. For now they are not
384        called anywhere.
385    o pkg/ggl90: make "useIDEMIX" useful
386      - re-organize code in s/r ggl90_calc a little to move computations that
387        are different for idemix into separate loops (changes verification
388        experiment idemix at truncation level, 12 digits remain -> updated)
389      - requires 2 new 2D fields KappaM, verticalShear
390      - make hFacI and recip_hFacI local 3D variables that are passed to
391        s/r ggl90_idemix
392      - fix and improve some comments
393    
394    checkpoint65j (2015/02/25)
395    o pkg/openad
396      - synchronize seawater.F with version in model/src: replace routine
397        body of sw_temp by calling sw_ptmp and fix/add a few comments.
398    o pkg/mnc:
399      - change default value of pickup_read/write_mnc params to FALSE
400        (since few features are missing in reading MNC pickup files).
401    o model/src:
402      - change default (background) vertical diffusivity for salt to be the
403        temperature (background) vertical diffusivity.
404      - change background vertical diffusivity in vertical mixing pkgs ggl90,
405        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
406        This makes ptracers default diffusivity (that uses salt diffKr) more
407        consistent with vertical mixing schemes.
408    o verification/testreport:
409      - fix typo in "-pcls" option ;
410      - put temp files in /tmp (instead of in local dir)
411      - add option "-ncad" to use genmake2 new option "-nocat4ad"
412      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
413    o pkg/ggl90 (idemix code):
414      - apply few fixes ; add some missing "_d 0" ; update output of exp.
415        global_ocean.90x40x15.idemix
416    o OpenAD
417      - enable active file I/O and begin removal of work-around code
418        for OpenAD for handling control variables (memory vs. active files)
419      - new CPP options file OPENAD_OPTIONS.h
420      - revert to genarr2d gradient check for hs94.1x64x5
421      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
422      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
423    o tools/genmake2:
424      - add option for an alternative Makefile (from Martin) where multiple
425        source files are sent to TAF (instead of all in one file).
426    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
427      - code provided by Carsten Eden as an extension of ggl90
428      - so far the code is turned on within ggl90 by setting a CPP-flag at
429        compile time; a runtime flag implementation is not yet complete
430      - tested in new verification experiment global_ocean.90x40x15.idemix
431    o verification:
432      - reduce length of the AD test run by half for experiments
433        global_ocean.cs32x15 (std + thsice) and isomip
434      - enable active file I/O for OpenAD, adjust verifications accordingly
435      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
436    o verification/testreport:
437      - fix two non-POSIX sed statements so that there are no error messages
438        on Mac OS X
439      - replace hostname -s with hostname | sed 's/\..*$//'
440    o model/src/seawater.F:
441      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
442        (following the matlab code), which would have avoided the bug caught
443        by Matt (see below) in the first place
444    o pkg/shelfice:
445      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
446        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
447      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
448        ice-shelf case (i.e., within surface level).
449      - add config summary in shelfice_check.F
450      - remove global variable recip_SHELFICElatentHeat and replace by a local
451        variable recip_latentHeat
452      - introduce diagnostics for friction velocity uStar (in case of
453        SHELFICEuseGammaFrict)
454      - change verification experiment isomip.htd:
455        + start from pickup (as input_ad at nIter0=8640)
456        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
457        + test SHELFICEuseGammaFrict = .TRUE.
458        + test SHELFICEadvDiffHeatFlux = .TRUE.
459    o model/src:
460      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
461        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
462        update output of experiments global_with_exf.yearly and isomip (all 6).
463    o pkg/shelfice:
464      - change setting of kTopC to also be zero where there is no ice-shelf.
465      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
466        ice-shelf is.
467      - first attempt to get RealFreshWaterFlux effects: for now, only without
468        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
469    o pkg/seaice: add the option to prescribe a fixed thickness PDF
470      for thermodynamic calculations
471      - because of divisions of the type 7/7 not exactly equal to 1, this change
472        affects results of some verification experiments by up to 4 digits:
473        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
474        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
475        adjoint: lab_sea, lab_sea.noseaicedyn
476        -> updated
477    
478    checkpoint65i (2015/01/23)
479    o model/src:
480      - change units of frictionHeating field from W to W/m^2
481      - fix bug in frictional heating from stratospheric drag in
482        S/R ATM_PHYS_TENDENCY_APPLY_V
483      - with synchronous time-stepping: move resetting to zero of frictionHeating
484        field from load_fields_driver.F to thermodynamics.F ;
485      - add diagnostics for frictional heating.
486    o model/src & gmredi K3D:
487      - add frictionHeating field to pickup-files (for synchronous time-stepping)
488      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
489      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
490        and name in pickup file).
491      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
492    o model/src:
493      - move (from ini_forcing.F) initialisation of all arrays in header file
494        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
495        (since Nov 2012) with option selectAddFluid=1.
496    o pkg/shelfice:
497      - change units (+ document) of newly added field "shelfIceMassDynTendency"
498      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
499    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
500    o pkg/seaice: two new runtime parameters:
501      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
502        long overdue
503      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
504        parameterization of tensil stress for fast ice (does not do anything yet)
505    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
506        for LSR: move checking overlaps out of JFNK-if-block
507    o pkg/atm_phys:
508      - move copy of grid and dynamical fields out of atm_phys_driver.F into
509        new S/R ATM_PHYS_DYN2PHYS.
510      - fix level height for Linear Free-Surf case (to be consistent with
511        fixed-in-time pressure levels).
512    o pkg/mom_common (bottomdrag):
513      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
514        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
515        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
516    o pkg/shelfice (u/v_drag):
517      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
518      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
519        (now similar to shelfice_u_drag.F)
520      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
521        from mom_vecinv.F (similar to mom_fluxform calls).
522    o pkg/mom_common (bottomdrag):
523      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
524      - add options for alternative discretisation of velocity norm in quadratic
525        bottom drag: averaging of grid-cell-center KE to U.point and V.point
526        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
527        improves when averaging only the other component (e.g. vVel for U bottom
528        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
529      - add options (bottomVisc_pCell) to account for partial-cell in bottom
530        friction (no-slip BC) thus getting the true distance from the bottom;
531        off by default since this also reduces model stability (explicit bottom
532        friction). Changes produce different machine truncation with linear-drag
533        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
534        front_relax (bvp & mxl, 10 & 11 digits).
535    o model/src & mom pkgs:
536      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
537        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
538      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
539        just copy level Nr value to level Nr+1.
540    o doc:
541      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
542    o pkg/streamice:
543      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
544        SHELFICE.h: move array shelficemass to init_varia, initialise
545        from array shelficemassinit, which is set in init_fixed and
546        has option to be set from file; introduce array
547        shelficeMassDynTend array, set thru file in init_fixed
548      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
549        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
550        pkg/streamice
551      - shelfice_thermodynamics.F: call shelfice_step_icemass if
552        SHELFICEMassStepping = .true.
553      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
554    
555    checkpoint65h (2014/12/17)
556    o verification/global_ocean.90x40x15, global_ocean_ebm:
557      - update to generic controls.
558    o pkg/ctrl:
559      - ctrl_map_ini_genarr.F: test for igen>0
560      - ctrl_init_variables.F: add call to CTRL_MAP_INI_GENTIM2D.
561      - move gentim2d part of ctrl_map_ini_genarr.F to
562        new separate routine : ctrl_map_ini_gentim2d.F
563      - ctrl_cost_driver.F,ctrl_init.F ctrl_map_ini_genarr.F:
564        add time variable weights and cyclic controls (time mean,
565        seasonal cycle, etc) capabilities to gentim2d
566    o pkg/ecco:
567      - move reading of error, conversion to weights from
568        ecco_cost_init_fixed.F to ecco_toolbox.F (ecco_readwei)
569    o global_oce_llc90, cs32:
570      - activte sbo.
571      - CTRL_SIZE.h : add maxCtrlProc.
572      - activate the new genctrl capabilities.
573      - update following reorganization of global_oce_input_fields.tar.gz  
574    o pkg/ctrl/ctrl_ad_diff.list:
575      - add missing ctrl_init_rec.f
576    o tools/OAD_support/keepOriginal:
577      - add ctrl_init_rec.F
578    o model/src/the_main_loop.F, pkg/ctrl/ctrl_map_ini_genarr.F:
579      - avoid recomputations of xx_gentim2d_dummy.
580    o momentum diagnostics:
581      - move filling of diagnostics Um_Diss & Vm_Diss from mom_fluxform.F and
582        mom_vecinv.F to timestep.F (to include Smag-3D contribution).
583    o pkg/seaice/seaice_lsr.F:
584      - fix computation of BU/BV, make sure they are non-zero, only necessary
585        for cubed sphere exchanges and SEAICE_OLx/y>0.
586        This makes calling s/r fill_cs_corner_rl obsolete (removed).
587    o verification/global_ocean.cs32x15/input.seaice
588      - add test for strong implicit coupling and restricted addtive Schwarz
589        methods for LSR
590      - update results/output.seaice.txt
591    o verification/tutorial_global_oce_biogeo:
592      - AD & OAD set-up: switch off ALLOW_OLD_VIRTUALFLUX (like in fwd set-up)
593        and set PTRACERS_EvPrRn(1,2) to zero (for DIC & ALK);
594        update output_adm,_oadm,_tlm.txt
595    o pkg/dic:
596      - change default to "#undef ALLOW_OLD_VIRTUALFLUX" in DIC_OPTIONS.h
597      - add a stop when ALLOW_OLD_VIRTUALFLUX is defined and PTRACERS_EvPrRn
598        for tracer 1 & 2 is set (to avoid double counting of dilution effect).
599    o verification/tutorial_global_oce_biogeo:
600      - AD & OAD set-up: do not set PTRACERS_EvPrRn for tracer 1 & 2 since
601        dilution is already added by pkg/dic ALLOW_OLD_VIRTUALFLUX ;
602        update output_adm,_oadm,_tlm.txt
603    o eesupp/src:
604      - add fill_cs_corner_rl.F (_RL-copy of fill_cs_corner_rs.F)
605        and call it in seaice_lsr when using nonzero SEAICE_OLx/y
606    o pkg/seaice: introduce strongly implicit coupling, intended for stabilizing
607      LSR (following Hutchings et al. 2004)
608      - introduce zetaZ as a global variable (requires adjustments in
609        seaice_evp.F and seaice_jfnk.F) and compute analoguously to etaZ
610        in seaice_calc_viscosities.F
611      - new flag SEAICEuseStrImpCpl (default off)
612      - add new terms zetaZ*du/dy and zetaZ*dv/dx on both sides of the
613        momentum equations
614      - JFNK-solver (preconditioner) adjusted to allow using this method
615        (where it does not have any positive effect)
616    o pkg/seaice
617      - add overlap for restrictive additive Schwartz method also to LSR, but
618        turn it off by default (because it only seems to work for non-cubed
619        sphere/llc topologies)
620    o pkg/autodiff
621      - add extra exchanges in addummy_in_steppging also for mnc output
622    o pkg/seaice:
623      - add extra exchanges before dumping adjoint fields in seaice_ad_dump.F
624        to avoid stripes in the adjoint output (similar to addummy_in_stepping.F)
625    o pkg/obcs:
626      - add option to specify domain-connected piece Id along OB though files
627        (for now, only used to diagnose PhiVel; default =1 -> global correction)
628      - modify obcs_diag_balance.F to process each connected-part separately;
629        exclude OB where Id = 0 but keep the full divergence there (-> constant
630        Psi along this portion of OB and all inflow derived from grad(Phi))
631      - add example of OB-conect files in verification/so_box_biogeo/input.
632    o pkg/diagnostics:
633      - improve treatment of Open-Boundaries in Velocity-Potential calculation:
634      a) use non zero matrix element across OB and solve for Phi 1 grid point
635         outside OB (i.e, where tracer OBCS are applied).
636      b) global imbalance of inFlow/outFlow across OB: instead of modifying
637         velocity across OB, spread it uniformly along the OB in the RHS.
638    
639    checkpoint65g (2014/11/19)
640    o pkg/diagnostcis:
641      - add preconditioner off-diagonal factor (diagCG_pcOffDFac) as run-time param
642    o pkg/my82,pp81,kl10:
643      - fix ALLOW_3D_DIFFKR implementation (previously had no effect): use 3-D
644        field diffKr as background diffusivity to set minimum diffusivity value.
645    o pkg/seaice:
646      - add new parameter SEAICEuseEVPrev (for revisited EVP by
647        Bouillon et al 2013)
648      - add SEAICE_evpAlpha/Beta to namelist
649      - modify seaice_evp code to able to use SEAICEuseEVPrev. These changes
650        involve trivial re-ordering of divisions/multiplications that should not
651        have any effects, but ... they do change the results of lab_sea.hb87 so
652        that only 2 digits of agreement remain, in line with the general
653        instability/fragility of the evp-code. For now, I do not care and just
654        update the verification experiment
655    o pkg/ctrl : add generic pre-processing (xx_genarr2d_preproc etc)
656      - remove xx_genarr2d_numsmooth etc
657      - use xx_genarr2d_preproc etc instead
658      - carry out smooth_correl2D at initialization stage rather than during
659        time stepping.
660      - get smoothOpNb from xx_gentim2d_preproc
661    o global_oce_cs32 :
662      - add test of generic ecco capabilities.
663    o pkg/exf/exf_getsurfacefluxes.F :
664      - add to tmpUE/tmpVN rather than re-initializing them (conventional behavior).
665    o pkg/ctrl,ecco :
666      - omit un-necessary arguments to ctrl_cost_gen.F unless ECCO_CTRL_DEPRECATED
667        is defined.
668    o pkg/seaice: add diagnostics for Delta (deformation parameter)
669    o model/src:
670      - when ALLOW_3D_DIFFKR is defined, add a Warning if any of the vertical
671        diffusivity (background) is specified but ignored.
672    o verification:
673      - in testreport, convert hostname to lower case for default output dir name
674    o model, pkg : add useCTRL, useECCO parameters (on/off run time switch).
675    o pkg/dic: add modifications from Hajoon:
676      - add iron sedimentation flux function of the flux of PO4 out of bottom layer
677      - light attenuation: add self-shading effect by climatological Chlorophyll
678        (read from file).
679    o pkg/seaice/seaice_preconditioner.F : fix cpp flags, so that code also
680        compiles when SEAICE_ALLOW_DYNAMICS is undefined
681    o global_oce_llc90,cs32 : ecco_v4 verification exps now use separate
682        AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h, ECCO_OPTIONS.h rather than
683        ECCO_CPPOPTIONS.h (i.e. replacing the deprecated, circumvoluted,
684        approach where CPP_OPTIONS.h includes an omnipotent
685        ECCO_CPPOPTIONS.h that superseeds pkgs '_OPTIONS.h').
686    o pkg/ctrl/ctrl_map_ini_genarr.F : include GMREDI_OPTIONS.h where
687        ALLOW_3D_KAPGM, ALLOW_3D_KAPREDI (to be added later) belong.
688    o pkg/seaice/SEAICE_SIZE.h : replace ALLOW_AUTODIFF_TAMC with ALLOW_AUTODIFF
689        to avoid needing AUTODIFF_OPTIONS.h anytime SEAICE_SIZE.h is included
690        (it seems that THSICE_SIZE.h, PTRACERS_SIZE.h have the same issue...)
691    o model/src, pkg/smooth, profiles, salt_plume, seaice, exf, ecco, ctrl :
692      add ECCO_OPTIONS.h, AUTODIFF_OPTIONS.h, CTRL_OPTIONS.h when needed
693      - ECCO_OPTIONS.h is needed when including ecco_cost.h, ecco.h
694      - AUTODIFF_OPTIONS.h is needed when including tamc.h, tamc_keys.h
695      - CTRL_OPTIONS.h is needed when including ctrl.h, optim.h, etc
696    o pkg/ctrl,ecco,exf :
697      - remove variables associated with NON-generic costs,
698        unless ECCO_CTRL_DEPRECATED is defined.
699      - remove NON-generic NON-obcs controls,
700        unless ECCO_CTRL_DEPRECATED is defined.
701    o pkg/ctrl : added ctrl_local_params.h
702    o pkg/ecco : added ecco_local_params.h
703    o verification : added ECCO_CTRL_DEPRECATED to most as and oad
704        experiments, which will progressively be removed once the
705        experiments are revised to use only generic controls/costs.
706    
707    checkpoint65f (2014/10/13)
708    o pkg/ctrl, ecco, seaice : minor changes in headers
709    o global_oce_llc90,cs32 : ecco_v4 verification exps now test generic
710        cost function and control capabilities added since checkpoint65c.
711    o pkg/ctrl: regroup all obcs ctrl variables in CTRL_OBCS.h.
712    o pkg/ecco: increase modularity and improve logic
713      - ecco_toolbox.F (new) : basic operations that are often used,
714        including ecco_zero, ecco_cp, ecco_cprsrl, ecco_diffmsk,
715        ecco_addcost, ecco_add, ecco_div, ecco_readbar.
716      - cost_gencal.F (new) : determine filnames and records.
717      - cost_genread.F, cost_generic.F : condense code using ecco_toolbox.
718      - cost_generic.F : use spzeroloc rather than hard-coded -9999,
719        and exploit the above functions leading to more compact code.
720      - cost_genread.F : rm un-necessary arguments, re-arrange args order.
721      - ecco_check.F, ecco_readparms.F : bring logic up to date (using_tpj,
722        using_ers, using_gfo, using_mdt is now only defined within gencost)
723    o pkg/ecco: extend generic cost capabilities
724      - pkg/ecco : added 3D gencost (ALLOW_GENCOST3D), added gencost
725        capabilities via gencost_preproc (+ _c,_i,_r related params),
726        gencost_posproc (+ _c,_i,_r related params), gencost_nrecperiod,
727        gencost_outputlevel arguments to cost_generic
728      - pkg/ecco/cost_genread.F (new) : interface between cost_generic
729        and active_read, making room for gencost_preproc to take effect.
730        Added preproc code ('climmon') to replace GENERIC_BAR_MONTH.
731      - pkg/ecco/cost_generic.F :
732        compute and store misfit maks*(model-data) in localdif that is
733        then used in cost and for output, output misfit if outlev.GT.0
734      - pkg/ecco/cost_averagesfields.F : depend on gencost_barskip
735        rather gencost_barfile for deciding whether to write barfile
736      - pkg/ecco/ecco_cost_driver.F : extract call to cost_profiles from cost_hyd
737      - pkg/ecco/ecco_cost_init_fixed.F : extract gencost weights from
738        ecco_cost_weights, re-activate ecco_summary, determine gencost_barskip
739      - pkg/ecco/ecco_summary.F : report gencost variables
740      - pkg/ecco/cost_gencost_customize.F : treat case of scatterometer costs
741    o pkg/sea/SEAICE_OPTIONS.h : add ALLOW_COST_ICE, ALLOW_SEAICE_COST_SMR_AREA
742    o pkg/ecco: internal re-organization
743      - resolve un-necessary dependancies within pkg/ecco and to pkg/ctrl
744        (rm includes of optim.h and ctrl.h, replace optimcycle with eccoiter,
745        mv relevant variables definition from ecco_cost.h to ecco.h,
746        make sure gencost routines only include ecco.h)
747      - throughout : add missing CCP switches, rm unused variables,
748        and rm un-necessary CPP switches
749      - throughout gencost routines : replace modelstartdate with
750        gencost_startdate when needed
751      - cost_bp_read.F : use arguments, instead of common blocs
752        so that it can be used also by (new) cost_gencost_bpv4.F
753      - ecco_init_varia.F : initialize RHOsumGlob_0, VOLsumGlob_0
754      - ecco_phys.F : compute etanFull
755      - ecco_readparms.F : rename using_topex as using_tpj, add
756        bpv4-grace to gencost list, initialize added parameters
757      - ecco_summary.F : include SIZE.h needed for augmented ecco.h
758    
759    checkpoint65e (2014/09/28)
760    o pkg/obcs:
761      - replaced the just-added CPP options with run-time variables
762        (see pkg/obcs/OBCS_PARAMS.h for details)
763    o pkg/obcs:
764      - add additional CPP options for sponge boundary layers
765        (see pkg/obcs/OBCS_OPTIONS.h for details)
766    o pkg/atm_phys:
767      - implement simple (obliquity only, assuming circular planet orbit)
768        seasonal cycle for incoming insolation ; used when run-time parameter
769        "select_incSW" is set to 1 ; by default (=0), uses old unchanged formula.
770    o pkg/exf, pkg/ecco, pkg/ctrl:
771      - add ctrlUseGen and .NOT.ctrlUseGen exclusive brackets
772      - activate gentim2d for xx_atemp,xx_aqh,xx_swdown,xx_lwdown,xx_precip
773      - implement gentim2d for xx_tauu, xx_tauv
774    o pkg/ctrl, pkg/ecco :
775      - fix and complement the generic controls implementation
776    o pkg/exf/exf_getclim.F, exf_getffields.F, exf_getsurfacefluxes.F,
777        pkg/shelfice/shelfice_thermodynamics.F,
778        verification/hs94.1x64x5/code_ad/ctrl_map_gentim2d.F,
779        verification/hs94.1x64x5/code_oad/ctrl_map_gentim2d.F :
780      - add weight in CTRL_GET_GEN calls
781    o pkg/ctrl :
782      - ctrl_get_gen.F : add weight as input parameter, and apply
783        it directly rather than using smooth_correl2Dw (to be retired).
784      - ctrl_map_gentim2d.F : add wgentim2d in CTRL_GET_GEN call
785    o pkg/ctrl :
786      - introduce run time switch ctrlUseGen (in ctrl.h, ctrl_check.F,
787        ctrl_init_variables.F, ctrl_readparms.F, ctrl_summary.F)
788      - re-activate ctrl_summary (call in ctrl_init.F)
789    o pkg/ctrl/ctrl_cost_gen.F :
790      - fix CCP brackets, remove un-necessary myiter, mytime
791    o pkg/ecco, pkg/ctrl :
792      - remove cost_genctrl.F (now pkg/ctrl/ctrl_cost_driver.F)
793      - remove cost_forcing_gen.F (now pkg/ctrl/ctrl_cost_gen2d.F)
794      - add ctrl_cost_driver.F (replaces pkg/ecco/cost_genctrl.F)
795      - add ctrl_cost_gen2d.F (replaces pkg/ecco/cost_forcing_gen.F)
796    
797    checkpoint65d (2014/09/15)
798    o pkg/ctrl/CTRL_GENARR.h, ctrl_readparms.F :
799      - add xx_genarr2d_bounds,xx_genarr3d_bounds,
800        xx_genarr2d_numsmooth, xx_genarr3d_numsmooth
801    o pkg/ctrl/ctrl_map_ini_genarr.F :
802      - remove compilation failure
803      - replace hard coded example
804      - use ctrl_map_ini_gen2D, 3D
805    o pkg/ctrl/ctrl_pack.F, ctrl_unpack.F :
806      - on/off switch based upon xx_genarr2d_weight,3d
807    o src/packages_init_variables.F :
808      - regroup pkg/estimation calls
809      - remove CTRL_MAP_INI, CTRL_MAP_INI_ECCO
810        (moved to ctrl_init_variables)
811    o cost/cost_init_varia.F :
812      - remove ecco_cost_init_varia
813        (moved to ecco_init_varia)
814    o ctrl/ctrl_init_variables.F :
815      - add CTRL_MAP_INI, CTRL_MAP_INI_ECCO
816      - add CTRL_MAP_INI_GENARR, SEAICE_CTRL_MAP_INI
817    o ctrl/ctrl_map_ini.F :
818      - remove ctrl_map_ini_genarr, seaice_ctrl_map_ini
819        (moved to ctrl_init_variables)
820    o ctrl/ctrl_map_ini_ecco.F :
821      - remove ECCO_PHYS (mv to ecco_init_varia)
822      - remove seaice_ctrl_map_ini (mv to ctrl_init_variables)
823    o ecco/ecco_ad_diff.list :
824      - add ecco_init_varia.f
825    o ecco/ecco_init_varia.F
826      - new routine
827    o pkg/streamice:
828      - move call to STREAMICE_INITIALIZE_PETSC from the_model_main.F
829        to streamice_init_fixed.F ; fix setting of STREAMICEisOn.
830      - from model/src, only call pkg/streamice routines if useStreamIce is TRUE.
831    o pkg/generic_advdiff:
832      - fix bug causing negatives in GAD_SMOLARKIEWICZ_HACK, introduced 8/8/2014.
833    o pkg/exf:
834      - exf_getffields.F : add xxg_atemp, xxg_aqh, xxg_swdown, xxg_lwdown,
835         xxg_precip capability
836      - exf_wind.F : no need for ALLOW_WSPEED_CONTROL cpp switch
837    o pkg/ctrl:
838      - ctrl_pack.F, ctrl_unpack.F : omit (un)packing of undefined xx_gentim2d
839    o model/src/load_fields_driver.F :
840      - move call to CTRL_MAP_GENTIM2D ahead of BULKF_FIELDS_LOAD, EXF_GETFORCING
841        so xx_gentim2d can be applied to e.g. exf fields in a timely manner.
842    o OpenAD verification experiments:
843      - Include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, and CTRL_OPTIONS.h
844        in src files (to enable to skip the ECCO_CPPOPTIONS.h);
845        for now, only in pkgs used in OpenAD verification experiments.
846      - Change all except one (halfpipe_streamice) OpenAD experiments to use pkg
847        specific option file (AUTODIFF_OPTIONS.h, COST_OPTIONS.h & CTRL_OPTIONS.h)
848        instead of using ECCO_CPPOPTIONS.h (with all relevant options in it).
849        This applies to both TAF (*/code_ad/) and OpenAD (*/code_oad/) tests.
850    o OpenAD verification tests:
851      - finish removing ALLOW_AUTODIFF_OPENAD (replaced by ALLOW_OPENAD);
852      - finish replacing ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for
853        tape/storage which are specific to TAF/TAMC) in pkgs used in OpenAD exp.
854      - leave ALLOW_AUTODIFF_TAMC undef in OpenAD verification tests (*/code_oad/)
855        and remove local copy of "tamc.h" (needed only if ALLOW_AUTODIFF_TAMC).
856    o model/src & generic_advdiff:
857      - change hard-coded loop-range in S/R APPLY_FORCING_T/S to set T & S
858        forcing over 0:sNx+1, 0:sNy=1 (instead of just 1:sNx,1:sNy): Model
859        dynamics requires valid tracer forcing only over tile interior but, for
860        some diagnostics, may need to extend it over 1 point in tile halo region.
861      - in gad_calc_rhs.F, update calls to gmredi_x/ytransport to get valid
862        tendency over i,j_Min,Max range. This allows to simplfy i,j_Min,Max
863        setting in temp/salt/ptracer_integrate.F
864    o pkg/dic:
865      - multiply tracer tendencies by maskInC (if ussing OBCS) before updating
866        gchem tracers: this allows to skip the 2nd call to OBCS_APPLY_PTRACER
867        in gchem_forcing_sep.F
868    o pkg/autodiff & obcs:
869      - add storage of current OB values for U & V (was already done for T & S).
870    
871    checkpoint65c (2014/08/30)
872    o pkg/dic:
873      - take out of dic_atmos.F the initialisation part (corresponding to istate=0)
874        and move it to new S/R DIC_INI_ATMOS ; also simplify the dependencies for
875        AD compilers (but still a Pb with multi-threading and Ajoint dependencies).
876    o verification:
877      - new experiment testing OBCS and DIC pkgs, using params & output from
878        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
879        passage: take OBCS from the last year of a 2 yrs simulation and initial
880        conditions from t=1.yr while keeping the same forcing.
881    o model/src:
882      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
883        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
884    o pkg/diagnostics (Stats-Diags):
885      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
886        a) refine region where stats are computed, excluding where arrhFac=0 ;
887        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
888        c) extend regional stats over the region edges (for U or V pt location).
889    o pkg/gchem:
890      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
891        pkg/dic is currently changing/updating ptracers values beyond the OB).
892    o verification (hs94):
893      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
894        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
895        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
896        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
897    o pkg/ptracers:
898      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
899        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
900      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
901        with AB-2 code (so that it get tested).
902    o model/src:
903      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
904        with AB-2 code (previously only available with AB-3 code).
905        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
906        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
907        there, by calling CYCLE_AB_TRACER).
908    o pkg/generic_advdiff:
909      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
910        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
911        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
912        S/R temp/salt/ptracers_integrate.F
913    o model/src & pkg/ptracers:
914      - remove common block variables gT,gS (in DYNVARS.h), except when
915         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
916      - remove common block variable gPtr.
917    o model/src & pkgs:
918      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
919         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
920         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
921         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
922      + change accordingly all calling S/R.
923      - use local temperature/salinity/ptracer tendency array (without bi,bj)
924        in S/R temp/salt/ptracers_integrate.F
925    o pkg/seaice:
926      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
927        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
928      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
929        in seaice_lsr
930      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
931        in s/r seaice_lsr_calc_coeffs
932    o pkg/mdsio:
933      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
934        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
935        too long (e.g., > MAX_LEN_FNAM/2 )
936    
937    checkpoint65b (2014/08/12)
938    o pkg/matrix:
939      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
940    o model/src:
941      - fix initialisation of geothermalFile; compile geothermal-flux code in
942        natl_box verification experiment.
943    o model/src & pkg/down_slope:
944      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
945      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
946        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
947        results at machine truncation level: update output of experiments
948        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
949    o pkg/diagnostics (Stats-Diags):
950      - do not cumulate the full volume when DIAGNOSTICS_FILL is
951        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
952        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
953        times (but Min,Max and StD are still wrong).
954    o model/src:
955      - add geothermal flux forcing: read in ini_forcing.F as time-constant
956        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
957    o model/src:
958      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
959        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
960        arrays are already updated while adjustments (filters, conv.adjustment) are
961        still applied later, in S/R TRACERS_CORRECTION_STEP.
962    o model/src:
963      - store in common bloc array "rhoInSitu" the virtual potential temperature
964        anomaly that is used to compute geopotential: this make the atmos code
965        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
966    o pkg/seaice/seaice_lsr.F
967      - rename integer variable ilcall to ipass (that's what it is called
968        in the residual diagnostics
969      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
970        default) for improved non-linear convergence of the first few steps
971      - adjust a few comments and add new ones to explain some of the store
972        directives
973    o pkg/generic_advdiff (& ptracers):
974      - re-work the code to check for valid advection scheme and for minimum
975        size of overlap (now stored in local common bloc in gad_advscheme.F)
976    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
977      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
978      - add an auxilliary variable "bet" and fix store directives and keys in
979        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
980        less exact gradients in my tests); but there are still
981        recomputation warning (although gradients are sort of OK), when
982        SEAICE_LSR_VECTORIZE is not defined, so this flag and
983        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
984      - update verification experiments lab_sea.
985      - change some comments in S/R seaice_calc_viscosities
986    o model/src:
987      - if staggerTimeStep=T, always apply exchange to velocity field in
988        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
989        (independent of using multi-dim advection or not); no effect on FWD run
990        but affects AD results (at machine truncation level): update output of
991        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
992        and isomip (oad: 12.d).
993    o pkg/generic_advdiff:
994      - stop if doAB_onGtGs is set to FALSE but ignored
995      - refine warning related to stability of tracer time-stepping
996        regarding internal wave dynamics.
997      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
998        on staggerTimeStep & implicitIntGravWave (will now get a warning
999        if potentially unstable).
1000    o pkg/kl10:
1001      - add new pkg "kl10" for mixing due to internal wave breaking, from
1002        http://www.sciencedirect.com/science/article/pii/S1463500310000144
1003        (contribution from Jody Klymak), tested in verification experiment
1004        verification/internal_wave/input.kl10/
1005    o isomip experiment:
1006      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
1007        (input.htd) and update the output.
1008    o cd_code experiments:
1009      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
1010        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
1011        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
1012        update the corresponding output.
1013    o pkg/seaice:
1014      - reduce the number of include files and store directives in
1015        S/R seaice_lsr_tridiagu/v
1016      - change the order of loops in one case in S/R seaice_lsr_tridiagv
1017        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
1018        get rid off one store directive (a TAF bug?)
1019      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
1020        S/R seaice_lsr_tridiagv to change the loop range for consistency
1021      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
1022      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
1023        S/R seaice_lsr_tridiagu/v (requires update of
1024        offline_exf_seaice/input.dyn_jfnk)
1025    
1026  checkpoint65a (2014/07/27)  checkpoint65a (2014/07/27)
1027  o model/src:  o model/src:
1028    - 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
# Line 18  o model/src: Line 1037  o model/src:
1037    - 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
1038      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.
1039      affects results at machine truncation level (e.g., ocean: if using      affects results at machine truncation level (e.g., ocean: if using
1040      SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)      SHORTWAVE_HEATING ; atmos: if using FrictionHeating or (atm_Rq<>0) moist
1041      moist correction due to vertical advection).      correction due to vertical advection).
1042    - update output of experiments: fizhi-cs-32x32x40 (13 digits),    - update output of experiments: fizhi-cs-32x32x40 (13 digits),
1043      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:      global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
1044      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 48  o pkg/seaice: more clean up Line 1067  o pkg/seaice: more clean up
1067      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
1068      this experiment):      this experiment):
1069      > size mitgcmuv_ad      > size mitgcmuv_ad
1070      text    data        bss     dec        hex        text    data        bss     dec        hex
1071      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
1072      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
1073      but only a moderate increase of 36% for global_ocean.cs32x15:      but only a moderate increase of 36% for global_ocean.cs32x15:
1074      text    data        bss     dec        hex      text    data        bss     dec        hex
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