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revision 1.1844 by heimbach, Fri Mar 29 23:21:39 2013 UTC revision 1.2049 by jmc, Mon Aug 18 20:16:53 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o verification/isomip, pkg/shelfic and OpenAD:  o pkg/ptracers:
8      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
9        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
10      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
11        with AB-2 code (so that it get tested).
12    o model/src:
13      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
14        with AB-2 code (previously only available with AB-3 code).
15        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
16        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
17        there, by calling CYCLE_AB_TRACER).
18    o pkg/generic_advdiff:
19      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
20        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
21        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
22        S/R temp/salt/ptracers_integrate.F
23    o model/src & pkg/ptracers:
24      - remove common block variables gT,gS (in DYNVARS.h), except when
25         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
26      - remove common block variable gPtr.
27    o model/src & pkgs:
28      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
29         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
30         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
31         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
32      + change accordingly all calling S/R.
33      - use local temperature/salinity/ptracer tendency array (without bi,bj)
34        in S/R temp/salt/ptracers_integrate.F
35    o pkg/seaice:
36      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
37        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
38      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
39        in seaice_lsr
40      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
41        in s/r seaice_lsr_calc_coeffs
42    o pkg/mdsio:
43      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
44        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
45        too long (e.g., > MAX_LEN_FNAM/2 )
46    
47    checkpoint65b (2014/08/12)
48    o pkg/matrix:
49      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
50    o model/src:
51      - fix initialisation of geothermalFile; compile geothermal-flux code in
52        natl_box verification experiment.
53    o model/src & pkg/down_slope:
54      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
55      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
56        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
57        results at machine truncation level: update output of experiments
58        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
59    o pkg/diagnostics (Stats-Diags):
60      - do not cumulate the full volume when DIAGNOSTICS_FILL is
61        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
62        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
63        times (but Min,Max and StD are still wrong).
64    o model/src:
65      - add geothermal flux forcing: read in ini_forcing.F as time-constant
66        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
67    o model/src:
68      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
69        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
70        arrays are already updated while adjustments (filters, conv.adjustment) are
71        still applied later, in S/R TRACERS_CORRECTION_STEP.
72    o model/src:
73      - store in common bloc array "rhoInSitu" the virtual potential temperature
74        anomaly that is used to compute geopotential: this make the atmos code
75        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
76    o pkg/seaice/seaice_lsr.F
77      - rename integer variable ilcall to ipass (that's what it is called
78        in the residual diagnostics
79      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
80        default) for improved non-linear convergence of the first few steps
81      - adjust a few comments and add new ones to explain some of the store
82        directives
83    o pkg/generic_advdiff (& ptracers):
84      - re-work the code to check for valid advection scheme and for minimum
85        size of overlap (now stored in local common bloc in gad_advscheme.F)
86    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
87      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
88      - add an auxilliary variable "bet" and fix store directives and keys in
89        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
90        less exact gradients in my tests); but there are still
91        recomputation warning (although gradients are sort of OK), when
92        SEAICE_LSR_VECTORIZE is not defined, so this flag and
93        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
94      - update verification experiments lab_sea.
95      - change some comments in S/R seaice_calc_viscosities
96    o model/src:
97      - if staggerTimeStep=T, always apply exchange to velocity field in
98        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
99        (independent of using multi-dim advection or not); no effect on FWD run
100        but affects AD results (at machine truncation level): update output of
101        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
102        and isomip (oad: 12.d).
103    o pkg/generic_advdiff:
104      - stop if doAB_onGtGs is set to FALSE but ignored
105      - refine warning related to stability of tracer time-stepping
106        regarding internal wave dynamics.
107      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
108        on staggerTimeStep & implicitIntGravWave (will now get a warning
109        if potentially unstable).
110    o pkg/kl10:
111      - add new pkg "kl10" for mixing due to internal wave breaking, from
112        http://www.sciencedirect.com/science/article/pii/S1463500310000144
113        (contribution from Jody Klymak), tested in verification experiment
114        verification/internal_wave/input.kl10/
115    o isomip experiment:
116      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
117        (input.htd) and update the output.
118    o cd_code experiments:
119      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
120        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
121        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
122        update the corresponding output.
123    o pkg/seaice:
124      - reduce the number of include files and store directives in
125        S/R seaice_lsr_tridiagu/v
126      - change the order of loops in one case in S/R seaice_lsr_tridiagv
127        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
128        get rid off one store directive (a TAF bug?)
129      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
130        S/R seaice_lsr_tridiagv to change the loop range for consistency
131      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
132      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
133        S/R seaice_lsr_tridiagu/v (requires update of
134        offline_exf_seaice/input.dyn_jfnk)
135    
136    checkpoint65a (2014/07/27)
137    o model/src:
138      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
139        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
140        (topo in p-coords, ice-shelf in z-coords); update output of experiments
141        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
142    o model/src:
143      - collect momentum forcing tendency into local 2-D array (passed as argument
144        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
145        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
146        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
147      - collect T & S forcing tendency into local 2-D array (passed as argument to
148        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
149        affects results at machine truncation level (e.g., ocean: if using
150        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
151        moist correction due to vertical advection).
152      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
153        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
154        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
155        obcs_ctrl (ad & fwd grd @ 12 & 7).
156    o pkg/ptracers & diagnostics:
157      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
158        title (to avoid some unexpected truncation); sort out ptracers diags units.
159      - collect ptracer forcing tendency into local 2-D array (passed as argument
160        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
161    
162    checkpoint65 (2014/07/18)
163    o pkg/fizhi:
164      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
165        affects results at machine truncation level. Update output of experiments
166        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
167    o pkg/seaice: more clean up
168      - rename TAF common block tapes to be more consistent and remove
169        unnecessary duplicates
170      - add store directives to remove more recomputations, but use smaller
171        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
172        The idea behind this flag is to reduce the memory footprint when the
173        adjoint of the LSR is not required. As of now, defining the flag
174        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
175        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
176        For experiment offline_exf_seaice, this means on a linux box with gfortran
177        nearly a factor of 10 (but keep in mind there is mostly seaice code in
178        this experiment):
179        > size mitgcmuv_ad
180        text    data        bss     dec        hex  
181        5100659 1216  220458952  225560827  d71c8fb
182        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
183        but only a moderate increase of 36% for global_ocean.cs32x15:
184        text    data        bss     dec        hex
185        6695027 1648 1014578664 1021275339 3cdf6ccb
186        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
187      - note: there are still recomputations in global_ocean.cs32x15 and
188        offline_exf_seaice and the gradient agreement changes (gets a
189        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
190      - in general, the AD gradients still are wrong
191    o OpenAD
192      - clean up code_oad/ directories somewhat by moving files
193        dontCompile, dontTransform, keepOriginal to OAD_support/
194    o model/src:
195      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
196        (not currently tested): add dissipation terms before NLFS rescaling of
197        tendencies (previously done after).
198    o pkg/diagnostics:
199      - write stats-diags in ascii file with more digits (same as in monitor).
200    o pkg/down_slope:
201      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
202        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
203    o model/src:
204      - new file "apply_forcing.F" containing all the code previously in
205        external_forcing.F, but with new argument list: pass, as new argument,
206        the current level tendency array to update (instead of a direct update
207        of the common bloc array). Change the corresponding calls.
208      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
209        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
210    o pkg/seaice/seaice_lsr, a little bit of clean up
211      - rearrange some code blocks, so that now all calculations for
212        setting up the right-hand-sides done within one single block
213        (I find that easier to read and understand)
214      - rearrange freedrift-code to reduce the number of ifdefs
215      - adjust some indentations and comments
216    
217    checkpoint64z (2014/07/10)
218    o model/src and several pkgs:
219      - change argument list of all S/R called from external_forcing.F and
220        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
221        to pass, as argument, the current level tendency array to update
222        (instead of a direct update of the common bloc array).
223      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
224      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
225    o pkg/seaice/seaice_lsr.F
226      - always initialize local arrays in seaice_lsr_tridiagu/v
227      - add more local tapes to seaice_lsr_tridiagu/v
228      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
229        keep it in bi/bj loop; this seems to be essential
230      - gradients are still wrong but only by 4-7 orders of magnitude
231        instead of 15 orders of magnitude, lab_sea improves a little
232    o pkg/seaice
233      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
234        generates unnecessary code in seaice_lsr_ad
235      - add more store directives in seaice_lsr to avoid unnecessary code
236        in seaice_lsr_ad
237      - exclude some residual computations in seaice_lsr when
238        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
239        in seaice_lsr_ad
240      - add more storing, a new tape (model/src/the_main_loop.F) and
241        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
242        and klockey should be checked by a specialist)
243      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
244        and update lab_sea after previous changes in pkg/seaice below
245    o pkg/autodiff:
246      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
247        viscFacInAd : run time parameters allowing for adjoint switches
248        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
249    o pkg/ecco:
250      - introduce cost_gencost_boxmean.F that computes a box mean
251        temperature (for use in adjoint sensitivity studies).
252    o model/src/set_defaults.F : initialize viscFacAdj to 1.
253    o pkg/mom_common/mom_calc_visc.F:
254      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
255    o pkg/seaice/seaice_summary.F:
256      - statement for SEAICEadjMODE now in autodiff_readparms.F
257    o pkg/seaice:
258      - remove some store directives and add new ones in an effort to get
259        finally rid off the recomputation warnings. This is successful
260        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
261        defined (i.e. no extensive recomputation warnings left), but there
262        are still too many recomputations on the solver iteration level
263      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
264      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
265        SEAICE_SIZE.h
266      - add a store directive in S/R seaice_calc_viscosities
267    o pkg/seaice (ITD code):
268      - fix definition of Hlimit for multi-threaded case
269      - use double precision arithmetic to compute Hlimit: this affects results;
270        update output of experiment seaice_itd.
271    o replace content of verification/seaice_itd
272      - instead of a 1D column use the configuration of offline_exf_seaice
273        to test the ice thickness distribution code with ridging
274      - this is a first shot at this experiment
275      - change of some defaults of ridging parameters SEAICEhStar (from
276        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
277        and lot of new comments.
278    
279    checkpoint64y (2014/06/20)
280    o pkg/seaice/seaice_reg_ridge.F:
281      - modify the regularization of very small volumes of ice; only check
282        total volume HEFF, and do not apply correction to individual ice
283        classes because that leads to funny patterns in the heat and fw-fluxes
284        into the ocean. Adjust seaice_itd/results/output.txt
285      - replace nITD by SEAICE_multDim in loop-ranges
286    o pkg/exf:
287      - add code to process the case field period = -12. with UV interpolation.
288      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
289        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
290    o verification/global_with_exf:
291      - switch all fields period to -12. (was previously untested) in input/data.exf
292        (but keep secondary test ".yearly" unchanged); update the reference output.
293    o pkg/cal:
294      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
295    o pkg/exf:
296      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
297        to replace logical switch "exf_verbose"
298      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
299    o pkg/sbo:
300      - update from Katherine Quinn: evaluate mass directly from density and SSH
301        (budget using Finite Volume method) instead of from bottom pressure.
302      - allow testreport to collect few selected SBO output ; tested in exp.
303        global_ocean.90x40x15 (after updating the results, to include SBO output).
304      - fix some multi-threading issues (in output part).
305    o model/src & most packages:
306      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
307      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
308        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
309        "data.{pkg}" exist ; and leave the S/R (return) just after.
310      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
311        + call LAND_READPARMS from packages_readparms.F
312    o pkg/seaice:
313      - remove code that resets useThSice in S/R seaice_readparms and
314        replace it by a warning in S/R seaice_check
315      - remove parameter MULTDIM, replace with nITD and runtime
316        parameter SEAICE_multDim (still hard-wired to nITD if
317        SEAICE_ITD is defined)
318    
319    checkpoint64x (2014/05/24)
320    o verification/lab_sea:
321      - update adjoint and TLM output following changes to pkg/salt_plume
322      - un-do the update after putting back local recip_Cp in few places.
323    o pkg/salt_plume: modifications by An Nguyen:
324      - add capability to do brine rejection (salt-plume) as function of
325        volume+tracers (instead of only salinity tracer).
326      - conserve volume by exchanging volume from each kLev to above to
327        accommodate in-coming brine volume
328      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
329      - switch KPP surf buoyancy due to brine forcing to 3-d
330        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
331      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
332      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
333        in East/West Arctic.
334    o pkg/sbo:
335      - incorporate modifications from Katherine Quinn to enable the use of sbo
336        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
337        output for future testreport verification (unfinished).
338    o pkg/atm_phys:
339      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
340        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
341        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
342    o pkg/seaice
343      seaice_calc_ice_strength.F: modify expression to avoid divisions
344        (affects truncation)
345      seaice_do_ridging.F: clean up the insectarium
346      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
347      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
348      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
349      - add some debugging information and error messages (warnings)
350    o model/src: modifications relatd to atmosphere p*:
351      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
352      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
353        of vertical profile tRef in geopotential background and anomaly.
354      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
355        and pkg/atm_phys.
356      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
357        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
358    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
359    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
360        not used right now, but can be used in BGC packages to fix conservation.
361    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
362        other packages too.
363    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
364        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
365    o model/src:
366      - since we have several heat capacity (even in model/src), define "recip_Cp"
367        as local variable (no longer in common block) to avoid any confusion.
368      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
369    o pkg/exf:
370      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
371        air density as function of air Temp, Humidity and atm pressure.
372    
373    checkpoint64w (2014/05/02)
374    o verification:
375      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
376        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
377        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
378        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
379        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
380    o model/src: for atmosphere in p* coords:
381      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
382      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
383        but not yet activated.
384    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
385      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
386      - this changes the results (but not for any verification experiment, because
387        none tests this), but avoids having an extra field in the restart files
388    o pkg/seaice: remove global variable TICE (not needed)
389      - replace by TICES or local variable where necessary (cost_seaice_test,
390        seaice_diagnostics_state)
391      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
392      - use specific read/write routines for reading and writing individual leves
393        of a multilevel field
394    o pkg/ctrl & model/inc:
395      - move additional anomaly fields of control vars (related to options:
396         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
397        from DYNVARS.h into new header file: CTRL_FIELDS.h
398    o pkg/seaice: some small modifications to the ridging code
399      - make fw2ObyRidge a global variable and add the freshwater flux to
400        seaice_growth
401      - pass actual thickness from seaice_prepare_ridging, so that it is
402        computed only in one place and compute it in the same way as in
403        seaice_growth
404      - initialise more fields in seaice_do_ridging that where cause floating
405        point exceptions over land
406    o pkg/seaice: preparations for ridging code and first real ridging code
407      - move most of "PART 1" of S/R seaice_growth into a new and separate
408        S/R seaice_reg_ridge that will both regularize the state variable after
409        advection call the actual ridging routine;
410      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
411        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
412      - remove ridging code from seaice_advdiff
413      - clean up remaining part 1 of seaice_growth in an attempt to make it
414        more readable (this is probably subjective)
415      - call seaice_itd_redist once in the initialisation phase to have the initial
416        conditions in the correct category
417      - finally: add new ridging routine for ITD code
418    
419    checkpoint64v (2014/04/11)
420    o pkg/ecco:
421      - add runtime parameters mdt[start,end]date[1,2]
422      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
423    o pkg/seaice:
424      - make deltaC a global variable, so that it can be used in ridging code
425      - first step towards ridging: introduce new routines that compute
426        ice strength based on ridging parameters
427      - add diagnostic for HSNOWITD
428      - add opnWtrFrac as a global variable (required for ridging scheme)
429    o pkg/salt_plume + pkg/seaice/seaice_growth.F
430      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
431        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
432    o verification/hs94.1x64x5:
433      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
434      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
435    o autodiff:
436      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
437        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
438        For now, only in pkgs used in verification/hs94.1x64x5.
439      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
440        which are specific to TAF/TAMC).
441      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
442        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
443        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
444      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
445        building mitgcmuv_ad (make adAll).
446    o pkg/ecco:
447      - cost_gencost_seaicev4.F:
448         reformulate proxy cost as function of sst and local param SEAICE_freeze
449         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
450      - add stop statement if old names siv4-[sst,vol] are used
451      - add snapshots + cost reports for atmospheric longwave
452      - remove factor 0.1 in front of wtau[u,v]
453      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
454         ALLOW_TMI_SST_COST_CONTRIBUTION
455    o pkg/atm_phys:
456      - add some diagnostics for Short-wave and for convection S/R.
457    o pkg/seaice/seaice_growth:
458      - fix a bug in the lateral melt parameterization for SEAICE_ITD
459        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
460      - rearrange loop order for better vector code in the same code block
461      - rewrite the floeDiameter formula to have fewer divisions
462      -  (miraculously) none of this changes the results of seaice_itd
463    o pkg/smooth:
464      - move param smooth2Ddiffnbt to pkg/ecco
465    o pkg/salt_plume:
466      - salt_plume_frac.F:
467         clean up local param names
468         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
469    o pkg/rw:
470      - add RS version of S/R READ_MFLDS_LEV.
471    o pkg/streamice:
472      - fix the restart test by writing/reading pickup_streamice files.
473    o pkg/seaice:
474      - refine checks for jfnk-related parameters
475      - comment out if statement with SEAICEuseIMEX parameter as long as there
476        is no IMEX code to avoid confusion and surprises
477    
478    checkpoint64u (2014/03/07)
479    o verification/MLAdjust:
480      - rename secondary test suffix:
481         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
482         0.leithD -> AhFlxF  + switch to flux-form
483         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
484         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
485    o pkg/mom_vecinv:
486      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
487        to be before mom_calc_visc.F)
488      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
489      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
490        this is simpler for the adjoint and for diagnostics.
491    o model/src + pkg/momentum:
492      - add input files for  2-D additional Western and Southern cell-edge wall
493         (e.g., to add "thin-wall" where it is =1).
494      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
495        using 2nd hFacZ that is computed from initial (fix domain) hFac
496      - known limitations of thin wall implementation: not yet coded for sigma
497        coords; not working with CD-scheme neither.
498    o pkg/seaice:
499      - rename recently introduced parameters from (wrong name) AB to
500        BDF (backward difference time discretisation)
501      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
502    o tools/adjoint_options:
503      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
504    
505    checkpoint64t (2014/02/01)
506    o pkg/ecco
507      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
508        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
509      - replace hard-coded record number and period which only work for monthly
510        with read-in runtime param that works for other periods (month,day,year)
511    o pkg/thsice
512      - corrected store directive fixes thsice adjoint gradient checks
513    o genmake2 & testreport:
514      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
515        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
516        Update testreport accordingly. No need to set "export OPENAD=true"
517        in adjoint_options/adjoint_oad anymore (will be removed later).
518    o pkg/shelfice:
519      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
520        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
521        so that surface forcing applies to k=kSurf if using pkg/shelfice.
522    o pkg/ctrl, pkg/grdchk, pkg/ecco:
523      - Changes to make GENARR more modular (i.e. invisible if not used)
524    o model/src/temp_integrate.F and salt_integrate.F
525      - re-include store directives that were removed on Dec 27th.
526    o model/src/external_forcing_surf.F
527      - add storage directives for EmPmR and PmEpR to avoid recomputation of
528        seaice_model in the adjoint that is problematic when seaice_model is
529        turned off in the adjoint. The resolved issue dated back to July when
530        EXTERNAL_FORCING_SURF call was moved.
531        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
532    o pkg/exf/exf_check.F
533      - fix a small bug again (originally found by Wentao Liu, now found again)
534      - streamline error output
535    o pkg/streamice and aim_v23:
536      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
537        Apple's /usr/bin/cpp knows what to do:
538        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
539        Target: x86_64-apple-darwin13.0.0
540    
541    checkpoint64s (2014/01/05)
542    o tools/adjoint_options:
543      - switch to fastopt.net TAF server (instead of default fastopt.de) for
544        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
545    o model/src:
546      - remove some unnecessary TAF storage directives in forward_step.F and
547        in dynamics.F (note: not always removed by TAF, e.g., double storage
548        of kappaRU,kappaRV in former version of dynamics.F).
549    o model/src & pkg/ptracers:
550      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
551        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
552        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
553      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
554      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
555      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
556    o useSingleCpuInput separates single-CPU input from single-CPU output;
557        for now only implemented for in exf_interp_read.F
558    o verification/advect_xy:
559      - fix missing EXCH call in local version of ini_salt.F and update output.
560    o momentum diagnostics:
561      - fix which deltaT is used in Total-Tendency diagnostics.
562      - fix typo in diagnostics for momentum tendency from AB.
563    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
564        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
565    
566    checkpoint64r (2013/12/08)
567    o verification/*/results:
568      - Update reference output of experiments that were passing with just 13 digits
569         (make it easier to detect future changes in results)
570    o model/src & pkg/ptracers:
571      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
572        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
573        to inside ptracers_integrate.F ; remove ptracers_advection.F
574    o coupling interface pkgs:
575        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
576      - change the config check to test the agreement of Ocean Depth
577        with ATM land/sea mask (instead of ATM orography);
578      - send to coupler the number of coupler time-steps to do for this run:
579        this allows to check for consistency and don't need anymore to be
580        specified in parameter file "data";
581      in coupler:
582      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
583      - improve report to log-file of config setting (pass log-file unit to few S/R)
584    o pkg/compon_communic:
585      - add coupling send/receive for non-tiled integer vector;
586      - add S/R to check and stop if any proc has an error (similar to
587        eesupp/src/stop_if_error.F but single thread and across Comm_World).
588    o pkg/exch2:
589      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
590        through list of all tiles my proc owns.
591    o model/src:
592      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
593        from rTrans) to simplify dependencies (no need to store rTrans anymore in
594        calling S/R); this affects AD results at machine truncation level:
595        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
596        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
597    o tools/build_options:
598      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
599    o coupling interface pkgs:
600        [compon_communic, atm_compon_interf & ocn_compon_interf]
601      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
602        to each S/R that needs it; remove un-used variables.
603      - change component tile registration (cpl_register.F in both compon_interf
604        and mitcomponent_tile_register.F) to pass the full list of tiles
605        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
606      - with pkg/exch2: adopt the same convention used for I/O to define mapping
607        towards coupler global array (unless W2_useE2ioLayOut=F):
608         a) can now use different tiling between atm & ocn comp.
609         b) no needs to modify the run-Off map when changing tiling (was needed
610            even if using the same tiling between atm & ocn).
611         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
612            full land tiles); not yet tested.
613      - check for valid mapping from comp. tile to coupler global array
614      - improve report of tile registration results to log file.
615    o pkg/exch2:
616      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
617        tile-registration (CPL_REGISTER);
618      - activate (un-comment) definition and setting of "W2_tileIndex" list to
619        store the local bi,bj indices of each tile;
620      - also print bi,bj in local report to log file;
621      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
622        Jun 2009 modif of pkg/exch2).
623    o testing on baudelaire:
624      - run 2 tests at a time: no significant slow down (since enough cpu) and
625        get the full set of test done earlier
626      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
627    o model/src/thermodynamics.F and routines called from it:
628      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
629        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
630        velocity (outp) by adding bolus velocity.
631      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
632        mass transport from velocity + lateral grid cell area
633      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
634      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
635     in thermodynamics.F
636      - remove k from thermodynamics.F and move it to temp_integrate.F
637        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
638        loop).
639      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
640        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
641        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
642        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
643      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
644        global_ocean.90x40x15, tutorial_global_oce_biogeo and
645        tutorial_tracer_adjsens (+ TLM output).
646    o tools/OAD_support and (verification/*/) code_oad:
647      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
648        module conversion ; remove unneeded CPP_EEOPTIONS.h.
649      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
650        version (closer to model/inc/CPP_OPTIONS.h).
651    o model/src:
652      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
653        retired list of parameters (routine FREEZE has been replace by surface
654        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
655    o pkg/gmredi:
656      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
657        velocity (same scheme but affects machine truncation) for GM_AdvForm.
658      - update output of FWD experiments: front_relax.bvp,
659        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
660    
661    checkpoint64q (2013/11/17)
662    o verification:
663      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
664        tutorial_global_oce_biogeo and global_ocean.90x40x15.
665      - generate new output (growth & melt) for seaice_itd experiment after
666        updating the input pickup_seaice files (previously wrong).
667    o pkg/cost:
668      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
669        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
670        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
671          cannot be applied to var in common block).
672        o allows to get results independent of tile-per-proc setting (if using
673          slower GLOBAL_SUM_SEND_RECV option).
674      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
675        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
676        forward gradients: update output).
677      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
678        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
679    o pkg/mom_common:
680      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
681        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
682        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
683        ensure that all field value that are used are set.
684    o tutorial_deep_convection (smag3d):
685      - add missing scaling in mom_calc_smag_3d.F;
686      - set smag3D_coeff in input.smag3d such that results do not change.
687    o pkg/dic:
688      - change dic_cost.F to compute cost on each tile first and then apply
689        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
690        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
691      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
692    o eesupp/src & pkg/mdsio:
693      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
694        (from pkg/mdsio) since they are no longer used for tape IO.
695      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
696        (+ keep a copy in pkg/atm_ocn_coupler).
697    o verification/isomip:
698      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
699    o tools/build_options:
700      - optfile linux_amd64_ifort11, fast (no ieee) case:
701        to get a working restart for all experiments, add "-fp-model source"
702        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
703    
704    checkpoint64p (2013/10/20)
705    o pkg/autodiff:
706      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
707        criteria, return to simple (default) tape IO format.
708    o pkg/mdsio (+ eesupp/src):
709      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
710        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
711      - fix globalFile and singleCpuIO options using simpler global mapping.
712      - new pairs of scatter/gather vector S/R (one for each type, generated from
713        template) corresponding to simpler global mapping.
714      - adread_write.F: switch to new S/R (but leave old calls commented) and write
715        to globalFile when parameter globalFiles is set to True.
716      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
717    o pkg/autodiff:
718      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
719        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
720        missing, just add a STOP if array type do not match.
721    o pkg/exf:
722      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
723         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
724         and rename array obsSIce to exf_iceFraction.
725    o tutorial_deep_convection:
726      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
727        for now all in this exp. code dir.
728      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
729        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
730    o eesupp/src:
731      - added SINGLE_DISK_IO option because reading of parameter files on
732        very large number of processors did not work with existing set-up
733    
734    checkpoint64o (2013/09/25)
735    o pkg/atm_phys & atm_compon_interf:
736      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
737    o tools/build_options:
738      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
739        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
740        remove CPP setting (was identical to genmake2 default).
741    o pkg/gmredi & model/src: Some updating and work done on the residual model.
742      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
743      - fixed up the calculation of the eddy stress and how it is added to the
744        external forcing via taueddy_external_forcing.F
745      - at the moment, it is very experimental and only works with the variable eddy
746        diffusivity calculated in gmredi_k3d.F
747    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
748        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
749    o testreport (& tools/do_tst_2+2):
750      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
751    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
752      - remove CPP='cpp -traditional -P' (this is genmake2 default)
753      - add switch (for big setups) to use 'medium' memory-model (but leave it
754        commented out for now). Note: needed with FC 19 to compile big setups.
755    o pkg/atm_compon_interf:
756      - regroup per field origin (model & pkgs) the coupling storage routines
757         (which accumalate in time each coupling field)
758      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
759        update accordingly + simplify aim_do_physics.F
760    
761    checkpoint64n (2013/08/26)
762    o pkg/bbl:
763      - update formulation to reduce dispersion of tracer properties in bbl
764      - replaced horizontal and vertical transport parameters with velocities
765      - changes results for verification/global_with_exf.yearly
766    o verification/halfpipe_streamice:
767      - change to matrix construction; update both Fwd & AD output.
768    o verification/tutorial_tracer_adjsens:
769      - OpenAD test: switch to vector-invariant momentum since fluxform with
770        rStar causes problems with OpenAD; update output.
771    o tools:
772      - genmake2: define a common prefix for all temp-file names ; move them
773        to local /tmp disk (but would be easy to move them back);
774      - xmakedepend: apply the same switch for temp-files.
775    o pkg/offline:
776      - changes for use with rStar (NLFS): assume that we continue to provide
777        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
778        output files) and apply r* scaling at each time-step (function of the time
779        varying Eta field); use normal pickup files (needed for restart with NLFS).
780    o adjoint with OpenAD:
781      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
782        package openad.  This package has to be compiled for all runs with OpenAD
783        instead of specifying code_oad_all as a modification directory.
784      - link the fortran templates from tools/OAD_support to the build directory
785        for preprocessing to avoid conflicts between different setups compiled
786        simultaneously and simplify cleanup.
787    o pkg/exf:
788      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
789        main model or other pkgs are exchanged in EXF_MAPFIELDS).
790    o model/src:
791      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
792        (similar to do_fields_blocking_exchanges.F).
793    o tools/genmake2:
794      - remove TAF output src code just before calling staf (when not doing a fresh
795        built, will stop if things go wrong with staf).
796      - fix target "adobj" (left from TAF version-2 transition)
797    o pkg/diagnostics:
798      - add a parameter to track the status of pkg/diagnostics activation;
799        this replace/extend the use of logical param "settingDiags" (to check
800        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
801        New S/R to print error message and stop when pkgStatus is not right.
802      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
803    
804    checkpoint64m (2013/08/13)
805    o model/inc:
806      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
807        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
808    o pkg/kpp & aim_v23:
809      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
810    o pkg/seaice:
811      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
812        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
813      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
814    o eesupp/src:
815      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
816        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
817    o switch to TAF version-2:
818      - add flow directives to "freeze" naming convention for ad-routines that
819        are used in I/O routines of adjoint state and associated common blocks
820        that are used in adcommon.h (backward compatible with version-1)
821      - update all ad-optfiles (in tools/adjoint_options + few local to some
822        verification exp) to switch to latest TAF version (currently 2.5.5);
823        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
824        out except for diva).
825      - the major change with TAF version-2 is that both the differentiated
826        routines and the forward routines (new) are returned as part of the TAF
827        output source code. Update genmake2 accordingly.
828      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
829        with version-2 when compared to TLM or FWD gradient); other experiments
830        output show minor changes (machine truncation level); update the few AD &
831        TLM output with 12 matching digits only (some prior to version-2 switch).
832    
833    checkpoint64l (2013/08/05)
834    o model/src:
835      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
836      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
837        when using TAF but only if using OpenAD.
838    o pkg/mom_common+fluxform+vecinv:
839      - always set horiz. viscosity arrays to background value before calling
840        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
841        only when using variable horiz. viscosity (useVariableVisc=T);
842      - simplify mom_vecinv.F (only 1 block for momViscosity).
843    o pkg/mom_common: variable horiz. viscosity in NH code
844      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
845        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
846      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
847        useBiharmonicVisc & useVariableVisc.
848      - fix old bug (already in 1rst implementation of variable horizontal viscosity
849        in calc_gw.F, version 1.27, 2006/06/20):
850        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
851        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
852      - change background horiz viscosity in vertical momentum (gW) to always be
853        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
854        any type of variable viscosity, e.g., viscAh/4Grid)
855      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
856        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
857        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
858        default viscAh,viscA4 is zero).
859    o model/src:
860      - extend length of drC & recip_drC from Nr to Nr+1.
861    o Divided Adjoint (DIVA) with MPI:
862      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
863      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
864        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
865    
866    checkpoint64k (2013/07/23)
867    o tools/OAD_support:
868      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
869        and remove it from genmake2.
870    o tools/build_options:
871      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
872        MPI_HEADER_FILES list (let genmake2 find the missing headers)
873    o verification/halfpipe_streamice:
874      - change to driving stress formulation; update both Fwd & AD output.
875    o tools/genmake2 and Divided Adjoint with MPI:
876      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
877      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
878      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
879        Makefile, which is set by genmake2, and check which mpi-headers are needed.
880        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
881      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
882    o testreport:
883      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
884        perform additional runs (number of additional runs is "add_DIVA_runs" taken
885        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
886    o verification/lab_sea (AD test):
887      - change to test Divided Adjoint Run in this set-up (both standard AD test
888        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
889    o pkg atm_ & ocn_compon_interf:
890      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
891        staggerTimeStep implementation) and disable (retired) corresponding
892        parameter.
893    o pkg/offline:
894      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
895      - add S/R OFFLINE_CHECK to print offline parameter summary
896        and stop if loading a file that is not used;
897      - enable to calculate GMRedi tensor, KPP mixing and convective index
898        when the corresponding file(s) is/are not specified (but pkg is used).
899      - comment out resetting of monitorFreq (to endTime) since it still useful
900        for monitoring CFL numbers and checking offline fields.
901    o OpenAD:
902      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
903        smaller standard output) and generate new (smaller) output (on baudelaire
904        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
905    o model/src:
906      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
907        (where external_forcing_adjust was called) and change list of arguments;
908      - merge external_forcing_adjust.F into external_forcing_surf.F
909      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
910        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
911        previously in file "balance_relax.F", now removed); remove corresponding
912        arrays in FFIELDS.h.
913      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
914        a hack for getting back surfaceForcingS (loaded from file) when using
915        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
916      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
917        (was getting only 11 digits for AD-grad, due to different truncation
918         error in AD code).
919    
920    checkpoint64j (2013/07/04)
921    o pkg/offline:
922      - to enable the use of other features with pkg offline (e.g., obcs),
923        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
924      - comment out "allowFreezing" (now active) in 2 offline testing exp.
925    o pkg/exf ALLOW_RUNOFTEMP
926      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
927      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
928      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
929    o pkg/atm_phys:
930      - allows to add some damping on uVel,vVel (strength only function of k).
931    o verification, ad-tests:
932      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
933        global_ocean_ebm and offline_exf_seaice.thsice.
934    o verification/halfpipe_streamice:
935      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
936        flux input boundary conditions to be ignored; a fix for this bug changed
937        verification results for forward test.
938      - add adjoint test.
939    o pkg/ptracers:
940      - allow to restart without SOM pickup (resetting SOM to zero).
941    o pkg/gmredi:
942      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
943      - It uses mixing length theory and suppression by steering level effects to
944        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
945        to JPO, for more details).
946      - It also uses the diffusivity to calculate an eddy induced streamfunction
947        based on a PV closure (rather than a buoyancy closure as in GM).
948      - New files added to pkg/gmredi:
949        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
950          induced overturning streamfunction (called from gmredi_calc_tensor)
951        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
952          for use in gmredi_k3d
953        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
954          the eddy diffusivity
955    
956    checkpoint64i (2013/06/18)
957    o pkg/cheapaml:
958      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
959        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
960        with pkg/cheapaml.
961    o utils/python: add subpackage for cubed sphere function, first example is
962        simple cs.pcol to plot 2D fields on a map
963    o pkg/streamice:
964      - This is a new package in MITgcm, which solves dynamic equations for ice
965         sheets and ice streams
966      - At the moment it is independent of atmosphere/ocean dynamics, or any
967        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
968        ed that this will change)
969      - There is a new verification exercise that tests it, halfpipe_streamice,
970        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
971        rectangular embayment
972      - halfpipe_streamice is forward-only for now, will have TAF test soon
973      - for questions, email dgoldber@mit.edu
974    o pkg/thsice:
975      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
976        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
977      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
978         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
979      - allow precip from pkg/cheapaml to make snow over seaice.
980    o pkg/cfc:
981      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
982      - remove atmos CFC 2-D arrays from common bloc (now local variables)
983      - change some hard-coded constant to run time parameter for reading and
984        and interpolating atmospheric CFC ; keep same default as previously.
985      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
986      - put arguments in standard order: myTime, myIter, myThid
987      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
988        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
989      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
990      - new routine to print summary of CFC params and check for consistency.
991    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
992      similar to thsice_advdiff.
993      Note that for the B-grid case the routine parameters uc/vc are overwritten.
994    o pkg/cfc:
995      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
996        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
997      - fix interpolation of atmphspheric CFC between Sorthern and Northern
998        hemisphere value.
999    o pkg/seaice:
1000      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
1001    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
1002                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
1003      - requires an additional time level that is stored in the pickup
1004      - you can start with AB2 from a pickup without this time level with
1005        pickupStrictlyMatch = .false.
1006    
1007    checkpoint64h (2013/05/26)
1008    o pkg/cheapaml:
1009      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
1010        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
1011      - consistent treatment of uWind,vWind location: assume everywhere in
1012        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
1013        (Note: was already the case for Tair,Qair advection);
1014        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
1015      - compute diabatic forcing only in the interior (excluding overlap regions)
1016      - fill in array "Qsw" (for short-wave heating);
1017      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
1018        before any update (consistent with MITgcm state var diagnostics);
1019      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
1020        non periodic ; + adjusted for uWind,vWind (C-grid).
1021    o pkg/seaice:
1022      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
1023        add explicitly pkg/exf in experiments that currently use pkg/seaice.
1024      - allows to compile pkg/seaice without pkg/exf.
1025    o tools/OAD_support:
1026      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
1027        of array "ourStepOf" in function rvNextAction (revolve.F90).
1028    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
1029      - change pkg name (to be used with other atmospheric physics pkg)
1030        but by-pass CVS when making the new pkg so that we keep the CVS history.
1031    o pkg/offline:
1032      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
1033        (previously called from pkg/dic_surfforcing_init.F)
1034    o model/src:
1035      - re-order sequence of calls within packages_init_variables.F, using
1036        standard order, except for:
1037         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
1038         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
1039    o new pkg: atm_phys
1040      - add entry point and source code (previously in contrib
1041          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
1042        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
1043      - re-order sequence of calls within packages_readparms.F,
1044         packages_init_fixed.F and packages_write_pickup.F
1045        (but skip packages_init_variables.F because of TAF issues).
1046      - update contrib/*/atm_gray/ experiment.
1047    o pkg/seaice (ITD code):
1048      - simplify and fix the writing of pickup-files for ITD case
1049    o pkg/seaice (ITD code):
1050      - introduce floe size dependent lateral melt for ITD case;
1051      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
1052      - update seaice_itd experiment main output.
1053    o pkg/thsice:
1054      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
1055        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
1056        changed accordingly pkg/atm2d.
1057    
1058    checkpoint64g (2013/05/01)
1059    o pkg/exf ALLOW_RUNOFTEMP
1060      - if defined,  river and glacier runoff temperature can be read-in from
1061        runoftempfile; runoftempfile needs to have same format as runofffile
1062    o pkg/thsice (& pkg/bulk_force):
1063      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
1064        for energy content of Precip + RunOff & Evap (like with pkg/exf).
1065      - change computation domain to always be the interior (without overlap).
1066      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
1067    o verification/tutorial_global_oce_biogeo:
1068      - add preliminary OpenAD setup (still has problems)
1069    o pkg/seaice:
1070      - turn some parameters for choosing the convergence criterion of
1071        the inexact Newton method (JFNK) into runtime parameters for convenience
1072      - clean up seaice_calc_viscosities.F: remove/retire two options for
1073        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
1074        the results of lab_sea/input because a division has been replaced by
1075        a multiplication with the reciprocal (sumNorm)
1076      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
1077        convergence of solver (changes results, of course), and to test some
1078        new features
1079    o model/src:
1080      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
1081      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
1082      - move forcing adjustment (balancing surface forcing) in specific S/R
1083        where might also be applied exchanges (if needed) to forcing arrays.
1084    o pkg/shelfice:
1085      - allow to specify the Ice-Shelf mass per unit area (instead of
1086        shelficeLoadAnomaly) and do the conversion from one to the other
1087      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
1088        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
1089        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
1090        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
1091      - update isomip experiment forward output (get machine truncation error
1092        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
1093    o verification/offline_exf_seaice:
1094      revise data.seaice in input.thermo and input_ad and update results accordingly
1095        HO = 0.2, SEAICE_areaLossFormula = 2,
1096        SEAICE_growMeltByConv = .TRUE.,
1097        SEAICE_doOpenWaterMelt = .TRUE.,
1098      Improve consistency with input.thsice and fix the spurious 500m ice corners
1099    o verification/global_ocean.cs32x15:
1100      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
1101        in icedyn (thsice+seaice-dyn) test and update output.
1102    o verification/offline_exf_seaice:
1103      - adjust list of tested variables (with testreport) and update
1104        standard test output with better slection of monitored fields.
1105    o pkg/cd_code:
1106      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
1107        experiment lab_sea.hb87
1108    o tools/genmake2:
1109      - change default makedepend from the system default to tools/xmakedepend:
1110        When no makedepend is specified, select tools/xmakedepend it the test pass,
1111        otherwise select the system default (if exist and pass the test) or
1112        try to build cyrus-makedepend ; stop if none of the 3 works.
1113    o pkg/exf & pkg/thsice:
1114      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
1115        for energy content of Precip + RunOff & Evap. Assumes:
1116       1) Rain has same temp as Air.
1117       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
1118       3) Run-Off comes at the temp of surface water (with same Cp)
1119       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
1120        put directly into Latent Heat flux & should use water-vapor heat capacity.
1121       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
1122        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
1123    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
1124        (compile when SEAICE_ALLOW_JFNK is defined)
1125    o pkg/thsice:
1126      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
1127        implementation): move THSICE_AVE call after the advection (called directly
1128        from thsice_do_advect.F).
1129    o verification/global_ocean.90x40x15 and OpenAD:
1130      New experiment for OpenAD is identical to the one in input_ad except that
1131        multiDimAdvection=.FALSE.,
1132      There is still an issue with this.
1133    o pkg/thsice:
1134      - account for ice velocity (ocean relative velocity) in turbulent heat flux
1135        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
1136        and offline_exf_seaice (main test).
1137    
1138    checkpoint64f (2013/03/31)
1139    o verification/OpenAD:
1140      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
1141    o verification/isomip, pkg/shelfice and OpenAD:
1142    - add OpenAD setup to this exp and make shelfice package work with OpenAD    - add OpenAD setup to this exp and make shelfice package work with OpenAD
1143  o verification/offline_exf_seaice: replace adjoint experiment.  o verification/tutorial_global_oce_biogeo:
1144      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
1145    o verification/offline_exf_seaice:
1146      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
1147  o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:  o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
1148    - add OpenAD setup to this exp and make ptracers package work with OpenAD    - add OpenAD setup to this exp and make ptracers package work with OpenAD
1149  o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean  o pkg/seaice/seaice_evp.F:
1150    stress (when the turningAngle is non-zero) over open water to avoid     mask the asymmetric contribution of the ice-ocean stress (when
1151    stripes in the EVP-solutions after many EVP-substeps. This does not change     the turningAngle is non-zero) over open water to avoid stripes
1152    the verification experiment (because turningAngle=0 in that experiment), but     in the EVP-solutions after many EVP-substeps. This does not change
1153    will affect other EVP solutions with turningAngle.ne.0     the verification experiment (because turningAngle=0 in that experiment),
1154       but will affect other EVP solutions with turningAngle.ne.0
1155  o verification, AD & TLM output:  o verification, AD & TLM output:
1156    - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple    - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
1157      additions and multiplications which affect results at machine truncation      additions and multiplications which affect results at machine truncation
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